Unclassified Unclassified tissue DNase-seq DNase-Seq DNase-seq Input control Input control N/A Unclassified Unclassified Liver Unclassified Unclassified P19 cells Unclassified Unclassified 0.5% formaldehyde 5min fixation Unclassified Unclassified bone marrow-derived macrophages Unclassified Unclassified embryonic stem cells Input control Input control none Embryonic stem cells Unclassified Unclassified C2C12 myoblasts Unclassified Unclassified peritoneal thioglycolate-elicited macrophages Histone H3K4me2 H3K4me2 (Millipore 07-030) Primary thioglycollate-elicited peritoneal macrophages Others Biotin Streptavidin beads murine primary activated B cells Unclassified Unclassified murine embryonic stem cells Unclassified Unclassified eWAT Histone H3K4me2 140226_H3K4me2 Input control Input control None (input) Immortalized MEF Unclassified Unclassified The testes were crosslinked with 1% formaldehyde treatment and fixation was stopped by addition of 0.125 mM glycine. After washing with PBS, samples were stored at -80 C. The crosslinked material from 100 mg testes was sonicated to 500 bp fragments by Covaris S2 (duty cycle; 20 %, cycle per burst; 200, 10 times for 30 seconds). Immunoprecipitation was performed by incubatin overnight at 4 C with 2 ug of anti-H3K27me3 (Millipore 07-449), 2 ug of anti-H3K4me1 (abcam ab8895), 4 ug of anti-H3K4me3 (abcam ab1012), and control IgG. Antibody-protein complex was captured with dynabeads protein A or G beads (life technologies) and DNA was extracted. Unclassified Unclassified large peritoneal macrophages Others Rpa1 RPA in vitro activated B cells Unclassified Unclassified Embryonic stem cells Histone H3K27ac H3K27ac (Abcam, ab4729) Mammary Unclassified Unclassified ESC Others Dmc1 Anti-DMC1 Santa Cruz (C-20, sc 8973) Testis Unclassified Unclassified Cortex Others Rad21 Scc1 (Abcam AB992) mouse embryonic fibroblasts (E13.5d) Others GFP Chromotek GFP trap Agarose Input control Input control none Others Epitope tags HA NIH/3T3 Tet-On 3G cells Others Lhx3 Lhx3.V5 anti-V5 (Abcam ab15828) ES-derived embryoid bodies with induced transcription factors Histone H3K4me3 H3K4me3(Cell signaling Technology, #9727) mouse embryo Others Stat1 STAT1 (santa cruz, sc-592) Primary bone marrow-derived macrophages (BMDM) Unclassified Unclassified mouse BMDM Unclassified Unclassified MEFs expressing OSKM for 48h Unclassified Unclassified E-myc Arf-/- Trp53+/+ lymphomas Histone H3K4me3 20130423_H3K4me3 Histone H3K4me3 H3K4me3 ( Abcam Cat# Ab1012 Lot# GR56209-1) Cultured MEFs (Mouse Embryonic fibroblasts) Histone H3K9acS10ph H3K9acS10ph ( Abcam Cat# Ab12181-50, Lot# 770587) Cultured MEFs (Mouse Embryonic fibroblasts) Input control Input control none mouse embryonic stem cells Histone H3K4me3 H3K4me3 (Diagenode) Synovial Fibroblasts Unclassified Unclassified pre-iPSC line 1(12.1) Unclassified Unclassified CorticalNeurons CorticalNeurons Others Stat1 Stat1 sc-346 A302-753A bone marrow Histone H3K9me2 H3K9me2 MEF Unclassified Unclassified mouse embryonic fibroblasts Others Ep300 anti-p300 primary CD4+ T cells from spleen and lymph nodes Unclassified Unclassified KH2 mouse embryonic stem cells Histone H3K4me2 20130423_H3K4me2 Unclassified Unclassified pancreas Histone H3K4me1 H3K4me1 (Abcam ab8895) Primary thioglycollate-elicited peritoneal macrophages Histone H3K4me3 H3K4me3 (Abcam ab8580) Hippocampal CA neurons Histone H3K4me1 H3K4me1 (Abcam ab8895) Hippocampal CA neurons Histone H3.3 H3.3 Primary Cortical Neurons (E16.5 DIV8) Unclassified Unclassified ERS480286 Input control Input control none embryonic stem cells Unclassified Unclassified bone marrow derived macrophages Unclassified Unclassified E9.5 full embryo Unclassified Unclassified nucleus accumbens Histone H3K27ac H3K27ac, Abcam, ab4729 CD4+ T cells Unclassified Unclassified Retina Unclassified Unclassified C3H10T1/2 cells Others Nr3c1 GR (Thermo Scientific, PA1-511A) Mammary Histone H3K27ac Anti-H3K27ac (Abcam # ab4729) Primary bone marrow-derived macrophages (BMDM) Histone H3K4me1 H3K4me1 (Active Motif, catalog# 39297, lot# 21008001) Immortalized MEF Others Mef2d anti-MEF2D (Flavell et al., 2008) retina Histone H3K36me3 H3K36me3 (Abcam, Ab9050, lot# GR10860-1) marrow derived MSC Histone H3K4me3 H3K4me3 (Abcam, Ab1012, lot# 956303) marrow derived MSC Histone H3K4me1 H3K4me1 (Abcam, Ab8895, lot# 961715) marrow derived MSC Histone H3K9ac H3K9Ac (Millipore, 06-942, lot# 31636) marrow derived MSC Histone H4K5ac H4K5Ac (Millipore, 07-327, lot# DAM1794310) marrow derived MSC Others Rxra RXR (Santa Cruz, N-197, sc-774, lot# G2310) marrow derived MSC Others Vdr VDR (Santa Cruz, C-20, sc-1008, lot# A0912) marrow derived MSC Histone H3K9K14ac H3K9acK14ac ( Millipore Cat# 06-599 Lot# 1969119) Cultured MEFs (Mouse Embryonic fibroblasts) Histone H3K27ac H3K27ac ( Abcam Cat# Ab4729 Lot# GR144577-2) Cultured MEFs (Mouse Embryonic fibroblasts) Histone H4K16ac H4K16ac ( Abcam Cat# Ab61240, Lot# GR284-15) Cultured MEFs (Mouse Embryonic fibroblasts) Others Spi1 PU1 sc-352 bone marrow Others Clock Mice were entrained to 12-hr light (L) and 12-hr dark (D) cycles for at least 2 weeks in a light-tight chamber at a constant temperature (23 ? 1?C). The LD entrained mice were transferred to constant darkness, and in the second day, the mice were sacrificed at different time for liver isolation. Nuclear extracts of the mouse liver were cross-linked by 1% formaldehyde, and then sonicated. The samples were used for ChIP with CLSP4 anti-CLOCK antibody. For control experiment, the DNA prepared by ChIP with 1D4 antibody and input DNA were also sequenced. Histone H3K4me3 H3K4me3 (Millipore, catalog# 17-614, lot# 1974075) Immortalized MEF Unclassified Unclassified K1ER cells Others Hdac3 HDAC3 liver Others Spi1 Anti-PU.1 (in-house rabbit polyclonal against the N-Terminal (aa. 1-100)) Primary bone marrow-derived macrophages (BMDM) Histone H4K8ac H4K8ac (Millipore 07-328) Primary thioglycollate-elicited peritoneal macrophages Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. MEL Unclassified Unclassified NIH/3T3 tet-on 3G cells Histone H3K4me3 custom-made H3K4Me3 antibody (Abmart) Preimplantation embryo Histone H3K27me3 H3K27me3(Diagnode, pAb-069-050) mouse embryo Unclassified Unclassified embryonic fibroblast chromatin Input control Input control none MLL-AF9/NrasG12D murine cell line Histone H3K79me1 Ab3261 Abcam Leukemic bone marrow Others Rela p65 (Santa Cruz sc-372) Primary thioglycollate-elicited peritoneal macrophages Others Stat5a STAT5A (Santa Cruz, sc-1081x) Mammary Unclassified Unclassified PDGF Neural Stem Cells Others Epitope tags Flag (Sigma, Cat. F1804) mESCs Others Stat5a STAT5A (Santa Cruz, sc-1081) Mammary Histone H3K4me2 H3K4me2 (Millipore, cat. no. 07-030) Splenic CD4+ T cells Input control Input control none ES cell culture Histone H3K27ac H3K27ac (Active Motif 39133) Embryonic stem cell (ESC) Histone H3K27me3 H3K27me3 (Active Motif 39155) Embryonic stem cell (ESC) Others Stag1 Stag1 (Peters laboratory ID A823) mouse embryonic fibroblasts (E13.5d) Others Dmc1 DMC1 (C-20) sc 8973 adult testis Unclassified Unclassified Primary Cortical Neurons (E16.5 DIV8) Others Stat3 STAT3 murine CD4+ T Unclassified Unclassified source Mmu1 Unclassified Unclassified source Mmu5 Unclassified Unclassified source Mmu4 Unclassified Unclassified source Mmu2 Unclassified Unclassified source Mmu3 Unclassified Unclassified Microglia Histone H3K4me2 20130620_H3K4me2 Unclassified Unclassified G1E-ER4+E2 cells Input control Input control none liver Input control Input control None Liver Input control Input control None (Input) Liver tissue Histone H3K27ac H3K27ac (Active Motif, catalog# 39133, lot# 21311004) Immortalized MEF Unclassified Unclassified E16.5 mouse embryonic cortex Histone H3K4me3 H3K4me3 (Millipore/EMD, 07-473, lot 2155413) spermatocytes Input control Input control N/A DIV7 mCTX neurons Others Nr3c1 GR, PA1-511A, Pierce; sc-1004, Santa Cruz Liver tissue Unclassified Unclassified embryonic cells Others Suz12 anti-Suz12 (D39F6 XP Cell Signaling) Embryonic Stem Cells Histone H3K27ac H3K27Ac (Abcam, ab4729) Primary bone marrow-derived macrophages (BMDM) Input control Input control NA NIH/3T3 Tet-On 3G cells Unclassified Unclassified Mouse embryonic stem cells Input control Input control N/A CD4+ T cells Input control Input control Input none ES-derived embryoid bodies with induced transcription factors Input control Input control none EpCAM+ epithelium from small intestine Unclassified Unclassified CD43 negative mouse resting B cells Others Rad21 RAD21 (Abcam: ab992) Embryonic Limb Bud Histone H3K27ac H3K27Ac (Diagenode: C1540174) Embryonic Limb Bud Histone H3K4me3 H3K4me3 (Milipore: 07-473) Embryonic Limb Bud Others Ctcf CTCF (Active motif: 613111) Embryonic Limb Bud Unclassified Unclassified Primary bone marrow-derived macrophages (BMDM) Input control Input control INPUT whole liver extract Histone H3K9me2 H3K9me2 H3K9me2 ChIP Cardiac biopsy Others Irf4 IRF4 Th17 in vitro Unclassified Unclassified whole hippocampus Unclassified Unclassified E-myc Trp53KI/ lymphomas Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. C2C12 Histone H3K27ac H3K27AC Abcam ab4729 hippocampal CA1 Histone H3K27me3 H3K27ME3 Millipore CS200603 hippocampal CA1 Histone H3K4me1 H3K4ME1 Abcam ab8895 hippocampal CA1 Histone H3K4me3 H3K4ME3 Abcam ab8580 hippocampal CA1 Histone H3K79me3 H3K79ME3 Abcam ab2621 hippocampal CA1 Histone H3K9ac H3K9AC Millipore 07-352 hippocampal CA1 Histone H3K9ac AcH3K9 (abcam, ab10812) regenerating liver harvested 12 h after PH Unclassified Unclassified Cell line Unclassified Unclassified spermatocytes Unclassified Unclassified CD4+ Th1 Input control Input control Input Input Cardiac biopsy Histone H3 H3 Abcam ab1791 hippocampal CA1 Histone H3K4me3 20130306_H3K4me3 Others Arntl BMAL1 Liver cells Unclassified Unclassified liver Input control Input control none (input) Heart Unclassified Unclassified Excitatory pyramidal neurons from mouse neocortex Unclassified Unclassified sorted murine lin-/Sca-1/c-Kit in vitro cultured cells Others Ctcf CTCF (Abcam ab70303 / Millipore 07-729) Mammary Input control Input control none Differentiated embryonic stem cells Histone H3K4me1 H3K4me1 (Abcam: 8898) Embryonic Limb Bud Histone H3K27ac H3K27ac Abcam ab4729 ES-derived embryoid bodies with induced transcription factors Others Rnf2 Rabbit anti-Ring1b Mouse embryonic stem cells Histone H3K4me3 Anti-H3K4me3 (Active Motif #39159) Primary bone marrow-derived macrophages (BMDM) Histone H3K4me1 Anti-H3K4me1 (Abcam # ab8895) Primary bone marrow-derived macrophages (BMDM) Others Cebpb Cebpb sc-150 bone marrow Unclassified Unclassified TauEGFP MEFs Others Stat5a STAT5 antibody C-17 liver tissue Unclassified Unclassified HPC-7 Cell Line Unclassified Unclassified Spleen Histone H2A.X H2A.X ESC Histone H3K4me2 20130306_H3K4me2 Input control Input control none heart Others Ahr SA-210 Liver Others Nrf1 NRF1 (Abcam, ab55744) embryonic stem cells Others Epitope tags Flag-M2 (Sigma, F1804) mouse embryonic stem cells Others Rela RelA bone marrow-derived macrophages Others Brd4 Brd4 (A301-985A; Bethyl) MLL-AF9/NrasG12D murine cell line Input control Input control native no antibody Embryonic stem cells Input control Input control crosslink no antibody Embryonic stem cells Histone H3K79me2 Ab3594 Abcam Leukemic bone marrow Histone H3K4me3 H3K4me3 Embryonic Stem Cells (ESCs) Others Rela RelA (Santa Cruz, catalgo# sc-372, lot# H1114) bone marrow-derived macrophages Others Creb1 CREB (Santa Cruz, catalog# sc-186 lot# C0614) bone marrow-derived macrophages Others Irf4 anti-IRF4 cultured TH2 cells Unclassified Unclassified KLRG1loIL7Rhi memory CD8 T cells Unclassified Unclassified KLRG1loIL7Rhi memory precursor CD8 T cells Unclassified Unclassified KLRG1hiIL7Rlo terminal effector CD8 T cells Unclassified Unclassified naive CD8 T cells Others Smc1a SMC1 antibody, Cat#A300-055A; RRID:AB_2192467 3T3-L1 preadipocytes Others Med1 MED1/TRAP220 antibody (M-255) Cat#sc-8998, RRID:AB_2144021 3T3-L1 preadipocytes Others Ctcf CTCF antibody, Cat#07-729; RRID:AB_441965 3T3-L1 preadipocytes Others Creb1 CREB CREB-1 Antibody (Santa Cruz Biotech, catalog# sc-186) Unclassified Unclassified immortalized cell line Unclassified Unclassified Isolated islets Histone H3K4me1 H3K4me1 (Abcam ab8895) Embryonic stem cell (ESC) Others Ep300 p300 Th17 in vitro Unclassified Unclassified A murine pre-B ALL carrying the human E2a:PBX transgene crossed to a CD3-/- was generously provided by Dr. Janetta Bijl. These cells were developed into a stable cell line expressing pre-B markers. Histone H3K4me1 H3K4me1 Abcam ab8895 ES-derived embryoid bodies with induced transcription factors Histone H3K27me3 H3K27me3 Active motif 39155, 39157 ES-derived embryoid bodies with induced transcription factors Others Myt1l Myt1lb (rabbit) TauEGFP MEFs Input control Input control NA splenic B220+ lymphocytes Others Nfkb1 Nfkb1 sc-114 bone marrow Others Irf4 Irf4 sc-6059 bone marrow Others Irf2 Irf2 ab65048 sc-498 bone marrow Histone H3.3 crosslink anti-H3.3 (09-838) Embryonic stem cells Unclassified Unclassified source ERS032733 Input control Input control none (input) ES cells Unclassified Unclassified Neuralized embryoid bodies Histone H3K27ac H3K27Ac (ab4729, Rabbit, 2 ug) splenic B220+ lymphocytes Histone H3K4me3 ab8580 (lot#1197461) 3T3-L1 cells Others Atf3 Atf3 sc-188 ab70005-100 bone marrow Histone H3K9me2 H3K9me2 DC Histone H3K4me1 H3K4me1 (Abcam, Ab8895, lot 720417) ES cells Others Rad21 RAD21 (Abcam, ab992) Splenic Histone H3K9me3 native anti-H3K9me3 (ab8898) Embryonic stem cells Unclassified Unclassified embryonic stem cells, mock treatment Others Med1 MED1 (M-255) 3T3-L1 pre-adipocytes (4h) Others Epitope tags anti-HA embryonic stem cells Histone H3K27ac H3K27ac (Abcam 4729) forebrain Others Spi1 PU.1 (Santa Cruz sc-352) Primary thioglycollate-elicited peritoneal macrophages Others Epitope tags 3FLAG M2 (Sigma Aldrich) 3T3-L1 cells (ATCC #CL-173) Input control Input control none ES cell Histone H3K4me3 H3K4me3 (Homemade, #28) mouse embryonic stem cells Others Biotin Dynabeads M-280 Streptavidin (Invitrogen) Mature B Others Stat2 Stat2 ab53149 sc-839 bone marrow Histone H3K27me3 H3K27me3 (abcam, ab6002) bone marrow Histone H3K27ac H3K27ac, #39133 liver Histone H3K4me3 H3K4me3 primary CD4+ T cells from spleen and lymph nodes Histone H3K27ac H3K27Ac (Abcam, cat. no. ab4729) Splenic CD4+ T cells RNA polymerase RNA polymerase II RNA Pol II (Rpb1 N-terminus) V6.5 mES cells Unclassified Unclassified source ERS032735 Unclassified Unclassified source ERS017586 Unclassified Unclassified source ERS017585 Input control Input control none Mouse back skins Input control Input control None Others GFP GFP IP Input control Input control None (Input DNA) Splenic Input control Input control none forebrain DNase-seq DNase-Seq DNase Input control Input control n/a n/a Histone H3K27me3 H3K27me3 (Millipore, 17-622) Thymus Others Tal1 TAL1 (sc12984) G1E-ER4 Histone H3K4me3 H3K4me3 mouse B cells Histone H3 H3 (Abcam, ab1791, lot GR135321-1) mouse embryonic fibroblasts Histone H3K27me3 H3K27me3 (Millipore, 07-449, lot 2194165) mouse embryonic fibroblasts Histone H3K9me3 H3K9me3 (Abcam, ab8898, lot GR130993-1) mouse embryonic fibroblasts Histone H3K9me2 H3K9me2 (AbCam, ab1220, lot GR139816-1) mouse embryonic fibroblasts Others Setdb1 Setdb1 (Santa Cruz Biotechnology, sc-66884, lot L1812) mouse embryonic fibroblasts Others Ctcf Ctcf (Millipore, 07-729, lot 2452497) Neural stem cells Others Cebpa C/ebp (Santa Cruz, sc-61) perfused primary hepatocytes Histone H3K27ac H3K27ac (Abcam Ab4729) ES cell culture Input control Input control no antibody ES cell culture Others Fosb sc48 DIV7 mCTX neurons Others Fos sc52 DIV7 mCTX neurons Others Onecut1 sc-13050 liver tissue Histone H2A.X H2A.X (Xiao lab) reprogramming from MEF cell Others Epitope tags native anti-HA (12CA5) Embryonic stem cells Histone H3K79me3 Ab2621 Abcam Leukemic bone marrow Histone H3K4me3 H3K4me3 (Abcam, Catalog# ab8580, Lot# GR47272-1) Embryonic stem cells Others Cebpa C/EBPa (sc-61, Santa Cruz) Haftl pre-B cells Histone H3K27ac H3K27ac (Abcam 4729) heart Others Jarid2 JARID2 Embryonic stem cells Others Epitope tags anti-HA (12CA5) Embryonic stem cells Others Ctcf CTCF adult mouse cortex Others Esr1 cocktail of Ab-10 from Labvision and sc-543 from Santa Cruz 7438 cells + Afos Others Nr3c1 cocktail of PA-510A and PA-511A from Affinity BioReagents and sc-1004 from Santa Cruz 7438 cells + Afos Others Esr1 cocktail of Ab-10 from Labvision and sc-543 from Santa Cruz 7438 cells Others Nr3c1 cocktail of PA-510A and PA-511A from Affinity BioReagents and sc-1004 from Santa Cruz 7438 cells Others Nr3c1 cocktail of PA-510A and PA-511A from Affinity BioReagents and sc-1004 from Santa Cruz Histone H3.3 H3.3 (rat monoclonal antibody using in Harada,A et al, The EMBO Journal, 2012.) Embryonic stem cells Histone H3K27me3 H3K27me3 (mouse monoclonal antibody provided by Dr. H. Kimura using in Kimura H et al., Cell Struct. Funct., 2008.) Embryonic stem cells Histone H3S10ph H3S10P (Millipore, cat# 04-817) Cultured MEFs (Mouse Embryonic fibroblasts) Others Hnf4g Hnf4g (Santa Cruz sc-6558X) Jejunal intestinal epithelial cells RNA polymerase RNA polymerase II Rabbit anti-N-terminal RNAP2 (Santa cruz sc-899) pre-B cell line B3 Input control Input control none Ventral tegmental area (brain) Histone H3K4me1 H3K4me1 (AbCam AB8895) Ventral tegmental area (brain) Histone H3K4me3 H3K4me2 (Millipore, Cat. # 07-030) Cranial neural crest cells Histone H3K27me3 H3K27me3 (Millipore, Cat. # 07-449) Cranial neural crest cells Histone H3K4me3 H3K4me3 (07-473, Millipore, lot: JBC1888194) bone marrow derived macrophages Histone H3K27me3 H3K27me3 (Milipore: 07-449) Embryonic Limb Bud Histone H3K4me1 anti-H3K4me1 Primary bone marrow-derived macrophages, no treatment, H3K4me1 ChIP Input control Input control none cultured NUP98-HOXA9 transformed mouse bone marrow LSK cells Unclassified Unclassified RA-treated P19 EC cells Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. G1E-ER4 Histone H3K27me3 H3K27Me3 Preimplantation embryo Histone H3K27ac abcam ab4729 Frontal Cortex Histone H3K27ac abcam ab4729 Hypothalamus Histone H3K27ac abcam ab4729 Amygdala Histone H3K4me3 H3K4me3 Active motif 39159, 39160 ES-derived embryoid bodies with induced transcription factors Histone H3K4me2 H3K4me2 Abcam ab7766 ES-derived embryoid bodies with induced transcription factors Others Isl1 Isl1 anti-Isl1 combination (DSHB 40.3A4, 39.3F7, 40.206) ES-derived embryoid bodies with induced transcription factors Others Cebpb C/EBP (Santa Cruz, C-19, sc-150, lot# F3011) marrow derived MSC Others Runx2 RUNX2 (Santa Cruz, M-70, sc10758, lot# D1411) marrow derived MSC Others Elf5 ELF5 (Santa Cruz, sc-9645) Mammary Histone H4K5ac H4K5Ac (Vendor: Millipore, cat# 07-327, lot# 2524676) bone marrow derived macrophages Others Rela p65 (Vendor: Santa Cruz, cat# sc-372, lot# A0314) bone marrow derived macrophages Histone H3K4me2 H3K4me2 (Vendor: Millipore, cat# 07030, lot#DAM1724042) bone marrow derived macrophages RNA polymerase RNA polymerase II RNApol2 (Santa Cruz sc-899X, Lot# L1510, Abcam ab26721, lot:GR84088-1) bone marrow derived macrophages Histone H3K27ac H3K27Ac (Vendor: Abcam, cat# ab4729, lot# GR132150-Y) bone marrow derived macrophages Others Smad2 SMAD2 (Cell signaling 5339) p19 cells Others Dmc1 anti-DMC1, Santa Cruz (C-20, sc-8973) whole adult testis Histone H3K9ac H3K9ac (Millipore 07-352) mouse embryonic fibroblasts (E13.5d) Histone H3K4me3 H3K4me2 (Millipore 07-030) mouse embryonic fibroblasts (E13.5d) Histone H3K4me1 H3(abcam, ab1791-100ug, lot GR210023-1 ) H3K4me1 (abcam,ab8895, lot GR193882-2) HSPCs Histone H3K4me3 H3(abcam, ab1791-100ug, lot GR210023-1 ) H3K4me3 (abcam,ab8580, lot GR190102-2)) HSPCs Histone H3K27ac H3(abcam, ab1791-100ug, lot GR210023-1 ) H3K27Ac (abcam,ab4729, lot GR144577-1) HSPCs Histone H3K27ac anti-histone H3 (acetyl K27) (Abcam, Cat# ab4729, Lot# GR184332-1) C2C12 cell line Others Elk1 ELK1 in house antibody Cultured MEFs (Mouse Embryonic fibroblasts) Others Srf SRF (sc-335) (Lot: D3013) Cultured MEFs (Mouse Embryonic fibroblasts) RNA polymerase RNA polymerase II Pol2 (Santa Cruz Biotechnology, N-20) Splenic B cell RNA polymerase RNA polymerase II RNA Pol II Macrophages Histone H2AK119Ub H2AK119ub (Diagenode, C15410002) Mouse embryonic fibroblast Histone H3K27me3 H3K27me3 (Diagenode, pAb-069-050) Mouse embryonic fibroblast Others Junb Junb ab28838 sc-46 bone marrow Input control Input control NA Mature B Others Dmc1 Anti-DMC1 (C-20) Anti-DMC1 9R_testis_SSDS Unclassified Unclassified source ERS032732 Histone H3K4me3 H3K4me3 Input control Input control None Liver tissue Histone H3K4me3 H3K4me3 07-473 spermatocytes Unclassified Unclassified sorted_microglia Others Epitope tags anti-FLAG M2 (Sigma F7425) Mouse embryonic fibrobrasts Input control Input control none mammary gland Input control Input control none testes Unclassified Unclassified P19Cl6 Unclassified Unclassified p19 cells Unclassified Unclassified E16 cortical neurons RNA polymerase RNA polymerase II Pol-II MMS-128P bone marrow Input control Input control NA Pro-B Histone H3 anti-H3 Macrophages Others Irf4 IRF4 murine CD4+ T Others Dnmt1 DNMT1 Others Irf4 anti-Irf4 Others BrdU anti-Br-dUTP source ERS023710 Unclassified Unclassified ES cells. HV+S+ FACs sorted population Unclassified Unclassified ES cells. HV-S+ FACs sorted population Histone H3K27me3 Abcam ab6002 anti-H3K27me3 CD4+CXCR5+CD62Llo T cells Others Aff3 Aff3 (Homemade#182) ES cell culture Unclassified Unclassified Mouse neuroblastoma cell line Input control Input control input Bone marrow derived macrophage- stimulated 30'/DMSO treated Histone H3S28ph H3S28ph Bone marrow derived macrophage- stimulated 30'/DMSO treated Input control Input control none primary T cells Histone H3K27ac H3K27ac (Active, Motif, lot 39133) ES cells Unclassified Unclassified Nucleus accumbens tissue Input control Input control None mouse embryonic stem cells Others Epitope tags FLAG (Sigma, F1804) Dnmt TKO ESCs Input control Input control None SV40T transformed fibroblasts Others Rorc Anti-RORgamma(t), eBioscience, AFKJS-9, 14-6988, E11084-325 Th17 cells Histone H3K27me3 H3K27me3 Embryonic Stem Cells (ESCs) Histone H3K27ac H3K27ac (Abcam 4729) liver RNA polymerase Polr3d anti-POLR3D (mouse and human) CS681 Ab, raised against peptide CSPDFESLLDHKHR {Chong et al 2001} Mouse Liver Histone H3K4me1 H3K4me1 (Abcam, catalog# ab8895, lot# GR46388-1) Primary B-cells Histone H3K4me3 H3K4me3 (Active Motif, catalog# 39159, lot# 1609004) Primary B-cells Others Myc c-Myc N262 (Santa Cruz, catalog# sc764, lot#G0111) Primary B-cells Histone H3K4me3 (rb) -H3K4me3 (#528; Ali Shilatifard) ES cell culture Others Epitope tags FLAG (Sigma, F3165) Embryonic stem cells Input control Input control none murine embryonic stem cells Histone H3K9me2 anti-H3K9me2; Abcam (ab1220) cardiomyocyte Others Pou5f1 Pou5f1/Oct4 V5 KH2 ES cells Histone H3K4me3 Histone H3 trimethyl Lys4 mammary gland Histone H3K27me3 H3K27me3 (Cell signaling, 9733S, lot unknown) ES cell line Input control Input control none, input-DNA Embryonic stem cell Others Gata1 GATA1_(SC-265) sc-265 GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. rat monoclonal antibody raised against mouse recombinant GATA1; recommended for detection of GATA1 of mouse, rat and human origin. Antibody Target: GATA1 G1E-ER4 Others Kmt2b Mll2 (Homemade, #9173) mouse embryonic stem cells Histone H3K27me3 Rabbit anti-H3K27me3 Mouse embryonic stem cells Others Ctcf CTCF (Upstate 07-729) mouse embryonic fibroblasts (E13.5d) Others Setdb1 SETDB1 3T3-L1 preadipocytes Histone H3K36me3 H3K36me3 ab9050 H3K36me3 IP Histone H3K4me3 H3K4me3 ab8580 H3K4me3 IP Input control Input control none OKSM reprogramming intermediates from Mouse Embryonic Fibroblasts Histone H3K4me1 H3K4me1 (ab8895, Abcam) Naive CD4 T cells Others Bcl6 Bcl6 antibody N-3 liver tissue Input control Input control none HL-1 cells Histone H3K27me3 H3K27me3 from T. Jenuwein Unclassified Unclassified source ERS005103 Input control Input control none input DNA Input control Input control none Frontal Cortex Histone H3K4me3 H3K4me3 liver tissue Others Stat3 STAT3 Th17 in vitro Histone H3K27me3 H3K27me3 Input control Input control None None iPSC Others Med1 Med1/TRAP220 Bethyl A300-793A iPSC Input control Input control WCE 3T3L1 Histone H4K20me1 H4K20me1 3T3L1 Histone H3K9me3 H3K9me3 3T3L1 Histone H3K79me2 H3K79me2 3T3L1 Histone H3K4me3 H3K4me3 3T3L1 Histone H3K27ac H3K27ac 3T3L1 Others Gata2 Gata2 FDCPmix Histone H3K4me1 H3K4me1 liver tissue Unclassified Unclassified NKT cells Input control Input control none none input RNA polymerase Polr2b RPB2 sc-67318 RPB2 IP Others Rag1 RAG1 thymocytes Histone H3K4me1 H3K4me1/2 (abcam 32356) B220 Others Suz12 Suz12 Abcam ab12073 mESC Histone H3K4me3 H3K4me3 (17-614 Millipore) Bone marrow derived dendritic cells Input control Input control none, input mouse primary CD4+ T cells Others Stat1 STAT1 (Santa Cruz Biotechnology, sc-592)(Lot #E1209) mouse primary CD4+ T cells Others Stat3 STAT3 (eBioscience, #14-6727-81)(Lot #E034014) mouse primary CD4+ T cells Histone H3K27ac H3K27ac (Abcam, catalog# ab4729, lot# GR183919-1) Mouse Embryonic day 14.5 Fetal Liver Histone H3K4me3 H3K4me3 (Millipore, catalog# 07-473, lot# 2289139) Mouse Embryonic day 14.5 Fetal Liver Histone H3K9me3 H3K9me3 (Abcam Ab8898) MEF cell culture Others Atrx Atrx Santa Cruz (sc-15408) Primary culutured mouse cortical neurons (DIV 8) Histone H3K9me3 H3K9me3 (Active Motif #39161) TT2 Unclassified Unclassified small peritoneal macrophages Histone H3K27ac H3K27ac abcam:ab4729, lot3221746 Heart Unclassified Unclassified hematopoietic stem and progenitor cells from E14.5 foetal liver Others Nlrc5 Rabbit polyclonal anti-mouse NLRC5 (aa 1139) custom antibody generated by Adipogen WT T-cells Histone H3K27me3 anti-H3K27me3 (C36B11 Cell Signaling) Embryonic Stem Cells Others Epitope tags HA antibody, Abcam ab9110 Embryonic Stem Cells Input control Input control none embryonic stem cells (ESC) Others Spi1 PU.1 (in-house rabbit polyclonal anti-mouse PU.1 1-100aa) Primary bone marrow-derived macrophages (BMDM) Others Irf8 IRF8 (in-house rabbit polyclonal anti-mouse IRF8 146-162aa) Primary bone marrow-derived macrophages (BMDM) Histone H3K27me3 H3K27me3 IP (abcam 6002) embryoid bodies Histone H3K27me3 H3K27me3 IP (abcam 6002) embryonic stem cells Histone H3K27me3 07-449 Millipore Leukemic bone marrow Input control Input control none (streptavidin-coated beads used to pulldown biotinylated Gata4; 11205D, M-280 Streptavidin Invitrogen) Heart Histone H3K9ac rabbit anti-H3K9ac (Millipore; 06-942) intestinal epithelial cells RNA polymerase RNA polymerase II RNA Pol II (Rpb1 N-terminus) SC-899 mouse heart Input control Input control none none Input, liver cells Histone H3K36me3 H3K36me3 Abcam ab9050 Hematopoietic stem cells (HSC) Histone H3K27me3 H3K27me3 Millipore 07-449 Hematopoietic stem cells (HSC) Input control Input control none ESC cells Unclassified Unclassified adult mouse cortex Histone H3K27ac H3K27ac adult mouse cortex Histone H3K9me3 H3K9me3 adult mouse cortex Others Myc Myc N262 (Santa Cruz, sc-764) embryonic fibroblasts, E13.5 Unclassified Unclassified Mouse embryonic day 11.5 (e11.5) hindbrain Others Epitope tags anti-FLAG M2 (Sigma, F1804) Neurospheres Histone H3K27me3 H3K27me3 (Abcam ab6002) Cerebellum Others Cebpb C/EBPbeta sc-150, santa cruz Histone H3K27ac anti-H3K27ac, ab4729, AbCam CD4+ T cells Others Stat2 anti-STAT2, ab124283, AbCam CD4+ T cells Others Stat1 anti- STAT1, sc-592, Santa Cruz Biotechnology CD4+ T cells Histone H3K79me3 Anti H3K79Me3 antibody from Abcam (ab8898) ESC cells Histone H3K27me3 anti-H3K27me3(Millipore 17-622) Differentiated embryonic stem cells RNA polymerase RNA polymerase II anti-RNA Pol II(8WG16) ab817 primary T-cells Unclassified Unclassified E8.5 full embryo Input control Input control None CD8 T cells Histone H3K27ac H3K27ac (Abcam ab4729) C2C12 myoblasts Histone H3K27me3 anti-H3K27me3; Millipore (07-449) cardiomyocyte Histone H3K27me3 H3K27me3 liver tissue Others Klf4 Klf4 (R&D AF3158) embryonic stem cells Histone H3K27me3 H3K27me3 (39155, Active Motif) mESC Others Hnf4a Hnf4a (Abcam ab41898) Jejunal intestinal epithelial cells Histone H3K4me1 H3K4me1 (Abcam ab8895) Jejunal intestinal epithelial cells Others Ctcf CTCF CD4+ Th1 Histone H3K9me3 H3K9me3 (abcam #8898) mouse embryonic fibroblasts Histone H3K27ac H3K27ac (abcam #4729) mouse embryonic fibroblasts Unclassified Unclassified Primary tissue Heart Histone H3K27me3 H3K27me3 (Millipore, 17-622 & 07-449) Heart Histone H3K27ac H3K27ac ( Abcam, ab4729) Heart Input control Input control none V5 KH2 ES cells RNA polymerase RNA polymerase II RNA Pol II Abcam Cat#ab5408 NAc dissection from 3-5 animals Histone H3K9me2 H3K9me2 Abcam Cat#ab1220 NAc dissection from 3-5 animals Histone H3K4me1 H3K4me1 Abcam Cat#ab1012 NAc dissection from 3-5 animals Histone H3K36me3 H3K36me3 Abcam Cat#ab9050 NAc dissection from 3-5 animals Histone H3K27me3 H3K27me3 Abcam Cat#ab6002 NAc dissection from 3-5 animals Histone H2A.XS139ph gammaH2AX in vitro activated B cells Unclassified Unclassified F1 2-1 129/Castaneus Female mESCs Histone H3K27me2 H3K27me2 (Cell signaling, 9728S, lot unknown) ES cell line Histone H3K27ac H3K27ac (Abcam ab4729, lot unknown) ES cell line Histone H2Bub H2Bub; Cell Signaling, 5546S Embryonic stem cells Histone H3K4me3 H3K4me3; Millipore, #04-745 Embryonic stem cells Others Smc3 rabbit anti-Smc3 mouse embryonic fibroblasts Others Ep300 p300 ChIP-Seq, sc-585 (Santa Cruz) Unclassified Unclassified V6.5 ES cells Others Nr1d1 Rev-erba, Cell Signaling Technology (CST#2124) liver Others Irf4 IRF4 Th0 in vitro Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. CH12 Histone H3K4me1 anti-K4me1 primary CD4+ T cells from spleen and lymph nodes Input control Input control none Mouse embryonic stem cells Histone H3K27me3 Millipore, 17-622 Wnt3KO EpiSCs Unclassified Unclassified C2C12 myoblast Unclassified Unclassified Mouse embryos Others Pparg PPAR (81B8, 2443s, lot# 2) marrow derived MSC Others Cebpa C/EBP (14AA, sc-61, lot# J1811) marrow derived MSC Others Nfib NFIB (Santa Cruz, sc-5567) Mammary RNA polymerase Polr2a anti-Polr2a antibody (Catalog #: MMS-126R, Covance) mpkCCD cells Input control Input control anti-IGG antibody (Catalog #:2729) mpkCCD cells Others Elob Elongin B; abcam, ab168836 Embryonic stem cells Histone H3K27ac anti-H3K27Ac (Abcam, ab4729) Primary bone marrow-derived macrophages (BMDM) Unclassified Unclassified neuroepithelia cells Input control Input control none, input-DNA FACS-purified Pou5f1-GFP-positive germ cells Others Myc c-Myc N262 (Santa Cruz sc764-X) tet-Myc liver tumor Histone H3K27me3 07-449 (lot#DAM162421) C3H10T1/2 cells Histone H3K4me3 ab8580 (lot#GR37544-1) C3H10T1/2 cells Histone H3K9ac ab4441 (lot#GR47329-1) C3H10T1/2 cells RNA polymerase RNA polymerase II Ser2P pol II CTD rat anti Ser2P-CTD 3E10 Chromotek cat. no. 3e10 S194 Myeloma B Cells RNA polymerase RNA polymerase II RNA pol II rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000) S194 Myeloma B Cells Input control Input control none peritoneal macrophage Others Gabpa Nrf2 (Cell Signaling Technology; D1Z9C) peritoneal macrophage Histone H3K4me3 H3K4me3 E11.5 embryonic hearts Histone H3K4me2 H3K4me2 E11.5 embryonic hearts Histone H3K4me1 H3K4me1 E11.5 embryonic hearts Unclassified Unclassified Epiblast stem cells Others Crebbp CBP (D6C5) Rabbit mAb Brown preadipocyte cell_CBP_ChIPSeq Input control Input control Brown preadipocyte cell_input DNA Unclassified Unclassified K4me1 ab9051 bone marrow Histone H3K4me3 H3K4me3 (Merck Millipore, catalogue number 04-745) E14 RNA polymerase RNA polymerase II RNA Polymerase II C57BL/6 LXRdKO mouse liver RNA polymerase RNA polymerase II RNA Polymerase II C57BL/6 wild type mouse liver Histone H3K27me3 Cell Signaling C36B11 ES cell Histone H3K9me3 Abcam ab8898 ES cell Unclassified Unclassified whole brain Histone H3K9ac H3K9Ac (ab4441; Abcam) AML cells Histone H3 H3 (ab1791; Abcam) AML cells Unclassified Unclassified Stably transfected P19 embryonic carcinoma cells Input control Input control none bone marrow macrophages Others Stat1 anti-STAT1 (santa cruz: sc-417) bone marrow macrophages Others Smad2 anti-Smad2/3 Cell Signaling Technology/8685 mouse embroid bodies Histone H3K9me2 Mouse anti-H3K9me2 (Abcam: ab1220) genomic DNA, Mnase Histone H3K4me2 Rabbit anti-H3K4me2 (Millipore: 07-030) genomic DNA, Mnase Histone H3.1 H3.1/2 Primary Cortical Neurons (E16.5 DIV8) Histone H3.3 H3.3 Adult Hippocampal NeuN- Cells (~7 weeks postnatal) Others Biotin M280 streptavidin Dynabeads Primary Cortical Neurons (E16.5 DIV8) Histone H3K27me3 H3K27me3 (Cell Signaling, 9733S, Lot 8) Terminally Differentiated Podocyte Others Vdr anti-VDR (Santa Cruz Biotechnology; sc-1008) proxmial half site of small intestine Input control Input control none F9 embryonal carcinoma cells Input control Input control none P19 embryonal carcinoma cells Histone H3K27me3 H3K27me3 primary CD4+ T cells from spleen and lymph nodes Others Rxra polyclonal anti-RXRa embryonal carcinoma cells Others Foxa2 FOXA2 Homogenized Mouse Liver Unclassified Unclassified Mouse nucleus accumbens 24 hr Unclassified Unclassified source 0HA74+75 Others Irf4 IRF4 M17 (sc-6059) Input control Input control none Mouse embryonic fibroblasts Input control Input control input spermatocytes Histone H3K27ac H3K27ac liver tissue Histone H3K27me3 H3K27me3 CD4+ Th1 Input control Input control none mESCs Input control Input control NA C3H10T1/2 cells Histone H3K27ac ab4729 (lot#741806) C3H10T1/2 cells Histone H3K4me1 ab8995 (lot#766313) C3H10T1/2 cells Input control Input control none Mouse embryonic fibroblast Others Nr1d1 Rev-erbalpha liver Histone H3K4me1 H3K4me1 3T3L1 Histone H3K36me3 H3K36me3 3T3L1 Histone H3K27me3 H3K27me3 3T3L1 Others Gata1 Gata1 FDCPmix Unclassified Unclassified ES-E14TG2a Histone H3K27ac H3K27Ac CD4+ Th1 Input control Input control none (input) mouse embryonic fibroblasts Others Rpa1 RPA thymocyte Others Hdac3 Anti-HDAC3, ab7030, Abcam Mouse liver Input control Input control input DNA control Mouse Histone H3K4me1 H3K4me1 Mouse embryos Histone H3K4me1 H3K4me1 P19Cl6 Unclassified Unclassified MIN6 cells Input control Input control none mouse embryo Input control Input control none E11.5 embryonic hearts Unclassified Unclassified RAG1-/-pro-B cells Unclassified Unclassified cortex Unclassified Unclassified MEF_WT Others Rag2 RAG2 thymocytes Histone H2A.XS139ph anti-gammaH2AX mIMCD3 RNA polymerase RNA polymerase II RNAPII Others Rxra RXR Others Pparg PPARg Others Tet3 TET3 Unclassified Unclassified ERS401876 Others Srf SRF bone marrow-derived macrophages Histone H3K4me1 anti-H3K4me1 (Abcam, ab8895) Primary bone marrow-derived macrophages (BMDM) Histone H3K27ac H3K27Ac Abcam AB4729 Embryonic stem cells Input control Input control Input Embryonic stem cells RNA polymerase RNA polymerase II RNA Pol II Abcam AB817 Embryonic stem cells Others Brd4 Brd4 (Bethyl; IHC-00396) primary T cells Input control Input control no antibody (input DNA sequencing) Embryonic stem cells Others Epitope tags anti-HA (Roche, Basel,Switzerland) Embryonic stem cells Histone H4K20me1 Anti- H4K20me1 Abcam (Cat. No. ab9051) mouse primary cortical neuron Histone H3K4me3 H3K4me3 pancreatic islets Input control Input control none (input) pancreatic islets Input control Input control Control none (input) CD4+CD8+ double positive thymocytes Histone H3K9me2 anti-H3K9me2 (Abcam; ab1220; Lot: GR138716-1) Murine MLL-AF9 leukemic cells Histone H3K9ac anti-H3K9ac (Abcam; ab4441; Lot: GR171767-1) Murine MLL-AF9 leukemic cells Histone H3 crosslink anti-H3 (ab1791) Embryonic stem cells Input control Input control None Embryonic fibroblast Others Meis1 Meis1/2 (Santa Cruz Biotechnology, sc-10599X, lot# C2912) Embryonic fibroblast Input control Input control none Neural progenitor cells Unclassified Unclassified Embryonic Stem Cells Unclassified Unclassified ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells Others Foxp3 Foxp3 antibody is a custom polyclonal antibody that has been affinity purified Activated Treg Others Biotin streptavidin-conjugated beads embryonic stem cells Histone H3K27me3 H3K27me3 (Millipore 07-449) ES cells Others Ebf1 abnova 1879-mol clone 1c12 Haftl pre-B cells Others Spi1 PU.1 (sc-352, Santa Cruz) Haftl pre-B cells Others Cebpb C/EBPb (sc-150, Santa Cruz) Haftl pre-B cells Histone H3K27ac H3K27Ac (ab4729, Abcam) Haftl pre-B cells Histone H3K27me3 H3K27Me3 (17-622, Millipore) Haftl pre-B cells Histone H3K4me1 H3K4Me1 (037-050, Diagenode) Haftl pre-B cells Unclassified Unclassified Nave CD4+ T cells Histone H3K27ac H3K27ac (Abcam, catalog# ab4729, lot# GR45851-1) Primary B-cells RNA polymerase RNA polymerase II RNAPII (Santa Cruz, catalog# sc-899, lot# F0112) Primary B-cells Unclassified Unclassified Primary thioglycollate-elicited peritoneal macrophages Others Runx3 Runx3 poly clonal home made Splenic CD8+ T cells Histone H3K36me3 H3K36me3 (Abcam, Ab9050, lot 707946) ES cells Histone H3K4me3 H3K4me3 (Active, Motif, lot 39159) ES cells Input control Input control input Rag1 -/- pro-B cells Others Atf3 ATF3 (Santa Cruz, catalog# sc-188, lot# L2214) bone marrow-derived macrophages Others Jund JunD (Santa Cruz, catalog# sc-74, lot3 A3015) bone marrow-derived macrophages Others Junb JunB (Santa Cruz, catalog# sc-46, lot# F1814) bone marrow-derived macrophages Others Fos Fos (Santa Cruz, catalog# sc-253, lot# I0808) bone marrow-derived macrophages Others Cebpd CEBPd (Santa Cruz, catalog# sc-151, lot# K1711) bone marrow-derived macrophages Others Cebpb CEBPb (in-house rabbit polyclonal antisera for mouse CEBP aa 22-195) bone marrow-derived macrophages Others Ctcf abcam, ab70303 activated B cell Others Ctcf abcam, ab70303 resting B cell Others Rad21 abcam, ab992 resting B cell RNA polymerase RNA polymerase II Anti Pol II antibody (QED Bioscience) ESC cells Others Epitope tags anti-HA antibody (ab9110, abcam) SHH medulloblastoma Unclassified Unclassified mouse embryonic stem cells Input control Input control input DNA Others Myc Anti-Myc (Santa-Cruz sc-764) Primary bone marrow-derived macrophages (BMDM) Input control Input control none Lgr5+ intestinal stem cells from adult mice Input control Input control none enterocyte from adult mice Histone H3K27ac H3K27ac (abcam, ab4729) Cranial neural crest cells Input control Input control none CD8+ T cell Histone H3K27me3 H3K27me3 antibody (Millipore, 07-449, lot 2652971) CD8+ T cell Others Smc5 Smc5 Calbiochem, DR1030 Splenic B Cells Others Brca1 Brca1 mouse monoclonal raised against mouse BRCA1 (160-300 amino acids) Splenic B Cells Others Rpa2 RPA Calbiochem, RPA34-20 Splenic B Cells Histone H2Bac AcH2B (in-house made rabbit whole antiserum) Unclassified Unclassified Mouse keratinocyte cell-line 2 Unclassified Unclassified Mouse keratinocyte cell-line 1 Histone H3K27me3 Histone H3 trimethyl Lys27 mammary gland Others Stat3 STAT3 (Santa Cruz, sc-482) Mammary Input control Input control None ZHBTc4 ES cells Histone H3K4me3 Anti-Trimethyl Histone H3 (Lys4) Antibody, (Millipore, clone: CMA304, catalog#: 05-1339, lot#: 2024897) Sorted cells Histone H3K27me3 Anti-trimethyl Histone H3 (Lys27) Antibody (Millipore, catalog#: ABE44, lot#: 1966928) Sorted cells Histone H2A.X H2A.X iPS cell from B cell Others Rpa2 anti-RPA32 Calbiochem NA19L, lot#D00127062 Primary B cells Histone H3K27me1 H3K27me1 (Millipore, 07-448, lot unknown) ES cell line Others Batf anti-BATF cultured TH2 cells Others Spi1 anti-PU.1 (rabbit polyclonal against the N-terminus (aa. 1-100)) Primary bone marrow-derived macrophages, no treatment, PU.1 ChIP Histone H3K27ac anti-H3K27ac Primary bone marrow-derived macrophages, no treatment, H3K27ac ChIP Histone H3K9me3 H3K9me3 3T3-L1 preadipocytes Others Meis1 anti-Meis1, Abcam, ab19867 RA-treated P19 EC cells, Meis1 ChIP Histone H3K27ac anti-H3K27ac, Abcam, ab4729 RA-treated P19 EC cells, H3K27ac ChIP Histone H3K4me1 anti-H3K4me1, Abcam, ab8895 RA-treated P19 EC cells, H3K4me1 ChIP Unclassified Unclassified ESC time-ChIP 12h timepoint Unclassified Unclassified ESC time-ChIP 6h timepoint Unclassified Unclassified ESC time-ChIP 3h timepoint Unclassified Unclassified ESC time-ChIP 0h timepoint Histone H3K27ac abcam, ab4729 activated B cell Input control Input control - embryonic forelmb bud, ChIP input Others Irf4 IRF4 (Santa Cruz, sc-6059, k1209) CD4+ T Cells Others Hdac3 HDAC3 Abcam ab7030 hippocampus Others Nr1h3 LXR (Santa Cruz sc-1000X, Lot:I0310, Abcam ab-41902, lot:GR9889-3, Active Motif 61177, lot:29111001) peritoneal thioglycolate-elicited macrophages Histone H3K27me3 H3K27me3 (Active Motif cat # 39155) B cell Unclassified Unclassified immunoprecipitated DNA primary lung tumor-drived cells Unclassified Unclassified Brown preadipocyte cell Histone H3K4me2 H3K4me2 (07-449, Upstate, Charlottesville, VA, lot 26335, cat#07-030) retina Histone H3K9ac H3K9ac Ab (Upstate 07-352, LOT# DAM1394804) Mature B Histone H3K4me3 H3K4me3 Ab (Abcam ab8580-100) Mature B Histone H3K27me3 H3K27me3 Ab (gift from T.Jenuwein) Pro-B Others Rnf2 Ring1B (custom-made) embryonic stem cells Unclassified Unclassified Epiblast stem cells_freed from Activin Others Med1 Med1 (A300-793A; Bethyl) MLL-AF9/NrasG12D murine cell line Unclassified Unclassified Differentiated trophoblast stem cells Unclassified Unclassified mouse ES cells E14 Histone H3K4me3 H3K4me3 (Abcam ab8580) whole adult testis Histone H3 anti-H3 (Abcam, catalog# ab1791) H3.F/F Histone H3 anti-H3 (Abcam, catalog# ab1791) H3.FC/FC Others Gata1 polyclonal rabbit a-GATA-1 produced in-house (H Im et al. PNAS 2005) ES-cell derived erythroid progenitors Input control Input control none Primary HSPC Cells Others Tcf3 sc-349 Haftl pre-B cells RNA polymerase RNA polymerase II Pol II (sc-899x, Santa Cruz) Haftl pre-B cells Unclassified Unclassified Primary B cells Others Ikzf1 Ikaros-N terminal Ab (IkN) Whole Thymus Others Ezh1 EZH1 (a generous gift from Dr. Sartorelli) Mammary gland Unclassified Unclassified Splenic CD4+ T cells Histone H3K27ac H3K27Ac (Active Motif, cat. no. 39135) Splenic CD4+ T cells Others Ncaph2 CAPH2 Bethyl A302-275A Embryonic stem cells Unclassified Unclassified Jejunal epithelial cells Others Rxra In house: peptide: mRXRa: PB105 (MDTKHFLPLDFSTQVNSSSLNSPTGRGC) P19 embryonal carcinoma cells RNA polymerase RNA polymerase II Santa Cruz sc-9001 P19 embryonal carcinoma cells Histone H3K27me3 Millipore 07-449 P19 embryonal carcinoma cells Histone H3K4me3 Abcam ab8580 P19 embryonal carcinoma cells Others Rxra In house: peptide: mRXRa: PB105 (MDTKHFLPLDFSTQVNSSSLNSPTGRGC) F9 embryonal carcinoma cells RNA polymerase RNA polymerase II Santa Cruz sc-9001 F9 embryonal carcinoma cells Histone H3K27me3 Millipore 07-449 F9 embryonal carcinoma cells Unclassified Unclassified Es cells nascent strands RNA polymerase RNA polymerase II polyclonal anti-RNA-PolII (H-224) embryonal carcinoma cells Others Rarg polyclonal anti-RARg embryonal carcinoma cells Histone H3K9me3 H3K9me3 Mouse nucleus accumbens 24 hr Others Esr1 ER Ab-10 Conditional Myb transformed myeloid cell line Others Stat3 STAT3 murine Irf4 deficient CD4+ T Histone H3K9me3 H3K9me3 (Ab8898) V6.5 mES cells Input control Input control input_DNA source ERS129490 Histone H3K27me3 H3K27-3me source ERS129492 Histone H3K4me3 H3k4-3me source ERS129491 Others Bcl11a Bcl11a source ERS129489 Histone H3K27me2 H3K27-3me source ERS129486 Histone H3K4me3 H3k4-3me source ERS129485 Others Bcl11a Bcl11a source ERS129484 Others Mbd3 source Mbd3_WT1 Unclassified Unclassified 0.5% formaldehyde 5min fixation. Unclassified Unclassified For comprehensive analysis of Ras-dependent changes in H3K27me content, we performed ChIP-seq analyses at various times after Ras induction. We sampled NIH 3T3 cells at 0, 2, 4, 7, and 12 days after infection with the H-Ras(G12V) retroviral vector. ChIP-seq libraries were prepared from ~40 ng each of ChIP and input DNA with the use of a TruSeq DNA LT Sample Prep Kit (Illumina, San Diego, CA). Libraries were clonally amplified in a flow cell and sequenced with the use of HiSeq Control Software 1.5 (Illumina) and a 48-nucleotide paired-end sequence. Image analysis and base calling were performed with the use of Real Time Analysis (RTA) 1.13 software. Unclassified Unclassified 0.5% formaldehyde 5min fixationThe H3f3a (purchased from Operon Biotechnologies) used for expression of H3.3. The cDNA were ligated into the Bidirectional Tet Expression Vector pT2A-TRETIBI (modified Clontech Tet-On system), which contains TolII transposon elements and EGFP cDNA located upstream of the cDNA sequence and which was modified from pT2AL200R150G (provided by Dr. Kawakami). The pT2A-TRETIBI/EGFP-H3.3 transfection was performed using Lipofectamine 2000 reagent (Life Technologies, Carlsbad, CA). C2C12 cells at 20% to 30% confluence were transfected with an expression vector, pCAGGS-TP coding transposase (provided by Dr. Kawakami), and pT2A-CAG-rtTA2S-M2 and incubated for 24 h. To create cell lines stably expressing GFP-H3.1 , transfected cells were cultured for 14-21 days in the presence of doxycycline and G418. Finally, the GFP positive cells in the stable lines were selected using fluorescence activating cell-sorting. Unclassified Unclassified 0.5% formaldehyde 5min fixationThe Hist1h3a (purchased from Operon Biotechnologies) used for expression of H3.1 . The cDNA were ligated into the Bidirectional Tet Expression Vector pT2A-TRETIBI (modified Clontech Tet-On system), which contains TolII transposon elements and EGFP cDNA located upstream of the cDNA sequence and which was modified from pT2AL200R150G (provided by Dr. Kawakami). The pT2A-TRETIBI/EGFP-H3.1 transfection was performed using Lipofectamine 2000 reagent (Life Technologies, Carlsbad, CA). C2C12 cells at 20% to 30% confluence were transfected with an expression vector, pCAGGS-TP coding transposase (provided by Dr. Kawakami), and pT2A-CAG-rtTA2S-M2 and incubated for 24 h. To create cell lines stably expressing GFP-H3.1 , transfected cells were cultured for 14-21 days in the presence of doxycycline and G418. Finally, the GFP positive cells in the stable lines were selected using fluorescence activating cell-sorting. Input control Input control none E14 Histone H3K79me2 H3K79me2 Unclassified Unclassified hippocampal tissue hippocampus Histone H3K27me3 H3K27me3 pancreatic islets Input control Input control NULL shLuc ES cells Others Smarca4 Brg1 (Abcam, ab110641) bone marrow-derived macrophages Unclassified Unclassified iWAT Unclassified Unclassified Primary tissue Fore Brain Input control Input control None (Total Input) Unclassified Unclassified Streptavidin pro-B Input control Input control none ESCs Input control Input control none RN2 Input control Input control n/a Testis Input control Input control WCE hippocampus Input control Input control MEF_Smarcb1-KO Histone H3K4me2 20130911_H3K4me2 Others Foxa1 Foxa1 liver Others Hdac3 HDAC3 Liver Others Sin3b Sin3B C2C12 myotubes RNA polymerase RNA polymerase II RNAP-II ab5408 Adult_Tissue Input control Input control IgG murine CD4+ T Input control Input control IgG source ERS129488 Input control Input control IgG source ERS129483 Histone H3K4me3 H3K4me3 T cells Input control Input control none AB1 ES cells Others Suz12 Suz12 (A302-407A; Bethyl) mouse embryonic stem cells Others Ep400 p400 (A300-541A; Bethyl) mouse embryonic stem cells Others Rad21 Bethyl 300-080A immortalized fibroblast Others Ctcf Millipore 07-729 immortalized fibroblast Histone H2AK119Ub H2AK119 ubiquitination Cell signaling D27C4/2 Lin- HSC RNA polymerase RNA polymerase II anti-Pol II (Santa Cruz, sc-899) Primary bone marrow-derived macrophages (BMDM) RNA polymerase RNA polymerase II anti-Ser2 Pol II (Chromotek, 3E10) Primary bone marrow-derived macrophages (BMDM) Histone H3K4me3 anti-H3K4me3 (Active Motif, #39159) Primary bone marrow-derived macrophages (BMDM) Histone H3K36me3 anti-H3K36me3 (Abcam, ab9050) Primary bone marrow-derived macrophages (BMDM) Histone H3K27ac anti-H3K27ac (Abcam, ab4729) Primary bone marrow-derived macrophages (BMDM) Histone H3K4me3 H3K4me3 (Abcam, ab8580) Bone marrow derived macrophages Histone H3K27ac H3K27ac (Abcam, ab4729) Bone marrow derived macrophages Others Nbn anti-Nbs1 (Abcam, ab32074) splenic B cells RNA polymerase RNA polymerase II RNAPolII (8WG16 monoclonal antibody) Bone marrow derived dendritic cells Histone H3K27ac H3K27ac NIH3T3 cells Histone H4K8ac H4K8ac (ab15823; Abcam) MLL-AF9/NrasG12D murine cell line Histone H3K27ac H3K27ac (ab4729; Abcam) MLL-AF9/NrasG12D murine cell line Histone H3K56ac H3K56ac (abcam, ab76307) Embryonic stem cells (ESCs) Histone H3K9ac H3K9ac (Millipore, 07-352) Embryonic stem cells (ESCs) Histone H3K27ac Abcam ab4729, lot: GR24371-1 Placenta Histone H3K27me3 H3K27me3 (Mllipore, 07-449, lot 2194165) Neural stem cells Histone H3K4me3 H3K4me3 (Millipore, 07-473, lot JBC1863338) Neural stem cells Others Smchd1 Smchd1 (Abcam, ab31865, lot GR52946-1) Neural stem cells Unclassified Unclassified Day10 Neurons Histone H4K20me1 H4K20me1 (Abcam, catalog# ab9051, lot# GR4867-1) Hippocampus Histone H3K9me3 H3K9me3 (Abcam, catalog# ab8898, lot# GR79978-1 and also 960144 earlier) Hippocampus Histone H3K4me1 H3K4me1 (Abcam, catalog# ab8895, lot# GR61280-1) Hippocampus Histone H3K36me3 H3K36me3 (Abcam, catalog# ab9050, lot# GR82518-1 and also 750267 earlier) Hippocampus Histone H3K27me3 H3K27me3 (Millipore, catalog# 07-449, lot# 1999681) Hippocampus Histone H3K27ac H3K27ac (Abcam, catalog# ab4729, lot# GR87165-1) Hippocampus Input control Input control none MEF cell culture Others Sirt1 Anti-Sirt1 (Upstate, 07-131) Satellite cells Histone H3K27ac H3K27ac (Active Motif, catalog# 39133, lot# 01613007) Immortalized MEF Others Smarca4 anti-BRG1 (Abcam, catalog# 110641, lot#YG081901C) Differentiated embryonic stem cells Histone H3K27ac H3K27ac (Active Motif, cat#: 39133, lot#: 105) Nave CD4 T cells RNA polymerase RNA polymerase II Anti- Pol II Santa Cruz Biotechnology (Cat. No. sc-899X) mouse primary cortical neuron Others Kdm1a Anti- LSD1 Abcam (Cat. No. ab17721) mouse primary cortical neuron Others Epitope tags Anti- M2 Sigma (Cat. No. A2220) mouse primary cortical neuron Histone H3K4me1 Anti-H3K4me1 Abcam (Cat. No. ab8895) mouse primary cortical neuron Histone H3K36me3 Anti- H3K36me3 Millipore (Cat. No. 07-549 ) mouse primary cortical neuron Histone H3K4me3 Millipore 07-473 Hematopoietic stem cells (HSC) Histone H3K27me3 Millipore 07-449 Hematopoietic stem cells (HSC) Others Stat3 STAT3 (Invitrogen, 13-7000) Pre-activated CD4+ T cells Others Tal1 Scl/Tal1 ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells Others Creb1 pCREB (Millipore, Ser 133, 06-519) MC3T3-E1 (pre-osteoblast) Input control Input control input mouse bone marrow derived macrophages Others Nr3c1 BuGR2, monoclonal (Pierce/ThermoFisher) mouse bone marrow derived macrophages Unclassified Unclassified Neural progenitor cells Histone H3K27ac H3K27Ac Anti-acetyl lysine 27 of histone H3 (Active Motif, catalog number 39133) CD4+CD8+ double positive thymocytes RNA polymerase RNA polymerase II Pol II (Santa Cruz, N20) ES cell culture Histone H3K4me1 H3K4me1 (Homemade #24) ES cell culture Histone H3K27ac H3K27ac (Abcam, ab4729) ES cell culture Histone H3K27me3 H3K27me3 (Homemade #67) ES cell culture Histone H3K79me2 anti-H3K79me2 (Abcam; ab3594; Lot: GR46675-1) Murine MLL-AF9 leukemic cells Histone H3K27me3 anti-H3K27me3 (Upstate; 07-449; Lot: DAM1421462) Murine MLL-AF9 leukemic cells Others Zic1 anti-Zic 1/2 C-terminus whole cerebellum Histone H3K27me3 H3K27me3 (Diagenode #pAb-069-050) primordial germ cells Histone H3K9me3 H3K9me3 (Active Motif #39161) primordial germ cells Unclassified Unclassified invitro differentiated murine cardiomyocytes (CM7/1) Unclassified Unclassified murine embryonic stem cells (CM7/1) RNA polymerase RNA polymerase II Pol2 Millipore:17-672, lot54931 Heart Histone H3K4me3 H3K4me3 Active Motif:39159, lot832164 Heart Others Fos sc7202 DIV7 mCTX neurons Histone H3K27ac ab4729 DIV7 mCTX neurons Histone H3K4me1 H3K4me1 (abcam ab8895) Pro B Histone H3K4me1 H3K4me1 (abcam ab8895) HSC Histone H3K27ac H3K27Ac Abcam AB4729 Neural Progenitors Others Epitope tags anti-FLAG M2 antibody (Sigma #F3165) mouse embryonic stem cells Histone H3K27me3 anti-H3K27me3 (07-449, Millipore) ES Cell(2i) Histone H3K9me3 anti-H3K9me3 (ab8898, Abcam) ES Cell(2i) Histone H3K4me3 anti-H3K4me3 (39159, Active Motif) ES Cell(2i) Unclassified Unclassified JMJD3-KO Nave CD4+ T cells Unclassified Unclassified WT Nave CD4+ T cells Unclassified Unclassified NIH3T3 fibroblasts Histone H4ac H4 Ac (Millipore, 06-866 ) NIH3T3 fibroblasts RNA polymerase RNA polymerase II Pol II (Santa Cruz Biotechnology, N20, sc-899) NIH3T3 fibroblasts Histone H3K27ac H3K27Ac ( abcam, ab4729) NIH3T3 fibroblasts Others Cdk9 CDK9 (Santa Cruz Biotechnology, sc-8338) NIH3T3 fibroblasts Others Brd4 BRD4 (C-terminus) made in house NIH3T3 fibroblasts RNA polymerase RNA polymerase II anti-RNAPII N-20 (Santa Cruz, sc-899) Embryonic Stem Cells Histone H3K27me3 H3K27me3 SV40T transformed fibroblasts Others Ezh2 EZH2 SV40T transformed fibroblasts Input control Input control None embryonic stem cells Histone H3K27me3 H3K27me3 mouse hippocampus Others Pou5f1 Oct4 (Santa Cruz sc-8628) embryonic stem cells (ESC) Others Cebpa CEBPA p30-GMP-blast cells, from pool of Biological repl_I_II_III, CEBPA ChIP Histone H3K4me1 Abcam, ab8895 Liver Others Meis1 Meis (Abcam, catalog# ab19867, lot# GR76623-1) c-kit+ bone marrow cells Others Tgif1 TGIF (H-172) (Santa Cruz Biotechnology, catalog# sc-9084, lot# K2608) c-kit+ bone marrow cells Others Crebbp CBP (CREBBP) Brindle 8690 primary CBP null MEF (e14.5) Others Crebbp CBP (CREBBP) Brindle 8690 primary wild type MEF (e14.5) Histone H3K4me3 anti H3K4me3, Diagenode pAb-003-050, Lot.: A5051-001P Pro-B cell Histone H3K9ac anti H3K9ac, Millipore 07-352, Lot: DAM1813175 Pro-B cell Histone H3K27me3 H3K27me3 (Millipore 07-449) in vitro differentiated cells Histone H3K9K14ac H3K9,K14ac (Millipore, Catalog# 06-599, Lot# 2019589) Embryonic stem cells Others Ep300 Sc-585x Haftl pre-B cells Histone H3K27me3 Millipore, 07-449 main olfactory epithelium Histone H3K27me3 H3K27me3 17-622, Millipore Heart Others Gata4 Gata4_Ab sc-1237x, Santa Cruz Heart Others GFP Custom GFP antibody Embryonic Stem Cells Unclassified Unclassified mouse embryo fibroblasts (MEF) Histone H3K27ac H3K27ac (Active Motif #39133) MC1-ZE7 ES cells Histone H2A.XS139ph H2AX (Millipore, Catalog# 05-636, Lot# 2116620) Mouse embryonic fibroblasts Histone H4K5ac H4K5ac (Millipore 07-327) Primary thioglycollate-elicited peritoneal macrophages Input control Input control input mouse embryonic stem cell Others Kmt2d MLL4 mouse embryonic stem cell Histone H3K27ac H3K27ac mouse embryonic stem cell Histone H3K4me1 H3K4me1 mouse embryonic stem cell Input control Input control none mouse brown preadipocytes, MLL4 KO, input Input control Input control none mouse brown preadipocytes, WT, input Others Kmt2d MLL4 mouse brown preadipocytes, MLL4 KO, MLL4 ChIP Others Kmt2d MLL4 mouse brown preadipocytes, WT, MLL4 ChIP Input control Input control Non-immune rabbit serum Splenic CD8+ T cells Input control Input control Non-immune rabbit serum Splenic NK cells Others Runx3 Runx3 poly clonal home made Splenic NK cells RNA polymerase RNA polymerase II anti-RNAPII (AC-055-100; Diagenode) 3T3-L1 adipocytes (Day 7) Others Pparg anti-PPAR (sc-7196; Santa Cruz) 3T3-L1 adipocytes (Day 7) Input control Input control none (input) embryonic fibroblasts treated with BAM factors Histone H4K8ac H4K8ac (Millipore 07-327) Bone marrow derived macrophages Histone H3K36me3 Abcam (ab9050) Embryonic stem cells Histone H3K36me2 Abcam (ab9049) Embryonic stem cells RNA polymerase RNA polymerase II S2 PolII, (ab5095, Abcam) Embryonic Stem Cells RNA polymerase RNA polymerase II Total PolII, (sc-899, Santa Cruz Biotechnology) Embryonic Stem Cells Input control Input control none Embryonic Stem Cells Histone H3K4me3 H3K4me3 Millipore 07-473 Hematopoietic stem cells (HSC) Others Rbpj anti-RBPJ antibody (custom-made) F9_RBPJ_ChIP-seq Others Mef2a MEF2 heart ventricles from 8 week old mouse RNA polymerase RNA polymerase II PolII heart ventricles from 8 week old mouse Others Esr1 Eralpha, Santa Cruz sc-542 uterus Others Suz12 Suz12 (Cell Signaling, D39F6) Primary CD4+ Th cells Unclassified Unclassified Hippocampal CA neurons Histone H3K4me3 Rabbit anti-Histone H3 trimethyl K4 (activemotif 35159, lot #: 01609004) Mouse Prostate Histone H3K4me1 Rabbit Anti-Histone monomethyl-H3 (Abcam ab8895, Lot GR61280-1) Mouse Prostate Others Erg Rabbit Anti-ERG (Epitomics Clone EPR3864) Mouse Prostate Others Ar Rabbit Anti-AR (Epitomics Clone ER179) Mouse Prostate Histone H3K9ac H3K9ac (Abcam, ab4441) Striatal Progenitor Cells Histone H3K27me3 H3K27Me3: Cell Signaling, C36B11 Haematopoietic progenitor cells Histone H3K4me3 H3K4Me3: Cell Signaling, C42D8 Haematopoietic progenitor cells RNA polymerase RNA polymerase II RNAPII N20 (Santa Cruz, sc-899) embryonic fibroblasts, E13.5 Histone H3K27ac H3k27Ac antibody (ab4729; Abcam) SHH medulloblastoma Unclassified Unclassified Mouse embryonic day 11.5 (e11.5) face Histone H3K27ac H3K27ac (Abcam ab4729) Mammary Histone H3K27me3 H3K27me3 (Abcam ab6002) Mammary Histone H3K27ac H3K27ac (active motif cat#:39133) Heart Others Ezh1 EZH1 (a gitf from Jian Xu) Heart Unclassified Unclassified Embryonic cortex Histone H4K16ac H4K16ac (Millipore Cat No 07329) Mouse Embryonic Fbroblast Others Esr1 cocktail of Ab-10 from Labvision and sc-543 from Santa Cruz 3617 cells expressing ER DBD mutant RNA polymerase RNA polymerase II RNAPII, Abcam, ab5131 Histone H3 H3 (Abcam, ab1791) Embryonic stem cells Histone H3K4me3 H3K4me3 (mouse monoclonal antibody provided by Dr. H. Kimura using in Hayashi-Takanaka,Y et al., Nucleic Acids Research, 2011. ) Embryonic stem cells Histone H3K27ac H3K27ac (mouse monoclonal antibody provided by Dr. H. Kimura using in Hayashi-Takanaka,Y et al., Nucleic Acids Research, 2011. ) Embryonic stem cells Input control Input control none Cerebellar Granule Cells Others Ep300 P300 antibody (N-15), Cat#sc-584; RRID:AB_2293429 3T3-L1 preadipocytes Others Ncor1 NCoR antibody, Cat#A301-145A; RRID:AB_873085 3T3-L1 preadipocytes Others Hdac3 HDAC3 antibody (H-99), Cat#sc-11417; RRID:AB_2118706 3T3-L1 preadipocytes Others Hdac2 HDAC2 antibody, Cat#A300-705A; RRID:AB_533399 3T3-L1 preadipocytes Others Smc1a SMC1 (Bethyl, A300-055A) Mammary Others Suz12 anti-SUZ12 (Bethyl A302-407A) Differentiated embryonic stem cells Histone H3K27ac anti-H3K27ac (ActiveMotif #39134) Differentiated embryonic stem cells Histone H3K27me3 H3K27Me3 CD8 T cells Histone H3K4me3 H3K4Me3 CD8 T cells Others Ehmt2 anti-G9a; Sigma (G6919) cardiomyocyte Others Epitope tags anti-FLAG (Sigma, catalog number F1804) Mouse Embryonic Stem Cells Histone H3K36me3 H3K36me3 liver tissue Histone H3K27ac H3K27ac (ABCAM ab4729) embryonic stem cells Others Smarcad1 ab67548(Abcam) Embryonic stem cells Others Suz12 Suz12 (Active motif, catalog# 39357, lot# 28612003) NIH/3T3 cells Unclassified Unclassified MEFs expressing OSKM and Esrrb for 48h Unclassified Unclassified pre-iPSC line 2(1A2) Histone H3K27ac H3K27ac (Abcam ab4729) Jejunal intestinal epithelial cells Others Epitope tags Mouse anti-FLAG (Sigma-Aldrich, F3165) and Rat anti-mCherry (ThermoFisher Scientific, M11217) testes Input control Input control Input DNA pre-B cell line B3 Histone H3K27me3 H3K27me3: Millipore #17-622 EpCAM+ epithelium from small intestine Histone H3K27ac H3K27Ac: Abcam 4729 EpCAM+ epithelium from small intestine Histone H3K4me3 H3K4me3: Millipore #07-473 EpCAM+ epithelium from small intestine Histone H2A.Z H2A.Z: Active Motif, #39113 EpCAM+ epithelium from small intestine Unclassified Unclassified H3K27me3 (Millipore, Cat. # 07-449) and H3K4me2 (Millipore, Cat. # 07-030) Cranial neural crest cells Others Epitope tags anti-HA (Roche 11867423001) Histone H3K4me3 H3K4me3: Millipore 07-473, lot # DAM1731494 (7.5uL per ChIP) Histone H3K36me3 H3K36me3: Abcam ab9050-100, lot # 136352 Histone H3K27me3 H3K27me3: Abcam ab6002-100, lot # 49749 Others Epitope tags HA (abcam #9110) mouse embryonic fibroblasts Others Cbx7 Rabbit anti-Cbx7 Mouse embryonic stem cells Unclassified Unclassified ES cell ES cell Others Elf4 Elf4 home made antibody Primary bone marrow-derived macrophages (BMDM); 7th day of differentiation Unclassified Unclassified A-MuLV transformed pro-B cells (Ebf1fl/fl;RERTCre), 2M 4-hydroxy-tamoxifen (4-OHT) treated Histone H3K9K14ac AcH3K9,14; Anti-acetyl-Histone H3 Antibody Histone H3K27me3 H3K27Me3,Cell Signaling, C36B11 Hematopoietic Stem Cells Histone H3K4me3 H3K4Me3, Cell Signaling, C42D Hematopoietic Stem Cells Histone H3K4me3 mouse ES cells, shluc control, H3K4me3 ChIP Others Epitope tags HA-antibody (Abcam, ab9110) ESC WITH LIF Input control Input control None Th1 cells Histone H3K9ac H3K9Ac (Abcam, ab4441) Th1 cells Others Rad51 Rad51 in vitro activated B cells Input control Input control none iPS cell from B cell Others Ctcf CTCF (Millipore, Cat. No. 07-729, Lot No. DAM1745366) Limb bud RNA polymerase RNA polymerase II Pol II murine embryonic stem cells Others Ezh2 Ezh2 (Cell signaling, 5246S, lot unknown) ES cell line Unclassified Unclassified day4 reaggregated Embryoid bodies Others GFP anti-GFP antibody (ab290, Abcam) Adipocite Input control Input control None Medial ganglionic eminence Others Tet1 Tet1 (home-made; same as the one used for ChIP-seq in PMID 21514197) mESCs Others Ep300 p300 mouse embryonic stem cell Histone H3K27ac H3K27Ac, Abcam Ab4729 whole cerebellum Input control Input control Mutation at binding site from ESC_WT Histone H3K27me3 H3K27me3 (Milipore: 07-449) Embryonic Midbrain Unclassified Unclassified ES cells. Ssea1+ fraction sorted after 30h of re-culture from the HV+S+ popultation. Unclassified Unclassified ES cells. Ssea1+ fraction sorted after 30h of re-culture from the HV-S+ popultation. Histone H3K4me3 H3K4me3 3T3-L1 preadipocytes Histone H3K27me3 H3K27me3 whole liver extract Histone H3K4me2 H3K4me2 whole liver extract Histone H3K36me3 H3K36me3 whole liver extract Histone H3K4me3 H3K4me3 (Abcam ab8580) Embryonic stem cell (ESC) Others Pparg PPARg immortalized brown adipocytes Others Batf Batf Th17 in vitro Others Batf Batf Th0 in vitro Histone H3K27me3 H3K27me3 (07-449, Millipore) Embryonic stem cell Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. Heart Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. Liver Input control Input control Input conditional KO Rb MEF Others Crtc2 CRTC2-ChIP 3T3-L1 preadipocytes Others Atoh1 GFP Atoh1 Binding sites Mouse Histone H3K27ac abcam, ab4729 resting B cell RNA polymerase RNA polymerase II Mouse anti-Pol II (Abcam, ab817) testes Histone H3K36me3 anti-H3K36me3 (Cell Signaling Technology, #4909) L-GMP transformed with MLL-AF9 Histone H3K9me3 anti-H3K9me3 (Abcam ab8898) L-GMP transformed with MLL-AF9 Others Rnf2 ActiveMotif, 39663 Wnt3KO EpiSCs Histone H3K4me3 H3K4me3 (Millipore, 06-598, lot JBC940052) Postnatal only nicotine received Histone H3K4me3 H3K4me3 (Millipore, 06-598, lot JBC940052) Postnatal only saccharin received Input control Input control none Bone marrow Others Fli1 Abcam ab15289 Bone marrow Histone H3K27me3 H3K27me3 Abcam, ab6002 Embryonic Stem Cell Others Suz12 Suz12 Cell Signaling, 3737 Embryonic Stem Cell Others Batf BATF (from Ken Murphy rabbit , not commercial available) CD4+ T Cells Histone H3K27me3 H3K27me3 (anti-trimethyl histone H3 Lys27 07-449 Millipore) Embryonic Stem cells mESCs Others Suz12 Suz12 (anti-Suz12 D39F6 Cell Signalling) Embryonic Stem cells mESCs Histone H3K4me3 H3K4me3 (anti-trimethyl histone H3 Lys4 07-473 Millipore) Embryonic Stem cells mESCs Others Neurog2 Ngn2 anti-Ngn2 (Santa Cruz sc-19233) ES-derived embryoid bodies with induced transcription factors Histone H3K9me3 H3K9me3 (1 ug/ml, Abcam ab8898) Olfactory Epithelium Others Nrf1 anti-Nrf1 antibody (ab34682, Abcam) embryonic stem cell Others Gtf3c1 TFIIIC-220 A301-291A Mouse embryonic stem cells Others Ncaph2 NCAPH2 A302-275A Mouse embryonic stem cells Others Med1 MED1 (Bethyl lab, A300-793A) Mammary Histone H3K4me3 Diagenode 15410003 Lot A5051-01P Undifferentiated ES cells Others Suz12 abcam12073 Lot 140428 -1 Undifferentiated ES cells Others Srebf1 Srebp1 (Santa Cruz sc-8984X, lot:G1811, sc-13551X, lot:E1613, sc367X, lot:G1212) peritoneal thioglycolate-elicited macrophages Unclassified Unclassified Rag2(-/-) pro-B cells Unclassified Unclassified Ebf1/ c-Kit+ fetal liver cells, pmys-EBF1C-IRES-GFP Histone H3K27me3 H3K27me3(Diagnode, pAb-069-050) mouse embryonic stem cells Histone H3K4me3 H3K4me3(Cell signaling Technology, #9727) MII oocyte Histone H3K9me3 H3K9me3 (Millipore and Abcam) Mouse skin Histone H3K27me3 H3K27me3 (EMD Millipore, 07-449) embryonic fibroblast chromatin Unclassified Unclassified pRb; M153 (Santa Cruz, sc-7905), C15 (Santa Cruz, sc-50), S855 (in-house, affinity-purified rabbit Ab), M136 (in-house, affinity-purified sheep Ab), Hyb4.1 (Developmental Studies Hybridoma Bank) embryonic fibroblast chromatin Others Tcf3 Tcf3 Act B cell Unclassified Unclassified Mouse Liver Others Pbx1 anti-Pbx1 (Abnova, Cat# H00005087, Lot# E5141-4A2) C2C12 cell line Others Suz12 Rabbit anti-Suz12 Mouse embryonic stem cells Others Nr3c1 GR Antibody Brown preadipocyte cell Histone H3K27me3 H3K27me3 (07-030, Upstate, Charlottesville, VA, lot 24440, cat.#07-449) retina RNA polymerase RNA polymerase II RNA Pol II (Rpb1 N-terminus) Santa Cruz SC-899 Embryonic stem cells Histone H3K9ac H3K9ac Ab (Upstate 07-352, LOT# DAM1394804) Pro-B Histone H3K4me3 H3K4me3 Ab (Abcam ab8580-100) Pro-B Histone H3K4me2 H3K4me2 Ab (Upstate 07-030, Lot# DAM1474881) Pro-B Others Biotin Dynabeads M-280 Streptavidin (Invitrogen) Pro-B Histone H3K27ac H3K27ac (abcam ab4729) tet-Myc liver tumor Histone H3K27ac H3K27ac (abcam ab4729) normal liver Histone H3K4me3 H3K4me3 (Active Motif #39159) tet-Myc liver tumor Histone H3K4me3 H3K4me3 (Active Motif #39159) normal liver RNA polymerase RNA polymerase II RNAPII (Santa Cruz sc899-X) tet-Myc liver tumor RNA polymerase RNA polymerase II RNAPII (Santa Cruz sc899-X) normal liver Others Myc c-Myc N262 (Santa Cruz sc764-X) normal liver Others Ep300 p300 (santa cruz sc-585 X, lot j2214) HPC7 Histone H3K27ac H3K27ac (Abcam,ab4729, lot GA104852-2) Liver Histone H3K4me3 H3K4me3 (Millipore, 07-473, lot 2019729) Liver Histone H3 H3 Abcam ab1791 Anterior Cingulate cortex Histone H3K27ac H3K27AC Abcam ab4729 Anterior Cingulate cortex Histone H3K27me3 H3K27ME3 Millipore CS200603 Anterior Cingulate cortex Histone H3K4me1 H3K4ME1 Abcam ab8895 Anterior Cingulate cortex Histone H3K4me3 H3K4ME3 Abcam ab8580 Anterior Cingulate cortex Histone H3K79me3 H3K79ME3 Abcam ab2621 Anterior Cingulate cortex Others Nr3c1 cocktail of GR Abs (3.3ul of each Ab): PA1-511A (ThermoScientific), MA1-510 (ThermoScientific), M-20 (sc-1004, Santa Cruz) liver Histone H3K27ac H3K27ac (abcam, ab4729) Mouse back skin Others Myod1 MyoD_(sc-32758) sc-32758 This gene encodes a nuclear protein that belongs to the basic helix-loop-helix family of transcription factors and the myogenic factors subfamily. It regulates muscle cell differentiation by inducing cell cycle arrest, a prerequisite for myogenic initiation. The protein is also involved in muscle regeneration. It activates its own transcription which may stabilize commitment to myogenesis. (provided by RefSeq) mouse monoclonal antibody raised against recombinant MyoD of mouse origin with an epitope mapping to amino acids 180-189. Antibody Target: MyoD C2C12 Others Myog Myogenin_(sc-12732) sc-12732 Myogenin is a muscle-specific transcription factor that can induce myogenesis in a variety of cell types in tissue culture. It is a member of a large family of proteins related by sequence homology, the helix-loop-helix (HLH) proteins. It is essential for the development of functional skeletal muscle. (provided by RefSeq) mouse monoclonal antibody; epitope mapping within amino acids 138-158 of myogenin of rat origin. Antibody Target: Myogenin C2C12 Histone H3K27ac H3K27ac (Abcam, ab4729, lot GR184333-2) Colon Histone H3K27ac rabbit polyclonal Anti-Histone H3K27ac antibody ChIP-seq_H3K27Ac_NKT2 Histone H3K27ac rabbit polyclonal Anti-Histone H3K27ac antibody ChIP-seq_H3K27Ac_NKT1 Histone H3 Rabbit IgG, Abcam ab1791 Oocyte Histone H3K36me3 Rabbit IgG, gift of Robert Klose Oocyte Histone H3K4me3 Rabbit IgG, Diagenode pAb-003-050 Oocyte Histone H3K4me2 Rabbit IgG, Abcam ab32356 Oocyte Input control Input control none (input) C2C12 cells Others Epitope tags HA (Covance, MMS-101P) C2C12 cells Input control Input control none (input) Embryonic stem cell (ES3) Others Epitope tags HA (Covance, MMS-101P) Embryonic stem cell (ES3) Histone H3K27me3 Anti-trimethyl-Histone H3 (Lys27) Antibody Brown preadipocyte cell_H3K27me3_ChIPSeq Histone H3K9me2 Anti-Histone H3 (di methyl K9) antibody mAbcam 1220 - ChIP Grade Brown preadipocyte cell_H3K9me2_ChIPSeq Histone H3K36me3 Anti-Histone H3 (tri methyl K36) antibody - ChIP Grade Brown preadipocyte cell_H3K36me3_ChIPSeq Histone H3K27ac Anti-Histone H3 (acetyl K27) antibody - ChIP Grade Brown preadipocyte cell_H3K27ac_ChIPSeq Histone H3K4me3 Anti-trimethyl-Histone H3 (Lys4) Antibody Brown preadipocyte cell_H3K4me3_ChIPSeq Histone H3K4me2 Anti-Histone H3 (di methyl K4) antibody - ChIP Grade Brown preadipocyte cell_H3K4me2_ChIPSeq Histone H3K4me1 Anti-Histone H3 (mono methyl K4) antibody - ChIP Grade Brown preadipocyte cell_H3K4me1_ChIPSeq Others Clock Anti-CTCF Antibody Brown preadipocyte cell_CTCF_ChIPSeq RNA polymerase RNA polymerase II ChIPAb+ RNA Pol II Brown preadipocyte cell_Pol_II_ChIPSeq Others Med1 CRSP1/TRAP220 Antibody Brown preadipocyte cell_Med1_ChIPSeq Others Pparg PPAR Antibody (H-100) Brown preadipocyte cell_PPAR_ChIPSeq Others Ebf2 Human/Mouse EBF-2 Antibody Brown preadipocyte cell_EBF2_ChIPSeq Others Cebpa C/EBP Antibody (C-19) Brown preadipocyte cell_C/EBP_ChIPSeq Others Cebpa C/EBP Antibody (14AA) Brown preadipocyte cell_C/EBP_ChIPSeq Others Pou5f1 Oct4 (Santa Cruz; sc-8628) embryonic stem cells Others Sox2 Sox2 (Santa Cruz; sc-17320) embryonic stem cells Others Stat5b Anti-Stat5B Total T Cells Others Stat5a Anti-Stat5A Total T Cells Input control Input control Rabbit IgG Total T Cells Input control Input control none whole adult testis Unclassified Unclassified GC B cells Unclassified Unclassified RAG-/-+ pre-B cells Histone H3K27ac H3K27ac (Abcam, ab4729) embryonic stem cells Histone H3K4me2 H3K4me2 APC-iPSC H3K4me2 ChIPseq Histone H3K4me3 H3K4me3 APC-iPSC H3K4me3 ChIPseq Histone H3K27me3 H3K27me3 APC-iPSC H3K27me3 ChIPseq Unclassified Unclassified APC-iPSC input DNA Input control Input control none none bone marrow Others Maff Maff bone marrow Others Egr2 Egr2 sc-20690 bone marrow Histone H3K4me3 K4me3 07-473 bone marrow Histone H3K27ac K27Ac ab4729 bone marrow Others Irf1 Irf1 ab52520 sc-640 bone marrow Others Ets2 Ets2 sc-351 bone marrow Others E2f4 E2f4 sc-512 bone marrow Others E2f1 E2f1 sc-193 bone marrow Others Ctcf Ctcf 07-729 bone marrow Others Ahr Ahr ab81937 bone marrow Others Dmc1 Anti-DMC1 (C-20) Anti-DMC1 13R_testis_SSDS Histone H3K9ac ab4441; Abcam Leukemic cells Histone H3 ab1791; Abcam Leukemic cells Input control Input control IgG whole brain Histone H3K27ac H3K27ac (Diagenode, pAb-196-050) Mouse embryonic fibroblasts Histone H3K27me3 H3K27me3 (Diagenode, pAb-195-050) Mouse embryonic fibroblasts Histone H3K4me3 custom-made H3K4Me3 antibody (Abmart) Embryonic stem cell Others Rad51 RAD51 (H92) sc 8349 adult testis Histone H3K4me2 H3K4me2 (Abcam, Ab7766) fibroblasts Input control Input control none, input mouse spinal cord microglia Histone H3K4me1 H3K4me1 mouse spinal cord microglia Histone H3K4me1 H3K4me1 AB8895 Embryonic stem cells Histone H3K27ac H3K27Ac AB4729 Embryonic stem cells Others Smad1 anti-Smad1 (clone 913C1b, Bio Matrix Research, Japan) mouse ESCs (E14) Input control Input control none mouse embroid bodies Others Stat5a STAT5A (Santa Cruz, sc-1081) Mammary gland RNA polymerase RNA polymerase II Pol II (abcam, ab5408) Mammary gland Others Ezh2 EZH2 (Diagenode, C15410039) Mammary gland Unclassified Unclassified Epiblast E6.25 Others Stat1 STAT1 (Santa Cruz, sc-346) Pre-activated CD4+ T cells Others Nr3c1 in-house GR antibody Cultured Klf15-/- embryonic fibroblasts Histone H4K16ac Rabbit anti-H4K16ac (Millipore 07-762) genomic DNA, Mnase Histone H3.3 H3.3 Adult Hippocampal NeuN+ Cells (~7 weeks postnatal) Unclassified Unclassified Adult Hippocampal NeuN+ Cells (~7 weeks postnatal) Histone H3K4me3 H3K4me3 (Millipore, 07-473, lot 2019729) embryonic fibroblasts (MEFs) Input control Input control N/A Pancreatic Beta Cells Unclassified Unclassified J1 Embryonic Stem Cells Histone H3 Histone H3 (Abcam, ab1791) J1 Embryonic Stem Cells Histone H2B Histone H2B (Abcam, ab1790) J1 Embryonic Stem Cells Histone H3K4me2 H3K4me2 (Millipore, cat#07-030, Lot # 2142243) Bone marrow Others Wdr5 WDR5 (anti-rabbit antibody made by our lab) Bone marrow Input control Input control none, input Bone marrow Histone H3K4me3 Abcam ab8580 F9 embryonal carcinoma cells Input control Input control none embryonic hindlimb bud, ChIP input Input control Input control none embryonic forelimb bud, ChIP input Others Epitope tags anti-FlagM2 (Sigma, 088k6018) mouse embryonic stem cells Others Cebpb C/EBPbeta Preadipocyte cell line Others Rest anti-REST (Santa Cruz, #H-290) Embryonic Stem Cells (ESCs) wildtype Others Tet1 Tet1 rabbit polyclonal antibodies Mouse ES cells Others Ezh2 Ezh2 Embryonic Stem cells Histone H3K36me3 H3K36me3 Embryonic Stem cells Histone H3K27me3 H3K27me3 Embryonic Stem cells Histone H3K4me3 H3K4me3 Embryonic Stem cells Others Smad3 Smad3 AB28379 Embryonic stem cells Histone H3K36me3 H3K36me3<AbCam#9050> primary CD4+ T cells from spleen and lymph nodes Histone H3K27me3 H3K27me3<Millipore #07-449> primary CD4+ T cells from spleen and lymph nodes Histone H3K4me3 H3K4me3<AbCam#8580> primary CD4+ T cells from spleen and lymph nodes Others Spi1 anti-PU.1 (T-21) Murine erythroleukemia (MEL) cells stably transfected with Gata-1 fused to ER RNA polymerase RNA polymerase II anti-Pol II Serine 2 phosphorylated Macrophages Others Ctcf CTCF Upstate, Cat# 07-729, Lot# 1350637 3T3-L1 Histone H3K36me3 H3K36me3 Abcam, Cat# ab9050, Lot# 136353 3T3-L1 Histone H3K27me3 H3K27me3 Upstate, Cat# 07-449, Lot# DAM1387952 3T3-L1 Histone H3K27ac H3K27ac Abcam, Cat# ab4729, Lot# 31456 3T3-L1 Histone H3K4me1 H3K4me1 Abcam, Cat# ab8895, Lot# 268176 3T3-L1 Histone H3K4me2 H3K4me2 Abcam, Cat# ab7766, Lot# 56293 3T3-L1 Histone H3K4me3 H3K4me3 Abcam, Cat# ab8580, Lot# 376637 3T3-L1 Others Terf2ip RAP1 embryonic fibroblast Others GFP anti-GFP (Cristea et al., 2005) Embryonic stem cells Histone H3K36me3 H3K36me3 (Abcam ab9050) Embryonic stem cells Unclassified Unclassified source 0ON489 Unclassified Unclassified source 0HA76 Unclassified Unclassified source 0QM43 Unclassified Unclassified source 0QM39 Unclassified Unclassified source tc141237_liver Unclassified Unclassified source mouse_1 Others Mbd3 source Mbd3_WT2 Others Mbd3 source Mbd3_null1 Unclassified Unclassified source mouse ChIP 1 Unclassified Unclassified ZHBTc4 is derived from ZHTc6 and maintained by tetracycline (Tc)-regulatable Oct-3/4 transgene. Both of Oct-3/4 locus are disrupted by IRES-zeocin and IRES-BSD KO vectors. It should be cultured in the absence of tetraycline to maintain the undifferentiated state. Others Clock Mice were entrained to 12-hr light (L) and 12-hr dark (D) cycles for at least 2 weeks in a light-tight chamber at a constant temperature (23 ? 1?C). The mice were sacrificed at different time for liver isolation. Nuclear extracts of the mouse liver were cross-linked by 1% formaldehyde, and then sonicated. The samples were used for ChIP with CLSP4 anti-CLOCK antibody. For control experiment, the DNA prepared by ChIP with 1D4 antibody and input DNA were also sequenced. Histone H3K9me3 ES cells carrying a doxycycline-inducible Kdm4b transgene was created using a piggyBac transposon-based expression system from the NCH.4.6 male mouse ES cell line (C57B6/N x C57B6/N) with normal karyotype, and named K4B-ES cells.K4B-ES cells were cultured in the presence or absence of doxycycline, and subjected to fixed chromatin preparation. The fixed chromatin samples (Dminus and Dplus) were used for chromatin immuno-precipitation using anti-histone H3K9me3 polyclonal antibody (Abcam ChIP-grade ab8898). ChIP-Seq libraries were prepared for the immuno-precipitated DNA as well as the input DNA of Dminus and D plus samples using the NEBNext? ChIP-Seq Library Prep Master Mix Set and Multiplex Oligos for Illumina (NEB) according to manufacturer's instructions. Histone H3K27ac H3K27Ac CD8 T cells Input control Input control IgG Input control Input control None None WCE Neural Progenitors Input control Input control none mESC Unclassified Unclassified MEF Input control Input control None Mature B cells Histone H3K4me3 H3K4me3 Liver tissue Histone H3K27me3 H3K27me3 T cells Input control Input control none e12.5 embryonic forebrain, input Input control Input control none Placenta Input control Input control none Hippocampus Histone H3K4me3 H3K4me3 (Millipore, catalog# 07-473, lot# DAM1817678) Hippocampus Histone H3K4me3 Rabbit anti-H3K4me3 (07-473) Testes Others Irf7 Irf7 GM-CSF treated myeloid cells Histone H3K27ac anti-H3K27Ac (Abcam AB4729) retina Histone H3K9me3 anti-H3K9me3 (Abcam; ab8898; Lot: GR88132-1) Murine MLL-AF9 leukemic cells Input control Input control miwi2KO_GermCellsTestis_MACS_inputDNA Input control Input control miwi2HET_GermCellsTestis_MACS_inputDNA Histone H3K9me3 a-H3K9me3 miwi2HET_Liver_H3K9me3 Input control Input control miwi2HET_Liver_inputDNA Others Epitope tags anti-Flag antibody iMN-ESCs Histone H3K36me3 H3K36me3 ES-E14TG2a Histone H3K27ac H3K27ac ES-E14TG2a Input control Input control None Mouse Prostate Histone H3K27me3 H3K27me3 (millipore 07-449) Heart Input control Input control input Histone H3K9me3 H3K9me3 liver tissue Input control Input control none NIH/3T3 cells Histone H3K27ac H3K27Ac liver Others Hnf4a HNF4A liver Others Prox1 PROX1 liver Unclassified Unclassified Primary tissue Whole Embryo Others Nr1h4 sc-13063 Liver Unclassified Unclassified DN2 Histone H3K4me3 Millipore 07-473 Histone H3K4me1 Abcam ab8895 Histone H3K27me3 Millipore 07-449 Others Foxa1 Santa sc-6553 Histone H3K27me3 Histone H3 trimethyl Lys27 Unclassified Unclassified Limb bud Input control Input control Granulocytes Unclassified Unclassified Promyelocytes Histone H3K4me3 H3K4me3 Th17 in vitro Histone H3K4me2 H3K4me2 Th17 in vitro Histone H3K27me3 H3K27me3 cerebellum Histone H3 H3 cerebellum Histone H2A.Z H2A.z cerebellum Others Chd4 Chd4 cerebellum Histone H3K4me3 Abcam, ab8580 Wnt3KO EpiSCs Histone H3K27ac Abcam, ab4729 Wnt3KO EpiSCs Input control Input control none Hypothalamus Input control Input control none Amygdala Histone H3 H3 Abcam, ab1791 Embryonic Stem Cell Unclassified Unclassified neuronal progenitor cells Histone H3K27ac H3K27ac Bone Marrow Histone H3K4me2 H3K4me2 Bone Marrow Input control Input control none marrow derived MSC Input control Input control IgG (Cell Signaling) Mouse skin Histone H3K27me3 H3K27me3 (Millipore) Mouse skin Histone H3K4me3 H3K4me3 (ActiveMotif) Mouse skin Unclassified Unclassified Bone marrow Others Kmt2c Mll3 Liver tissue Histone H3K4me3 H3K4me3 (Millipore, 17-614) Mammary Input control Input control none Colon Input control Input control MEF, Input Histone H3K27me3 H3K27me3 control_E13.5_cortex Histone H3K27me3 H3K27me3 control_P1_cortex Unclassified Unclassified Follicular B cells Others Sin3a mSin3A CD8 T cells Others Egr1 Egr1 ab54966-100 sc-110 bone marrow Others Rel Rel sc-71 sc-70 bone marrow Others Stat3 Stat3 A302-406A bone marrow Others Rela Rela A301-824A sc-372 bone marrow Others Relb Relb A302-183A sc-226 bone marrow Others Hif1a Hif1a NB100-134 bone marrow Unclassified Unclassified H3K4Tm3 ACH3_ChIPseq Histone H3K9ac H3K9Ac TMK4_ChIPseq Histone H3K9me3 Antibody H3K9me3 (Abcam ab8898-100, lot. 733953) Embryonic Stem cells Input control Input control MEF_Smarca4-KO Input control Input control none fibroblasts Input control Input control none Mammary gland Unclassified Unclassified EpiLC Unclassified Unclassified EpiSC Others Rag2 RAG2 preB Unclassified Unclassified immortalized fibroblast Histone H3 H3Pan Liver tissue Histone H3K9me3 H3K9me3 Liver tissue Input control Input control none KH2 Histone H3K27me3 H3K27me3 Doxycycline-induced MEFs Histone H3K4me2 H3K4me2 Doxycycline-induced MEFs RNA polymerase RNA polymerase II Pol II MEF Histone H3K4me3 H3K4me3 MEF Histone H3K9ac H3K9Ac MEF Histone H3K36me3 H3K36me3 MEF Histone H4K8ac anti-H4K8Ac Macrophages Histone H4K5ac anti-H4K5Ac Macrophages Histone H4K12ac anti-H4K12Ac Macrophages Histone H3ac anti-H3Ac Macrophages Others Brd3 anti-Brd3 Macrophages Others Brd2 anti-Brd2 Macrophages Others Paxip1 PTIP mouse B cells Others Spi1 anti-PU.1 (T-21) ES-cell derived erythroid progenitors RNA polymerase RNA polymerase II anti-Pol II total Macrophages Histone H3K4me3 anti-H3K4me3 Macrophages Others Cdk9 anti-CDK9 (P-TEFb) Macrophages Histone H4ac anti-H4Ac Macrophages Others Brd4 anti-Brd4 Macrophages Others Brd4 BRD4 Others BrdU anti-Br-dUTP source ERS028740 Others BrdU anti-Br-dUTP source ERS028739 Others BrdU anti-Br-dUTP source ERS023709 Others BrdU anti-Br-dUTP source ERS023708 Others BrdU anti-Br-dUTP source ERS023707 Unclassified Unclassified No Unclassified Unclassified ChIP Input control Input control none, input bone marrow-derived macrophages Input control Input control none newborn lens, input Histone H3K27ac anti-H3K27ac Flt3L cultured dendritic cells Histone H3K4me1 anti-H3K4me1 Flt3L cultured dendritic cells Others Ep300 anti-p300 Flt3L cultured dendritic cells Others Cebpb CEBPb, sc-150, Santa Cruz Liver tissue Input control Input control none embryonic fibroblast Others Sumo2 SUMO2 Bone marrow derived dendritic cells Others Sumo1 SUMO1 (Y299 monoclonal antibody) Bone marrow derived dendritic cells Input control Input control none CD4 T cells Others Fgfr1 FGFR1 (Abcam, ab10646) Embryonic Stem Cells Input control Input control none, input_ mouse primary CD4+ T cells Others Setdb1 Setdb1 Santa Cruz (H-300 sc-66884) C2C12 Unclassified Unclassified HA (homemade) GATA1 null erythroblasts Input control Input control none Satellite cells Histone H4K16ac Anti-H4K16ac (Millipore, CS204361) Satellite cells Histone H3K79me3 H3K79me3, Diagenode cat#pAb-068-050 Hematopoietic progenitor cells Histone H3K79me2 H3K79me2, Abcam ab3594 Hematopoietic progenitor cells Others Irf1 IRF1 (santa cruz, sc-640) Primary bone marrow-derived macrophages (BMDM) Others Stat2 STAT2 (santa crus, sc-950) Primary bone marrow-derived macrophages (BMDM) Input control Input control none Mouse kidney cortex, input Others Wt1 WT1 (Santa Cruz, sc-192, Lot F1711) Mouse kidney cortex, WT1 ChIP Input control Input control none embryonic hindlimb Others Rnf2 39663, Active Motif mouse embryonic stem cells E14 Histone H3K27ac H3K27ac (Abcam ab4729) Brown adipose tissue Others Brd2 Brd2 (Bethyl; IHC-00612) primary T cells Histone H3K27ac H3K27ac mouse saline NAc H3K27ac ChIPseq Histone H3K27ac H3K27ac mouse cocaine NAc H3K27ac ChIPseq Input control Input control mouse IgG (278-010, Ancell) Primary proliferating myoblasts Histone H3K4me3 H3K4me3 (Abcam ab1012) TT2 Others Ctcf CTCF (Cell Signaling 2899) Embryonic stem cells Others Ppara PPAR alpha (Santa Cruz: H-98, sc-9000) burst-forming unit erythroid (BFU-E) Others Nr3c1 GR (Santa Cruz: H300, sc-8992) burst-forming unit erythroid (BFU-E) Others Suz12 SUZ12 (Abcam, 12073) MLL-AF9-puro transformed murine leukemia cell line Histone H3K27me3 H3K27me3 (Millipore 07-449) MLL-AF9-puro transformed murine leukemia cell line Input control Input control none MLL-AF9-puro transformed murine leukemia cell line Others Prdm5 Prdm5 MC3T3 mouse cell line Histone H3K27ac Anti-Histone H3 (acetyl K27) antibody activated B cell Histone H3K27me3 H3K27me3 (Abcam, ab6002) Spermatocytes Histone H3K27me3 H3K27me3 Abcam ab6002) CD43- splenic B cells Histone H3K4me3 H3K4me3 (Abcam ab8580) CD43- splenic B cells RNA polymerase RNA polymerase II RNA Pol II (N-20)(Santa Cruz sc-816x) CD43- splenic B cells Input control Input control None (input) CD43- splenic B cells RNA polymerase RNA polymerase II serine 5-phosphorylated RNA Polymerase II (Abcam) in vitro activated B cells Histone H3K4me1 H3K4me1 Abcam: ab8895, lot667543 Heart Histone H3K4me3 H3K4me3 Abcam #ab8580 Differentiated motor neuron Histone H3K27me3 H3K27me3 Abcam #ab6002 Differentiated motor neuron Others Nr3c1 GR, sc-1004, Santa Cruz bone marrow-derived macrophages Others Gad1 crosslink anti-DAXX (sc-7512) Embryonic stem cells Histone H3K9me3 crosslink anti-H3K9me3 (ab8898) Embryonic stem cells Others Pknox1 Prep1(N-15X) (Santa Cruz Biotechnology, sc-6245X, lot# F2003) Embryonic fibroblast Unclassified Unclassified Hepa1-6 hepatoma cells Others Epitope tags HA antibody, Abcam ab9110 embryonic fibroblasts Input control Input control none embryonic fibroblasts, E13.5 Others Myc c-Myc N262 (Santa Cruz, catalog# sc764, lot# G0111) embryonic fibroblasts, E13.5 Histone H3K4me3 H3K4me3 (Abcam, 8580) Dnmt TKO ESCs Input control Input control none WT MEF Others Sox3 R&D hSOX3 (AF2569) Neural Progenitor Cells Others Atrx ATRX SV40T transformed fibroblasts Others Hdac1 HDAC1 (Abcam, ab7028) embryonic stem cells Others Gtf2b anti-GTF2B (sc-225) whole heart Histone H3K36me3 Abcam (ab9050) primary Rag2 -/- thymocytes Histone H3K27ac H3K27ac ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells Histone H3K4me1 H3K4me1 ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells Others Olig2 DF308 (Olig2) Others Otx2 Otx2 (Abcam ab21990-100ug) embryonic stem cells (ESC) Input control Input control none epiblast like cells (EpiLC) Histone H3K27me3 H3K27m3(Millipore #07-449) primary NK cells from spleens purified by negative selection Histone H3K36me3 H3K36m3(AbCam #9050) primary NK cells from spleens purified by negative selection Histone H3K4me3 H3K4m3(Millipore #04-745) primary NK cells from spleens purified by negative selection Others Cebpb CEBPb (sc-150) BV2 cells Others Cebpa CEBPa (sc-61) BV2 cells Others Spi1 PU.1 (sc-352) BV2 cells Histone H3K4me2 H3K4me2 (Millipore 07-030) BV2 cells Others Baz1a ACF1 nucleus accumbens tissue Others Smarca5 SNF2H nucleus accumbens tissue Input control Input control none nucleus accumbens tissue Input control Input control none In vitro effector CD8+ T cells Others Irf8 ICSBP Antibody (Santa Cruz biotechnology inc., C-19) Flt3 ligand derived dendritic cells Others Ncoa2 SRC-2 antibody (Bethyl Laboratories, catalog number A300-346, lot number A-1) Liver Others GFP Custom GFP antibody from MPI-CBG anti-GFP 2007 (Vermeulen et al., 2010) Embryonic Stem Cells (ESCs) Others Rnf2 RING1B ab (Atsuta et al., 2001; PMID 11289226) Embryonic stem cells, tamoxifen treated, RING1B ChIP Others Rnf2 RING1B ab (Atsuta et al., 2001; PMID 11289226) Embryonic stem cells, untreated control, RING1B ChIP Others Kdm2b KDM2B ab (Farcas et al., 2012; PMID 23256043) Embryonic stem cells, tamoxifen treated, KDM2B ChIP Others Kdm2b KDM2B ab (Farcas et al., 2012; PMID 23256043) Embryonic stem cells, untreated control, KDM2B ChIP Unclassified Unclassified E36 ES cells Unclassified Unclassified E36 ES cells EED KO Others Ezh2 anti-Ezh2 : BD Transduction Laboratories ref : 612666 TT2 Histone H3K9ac anti-H3K9ac (active motif 39918) whole heart Histone H3K27ac H3K27ac mouse brown preadipocytes, MLL4 KO, H3K27ac ChIP Histone H3K27ac H3K27ac mouse brown preadipocytes, WT, H3K27ac ChIP Histone H3K4me3 H3K4me3 mouse brown preadipocytes, MLL4 KO, H3K4me3 ChIP Histone H3K4me3 H3K4me3 mouse brown preadipocytes, WT, H3K4me3 ChIP Histone H3K4me1 H3K4me1 mouse brown preadipocytes, MLL4 KO, H3K4me1 ChIP Histone H3K4me1 H3K4me1 mouse brown preadipocytes, WT, H3K4me1 ChIP Histone H3K4me1 Monoclonal anti-H3K4me1 Splenic CD8+ T cells Others Egr2 Anti-EGR2 (Covance, PRB-236P D13BF00486) T cells Input control Input control none (input) embryonic fibroblasts Histone H3K4me3 Anti-H3K4me3 Millipore (#07-473) Testis Others Irf4 anti-Irf4 (Santa Cruz; sc-6059) purified primary B cells from Bi-8i mice; stimulated for 3 Days; anti-Irf4 ChIP Others Irf4 anti-Irf4 (Santa Cruz; sc-6059) purified primary B cells from Bi-8i mice; stimulated for 1 Days; anti-Irf4 ChIP Unclassified Unclassified neonatal tail tip fibroblasts, Hotair knockout Unclassified Unclassified neonatal tail tip fibroblasts, Hotair wildtype Histone H3K27me3 H3K27me3 (Millipore 07-449) CM stage cultures, H3K27me3 Histone H3K27me3 H3K27me3 (Millipore 07-449) CP stage cultures, H3K27me3 Histone H3K27me3 H3K27me3 (Millipore 07-449) MES stage cultures, H3K27me3 Histone H3K4me1 H3K4me1 (Abcam ab8895) CM stage cultures, H3K4me1 Histone H3K4me1 H3K4me1 (Abcam ab8895) CP stage cultures, H3K4me1 Histone H3K4me1 H3K4me1 (Abcam ab8895) MES stage cultures, H3K4me1 Histone H3K4me1 H3K4me1 (Abcam ab8895) ESC stage cultures, H3K4me1 Input control Input control none (input) bone marrow-derived macrophages Others Rad21 abcam, ab992 activated B cell Histone H3K27me3 H3K27me3 (Millipore 07-449) hindlimb muscles Histone H3K4me3 H3K4me3 (Abcam 8580) hindlimb muscles Input control Input control mIgG (sc-2025, SantaCruz) mIgG1 Input control Input control none Five-day cultured Th2 cells generated from primary splenic CD4_T cells Input control Input control N/A (input sample) ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells Input control Input control No antibody ESC Input control Input control Control IgG SHH medulloblastoma Unclassified Unclassified Mouse embryonic day 11.5 (e11.5) midbrain Histone H3K9me3 H3K9me3 (Abcam, 8898) Embryonic stem cells Others Tbx21 anti-T-bet, sc-21003, Santa Cruz Biotechnology CD4+ T cells Others Biotin Streptavidin T1 dynabeads (Invitrogen) RAW macrophages Histone H2A.Z anti-H2AZ (Abcam, Cat # ab4174, Lot # GR216098-1) murine embryonic stem cells Histone H4ac anti-H4ac (Millipore, Cat # 06-598, Lot # 2510372) murine embryonic stem cells Others Epitope tags anti-FLAG (Sigma M2 F1804) Differentiated embryonic stem cells Histone H3K36me3 anti-Histone H3 K36me3 ab9050 primary T-cells Others Cbfb CBF CD8 T cells Input control Input control input DNA Mouse Embryonic Stem Cells Others Mef2c anti-Mef2c; Abcam (ab43796) cardiomyocyte Histone H3K9me3 H3K9me3 (diagenode, Cat. C15410193) hippocampus Histone H3K27ac H3K27ac (Abcam, ab4729) H3K27ac_WT Input control Input control IgG liver tissue Others Suz12 Sox2 (R&D AF2018) embryonic stem cells Others Pou5f1 Oct4 (Santa Cruz SC-8628) embryonic stem cells Others Ep300 p300 (sc-585, Santa Cruz Biotechnology) mESC Others Cebpb Anti-CEBPb (Santa Cruz sc-150X) Primary bone marrow-derived macrophages (BMDM) Others Junb Anti-JunB (Santa Cruz sc-46x) Primary bone marrow-derived macrophages (BMDM) Others Irf1 Anti-IRF1 (Santa Cruz sc-640) Primary bone marrow-derived macrophages (BMDM) Others Stat1 Anti-STAT1 (Santa Cruz sc-592) Primary bone marrow-derived macrophages (BMDM) Others Fosl1 MEFs expressing OSKM and Flag-Fra1 for 48h Unclassified Unclassified MEFs expressing Oct4,Sox2,Klf4 from pMX vector for 48h Unclassified Unclassified MEFs expressing Oct4,Sox2 from pMX vector for 48h Histone H3K27ac H3K27ac (39133, Active Motif) mESC Input control Input control none Treg cells from FoxP3A384T:hCD2 mice Input control Input control none Treg cells from FoxP3WT:hCD2 mice Others Foxp3 FoxP3 (affinity purified rabbit polyclonal antibody, generated in house) Treg cells from FoxP3A384T:hCD2 mice Input control Input control Mitotic Input Others Sox2 Sox2 Y-17 (sc-17320, Santa Cruz) Mitotic ChIP Others Sox2 Sox2 Y-17 (sc-17320, Santa Cruz) Asynchronous ChIP Input control Input control none Cranial neural crest cells Others Nfe2l1 Cell Signaling Technology, anti-TCF11 (D5B10) Wild-type MEFs immortalized with SV40 large T antigen and treated with MG132. Unclassified Unclassified Wild-type MEFs immortalized with SV40 large T antigen and treated with MG132. Unclassified Unclassified Primary tissue Lung Unclassified Unclassified Primary tissue Skeletal Muscle in Embryo Others Gabpa GABP- antibody from Santa Cruz (sc-22810) Primary bone marrow-derived macrophages (BMDM); 7th day of differentiation Histone H3K27ac H3K27ac (Abcam, catalog# #4729, lot# GR132150-1) HFD-chow, liver Histone H3K27ac H3K27ac (Abcam, catalog# #4729, lot# GR132150-1) Chow-chow, liver Histone H3K27ac H3K27ac (Abcam, catalog# #4729, lot# GR132150-1) HFD, liver Histone H3K27ac H3K27ac (Abcam, catalog# #4729, lot# GR132150-1) Chow, liver Others Pax6 Rabbit anti-Pax6 (Biolegend, 901301) Min6 cells Others Epitope tags Flag antibody Embryonic stem cell Histone H4K12ac AcH4K12; Anti-Histone H4 (acetylated) (acetyl K12) antibody Others Irf4 Santa Cruz Biotech/sc-6059x stromal adherent IKDN pre-B cell progenitors derived from IKDN CD2 Cre mice Input control Input control N/A NAc dissection from 3-5 animals RNA polymerase RNA polymerase II Ser-2-Phosphorylated RNA polymerase II: Active Motif, clone 3E10 ESC shPhf5a WITH LIF Others Epitope tags Flag-Tag ChIP-Seq Reconstitute Flag tag MEF cell Histone H2A.X H2A.X ES cell Input control Input control None Trophoblast stem cells Input control Input control no antibody Embryonic stem cells Histone H3K4me1 H3K4me1 (Abcam, ab8899, lot unknown) ES cell line Others Lhx6 LHX6 polyclonal (Genscript) Basal ganglia Others Nkx2-1 NKX2-1 polyclonal (Santa Cruz Biotechnology #sc-13040 RRID:AB_10015210) Basal ganglia Others Epitope tags anti-FLAG M2: Sigma (F3165) mESCs Others Chd4 anti-Chd4: Abcam (ab70469) mESCs Histone H3K27ac H3K27Ac (Abcam, ab4729, Lot:GR200563-1) Liver tumor cell line, sgp53/Cas9, H3K27Ac ChIP Histone H3K4me1 H3K4me1 (Abcam; ab8895, Lot:GR114265-2) Liver tumor cell line, sgp53/Cas9, H3K4me1 ChIP Histone H3K4me3 H3K4me3 (Abcam, ab8580, Lot:GR164706-1) Liver tumor cell line, sgMll3/Cas9, H3K4me3 ChIP Histone H3K27ac anti-H3K27ac Primary bone marrow-derived macrophages, IL4 for 4hrs, H3K27ac ChIP Histone H3K4me1 anti-H3K4me1 Primary bone marrow-derived macrophages, IL4 for 4hrs, H3K4me1 ChIP Others Epitope tags Monoclonal ANTI-FLAG M2, Clone M2 (SIGMA, F1804) Neural progenitor like cells RNA polymerase RNA polymerase II Pol2 MMS-126R RNA Polymerase II mouse monoclonal, clone 8WG16. Antibody Target: POL2 MEL Others Rorc RORg Th17 in vitro Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal. Antibody Target: H3K4me1 MEL Histone H3K4me3 H3K4me3 (04-745, Millipore) Embryonic stem cell Histone H3K27me3 anti-H3K27 (Diagenode, catalog# pAb-069-050) ESCs Histone H3K4me3 H3K4me3 (Abcam, ab8580) retina Histone H3K9me3 In house anti-H3K9me3 #4861 Embryonic Fibroblasts Histone H3K9me3 In house anti-H3K9me3 #1926 Embryonic Fibroblasts Histone H3K4me3 H3K4Me3 (Millipore,17-614) spleen + lymph nodes Histone H3K27ac H3K27Ac (Diagenode, C15410196) spleen + lymph nodes Histone H3K36me3 H3K36Me3 (Diagenode, C15410192) spleen + lymph nodes Input control Input control WCE Day5 motor neurons Others Epitope tags anti-V5 (Abcam, ab15828) Pseudo IP against V5 Histone H3K27ac Abcam, ab4729 EpiSCs Histone H3K4me3 H3K4me3 (Millipore, 06-598, lot JBC940052) Pre and postnatal nicotine received Histone H3K4me3 H3K4me3 (Millipore, 06-598, lot JBC940052) Pre and postnatal saccharin received Others Jun cJUN (Abcam, ab31419, GR30-33) CD4+ T Cells Input control Input control none (genomic DNA) Embryonic Stem cells mESCs Input control Input control none E11.5 Embryo Trunk Input control Input control none thymus Input control Input control none (input) quadriceps muscle Others Hdac3 HDAC3 quadriceps muscle Histone H3K56ac H3K56ac (abcam, ab76307) Murine PDAC Others Smarca4 Brg1 (ab110641; Abcam) RN2 Others Nr1d1 Rev-erb alpha (Cell Signaling, catalog number CS2124, rabbit antibody) Brown adipose tissue Unclassified Unclassified Ebf1/ c-Kit+ fetal liver cells, pmys-EBF1wt-IRES-GFP Unclassified Unclassified Ebf1/ c-Kit+ fetal liver cells, pmys-Empty-IRES-GFP Histone H3K27me3 H3K27me3(Diagnode, pAb-069-050) mouse trophoblast stem cells Histone H3K4me3 H3K4me3(Cell signaling Technology, #9727) mouse trophoblast stem cells Others Kat2b Kat2b (Abcam; ab12188) isolated mouse islet Unclassified Unclassified NSC time-ChIP 12h timepoint Unclassified Unclassified NSC time-ChIP 6h timepoint Unclassified Unclassified NSC time-ChIP 3h timepoint Unclassified Unclassified NSC time-ChIP 0h timepoint Input control Input control none V6.5 embryonic stem cells Others Morc3 1 L anti-MORC3 antibody (100-401-N96S, Rockland) V6.5 embryonic stem cells Histone H3K27me3 H3K27me3 (Abcam ab6002) Spermatogonial stem and progenitor cell (SSC) Histone H3K4me3 H3K4me3 (Abcam ab8580) Spermatogonial stem and progenitor cell (SSC) Input control Input control none Spermatogonial stem and progenitor cell (SSC) Histone H3K27me3 H3K27me3 (Abcam ab6002) multipotent adult spermatogonial-derived stem cell (MASC) Histone H3K4me3 H3K4me3 (Abcam ab8580) multipotent adult spermatogonial-derived stem cell (MASC) Histone H3K27me3 H3K27me3 (Millipore 07-449, Lot. 2382150) Forelimb Others Spi1 anti-PU.1 (SantaCruz, sc-352x) Primary bone marrow-derived macrophages (BMDM) Others Irf1 anti-IRF1 (SantaCruz, sc-640x) Primary bone marrow-derived macrophages (BMDM) Others Irf8 anti-IRF8 (SantaCruz, sc-6058x) Primary bone marrow-derived macrophages (BMDM) Others Epitope tags anti Myc-tag antibody (CST, 9B11, mouse mAb) Crosslinked chromatin ES cells Unclassified Unclassified cultured mouse pre-B-cell ALL Input control Input control Santa Cruz SC-2025 Quiescent B cells, lipopolysaccharide (LPS) treatment for 4hrs Histone H3K27me3 H3K27Me3 Embryonic stem cell Histone H3K4me3 H3K4Me3 - Abcam, ab8580 H3K4Me3.F/F Histone H3K4me3 H3K4Me3 - Abcam, ab8580 H3K4Me3.FC/FC Histone H3K4me2 H3K4Me2 - Abcam, ab32356 H3K4Me2.F/F Histone H3K4me1 H3K4Me1 - Abcam, ab8895 H3K4Me1.F/F Histone H3K4me1 H3K4Me1 - Abcam, ab8895 H3K4Me1.FC/FC Input control Input control N/A (input) myeloid leukemia Histone H3K79me2 Abcam anti-H3K79me2 (ab3594) myeloid leukemia Input control Input control None embryoid bodies, WT, RA, input Input control Input control None embryoid bodies, WT, no RA, input Input control Input control None embryoid bodies, UTX depleted, RA, input Input control Input control None embryoid bodies, UTX depleted, no RA, input Histone H3K4me3 Anti-H3K4me3 (Millipore: 17-614, lot# 2109590) embryoid bodies, WT, RA, H3K4me3 ChIP Histone H3K4me3 Anti-H3K4me3 (Millipore: 17-614, lot# 2109590) embryoid bodies, WT, no RA, H3K4me3 ChIP Histone H3K4me3 Anti-H3K4me3 (Millipore: 17-614, lot# 2109590) embryoid bodies, UTX depleted, RA, H3K4me3 ChIP Histone H3K4me3 Anti-H3K4me3 (Millipore: 17-614, lot# 2109590) embryoid bodies, UTX depleted, no RA, H3K4me3 ChIP Histone H3K27me3 Anti-H3K27me3 (Millipore: 07-449, lot# 2382150) embryoid bodies, WT, RA, H3K27me3 ChIP Histone H3K27me3 Anti-H3K27me3 (Millipore: 07-449, lot# 2382150) embryoid bodies, WT, no RA, H3K27me3 ChIP Histone H3K27me3 Anti-H3K27me3 (Millipore: 07-449, lot# 2382150) embryoid bodies, UTX depleted, RA, H3K27me3 ChIP Histone H3K27me3 Anti-H3K27me3 (Millipore: 07-449, lot# 2382150) embryoid bodies, UTX depleted, no RA, H3K27me3 ChIP Unclassified Unclassified mouse embryonic stem cells (E14) Histone H3K27ac H3K27ac Antibody Brown preadipocyte cell Others Creb1 p-CREB Antibody Brown preadipocyte cell Others Cebpa C/EBP Antibody (C-19) Brown preadipocyte cell RNA polymerase RNA polymerase II Anti-polII (Santa Cruz # sc-899) Primary bone marrow-derived macrophages (BMDM) Histone H3K27me3 H3K27me3 (Cell signaling, cat n. 9733BF) Tumor (glioma) Histone H3K27ac H3K27ac (ab4729, Abcam) FACS-purified Pou5f1-GFP-positive germ cells Histone H3K27me3 H3K27me3 (07-449, Millipore) FACS-purified Pou5f1-GFP-positive germ cells Histone H3K4me3 H3K4me3 (04-745, Millipore) FACS-purified Pou5f1-GFP-positive germ cells Histone H3K27ac H3K27ac (abcam ab4729) tet-Myc liver tumor (tet-Myc inactivated for 16h) Histone H3K4me3 H3K4me3 (Active Motif #39159) tet-Myc liver tumor (tet-Myc inactivated for 16h) RNA polymerase RNA polymerase II RNAPII (Santa Cruz sc899-X) tet-Myc liver tumor (tet-Myc inactivated for 16h) Others Myc c-Myc N262 (Santa Cruz sc764-X) tet-Myc liver tumor (tet-Myc inactivated for 16h) Input control Input control None CD8 T cell Histone H3K27me3 Millipore, 17-622 CD8 T cell Histone H3K27ac Abcam, ab4729 CD8 T cell Histone H3K4me3 Millipore, 17-614 CD8 T cell Histone H3K4me1 Abcam, ab8895 CD8 T cell Histone H3K27me3 anti-trimethyl-histone H3 (Lys27) (Millipore, Cat# 07-449, Lot# 2607758) C2C12 cell line Histone macroH2A1 anti-mH2A1 (Abcam, Cat# ab37264, Lot# GR132054-1) C2C12 cell line Histone H3K4me3 H3K4me3 (Millipore, 07-473, lot 2019729) Visceral yolk sac endoderm Input control Input control IgG (Thermo scientific, 23212, lot LI150449) embryonic stem cells Others Tfe3 TFE3 (Sigma, Catalog# HPA023881, Lot# E96562) MEF RNA polymerase RNA polymerase II CstF77 rabbit anti-human CstF77 (this work) S194 Myeloma B Cells Others Ep300 p300, SantaCruz: sc-585x C1C12 myotubes differentiated for 96h Others Ep300 p300, SantaCruz: sc-585x Growing C1C12 myoblasts Histone H3.3 Millipore:ChIPAb+TM histone H3.3-ChIP validated antibody (cat 17-10245) 3Rb_Anti-H3.3_ChIP-seq Histone H3.3 Millipore:ChIPAb+TM histone H3.3-ChIP validated antibody (cat 17-10245) Cg_Anti-H3.3_ChIP-seq Histone H3.3 Millipore:ChIPAb+TM histone H3.3-ChIP validated antibody (cat 17-10245) 1Rb_Anti-H3.3_ChIP-seq Histone H2A.XS139ph Millipore: anti-phospho-Histone H2A.X (Ser139) Antibody, clone JBW301 3Rb_Anti-gH2AX_ChIP-seq Histone H2A.XS139ph Millipore: anti-phospho-Histone H2A.X (Ser139) Antibody, clone JBW301 1Rb_P Anti-gH2AX_ChIP-seq Histone H2A.XS139ph Millipore: anti-phospho-Histone H2A.X (Ser139) Antibody, clone JBW301 1Rb_M Anti-gH2AX_ChIP-seq Histone H3K27ac H3K27ac (abcam, ab4729) Mouse skin SCC Histone H4ac Rabbit Anti-acetyl-histone H4 C2C12_MLXWT-H4AC Histone H4ac Rabbit Anti-acetyl-histone H4 C2C12_MLXDN-H4AC Histone H3K27ac rabbit polyclonal Anti-Histone H3K27ac antibody ChIP-seq_H3K27Ac_NKT17 Unclassified Unclassified GFP pos medullary thymic epithelial cells Unclassified Unclassified GFP neg medullary thymic epithelial cells Input control Input control none Primary CD4_T cells isolated from 6-8 week old mice (C57BL/6) Histone H3K27me3 H3K27me3 (Millipore, 17-622) H3K27me3_WT Histone H3K36me3 H3K36me3 (Abcam, ab9050) ESC shPhf5a WITH LIF Histone H3K36me3 H3K36me3 (Abcam, ab9050) ESC shControl WITH LIF Histone H3K79me2 H3K79me2 (Active Motif, 39143) ESC shPhf5a WITH LIF Histone H3K79me2 H3K79me2 (Active Motif, 39143) ESC shControl WITH LIF Histone H3K4me3 H3K4me3 (Millipore, 07-473) ESC shPhf5a WITH LIF Histone H3K4me3 H3K4me3 (Millipore, 07-473) ESC shControl WITH LIF RNA polymerase RNA polymerase II Ser-2-Phosphorylated RNA polymerase II: Active Motif, clone 3E10 ESC shControl WITH LIF Others Paf1 Paf1 antibody, serum purified ESC shPhf5a WITH LIF Others Paf1 Paf1 antibody, serum purified ESC shControl WITH LIF Histone H2A.X anti-H2AX (Abcam, catalog# ab11175) H2AX.F/F Histone H2A.X anti-H2AX (Abcam, catalog# ab11175) H2AX.FC/FC RNA polymerase RNA polymerase II monoclonal anti-RNAPII clone 4H8 (Francis Crick Institute) RNAPolII.F/F RNA polymerase RNA polymerase II monoclonal anti-RNAPII clone 4H8 (Francis Crick Institute) RNAPolII.FC/FC Input control Input control anti-IgG (Sigma, catalog# M8642) IgG.F/F Input control Input control anti-IgG (Sigma, catalog# M8642) IgG.FC/FC Histone H2A.XS139ph anti-gH2AX (Abcam, catalog# ab2893) gH2AX.F/F Histone H2A.XS139ph anti-gH2AX (Abcam, catalog# ab2893) gH2AX.FC/FC Others Dnmt3a Dnmt3a (Abcam ab2850, rabbit) MEF Others Dnmt3a Dnmt3a (Abcam ab13888, mouse) MEF Histone H2BK20ac H2BK20ac ( Abcam ab52988, lot 527003) BV2 microglia cells Histone H3K27ac Abcam ab4729, Lot: 509313 BV2 microglia cells Others Smc1a SMC1 Chromatin IP against SMC1 Others Dmc1 Anti-DMC1 (C-20) Anti-DMC1 B6_testis_SSDS Others Rxra RXR C57BL/6 LXRdKO mouse liver Others Rxra RXR C57BL/6 wild type mouse liver Others Nr1h3 LXR C57BL/6 wild type mouse liver Input control Input control none (input) Rods from WT mouse retina Input control Input control none Primary keratinocytes trancduced with AhRCA-HA Others Ahr HA (abcam, ab9110) Primary keratinocytes trancduced with AhRCA-HA Histone H2Bub H2Bub, Millipore: 05-1312, clone 56 C1C12 myotubes differentiated for 96h Histone H2Bub H2Bub, Millipore: 05-1312, clone 56 Growing C1C12 myoblasts Input control Input control None B1A B cells Histone H3K4me3 H3K4me3 Germinal Center B cells Input control Input control None Germinal Center B cells Histone H3K4me1 H3K4me1 Marginal Zone B cells Input control Input control None Marginal Zone B cells Histone H3K4me1 H3K4me1 Follicular B cells Input control Input control None Follicular B cells Input control Input control None Pre B cells Input control Input control None Pro B cells Histone H3K4me3 custom-made H3K4Me3 antibody (Abmart) Growing oocyte Input control Input control Control mouse intestinal stem cells Input control Input control IgG adult testis Input control Input control none E8.5 whole embryos Histone H3K9me2 anti-H3K9me2 (Abcam ab1220) E8.5 whole embryos Histone H3K4me1 H3K4me1 (Abcam, catalog# ab8895, lot# GR114265-2) Primary HSPC Cells Histone H3K27ac H3K27ac (Abcam, catalog# ab4729, lot# GR183919-1) Primary HSPC Cells Others E2f3 anti-E2F3 (Santa Cruz, catalog# sc-878x, lot# E1712) mouse embryonic fibroblasts Unclassified Unclassified wild-type E14 cells Histone H3K27me3 H3K27me3 (Millipore, 07-449) Epiblast E6.25 Others Esr1 Antibody Mix: MC20 (SantaCruz) + ab10 (TE111-SD1) (Abcam) liver Histone H3K36me3 H3K36me3 primary CD4+ T cells from spleen and lymph nodes Others Nr3c1 in-house GR antibody Cultured WT embryonic fibroblasts Histone H4K8ac Rabbit anti-H4K8ac (Millipore: 07-328) genomic DNA, Mnase Others Crotonyl lysine Rabbit anti-crotonllysine (PTM Biolabs: #PTM-501) genomic DNA, Mnase Histone H3K27me3 Mouse anti-H3K27me3 (Abcam: ab6002) genomic DNA, Mnase Unclassified Unclassified HA.11 Primary Cortical Neurons (E16.5 DIV8) Input control Input control none Basal Ganglia and Septum Others Otx2 anti-OTX2 (R&D, catalog# AF1979, lot# KNO0211051) Basal Ganglia and Septum Histone H3K4me3 Anti-H3K4me3 (Millipore) pooled bone marrow Input control Input control None WCE Embryonic stem cells Histone H3K27me3 H3K27me3 (07-449, Millipore) Naive CD4 T cells Others Trim28 crosslink anti-KAP1 (ab10483) Embryonic stem cells Others Trim28 crosslink anti-KAP1 (ab22553) Embryonic stem cells Others Sox11 Sox11 (M. Wegner) Neurons Others Sox2 Sox2 (Millipore) Neural progenitor cells Others Sox3 Sox3 (T. Edlund) Neural progenitor cells Histone H2A.Z H2AZ (abcam, ab4174, GR35527-1) murine embryonic stem cells Histone H3 H3 (abcam, ab1791, GR204148-1) murine embryonic stem cells Input control Input control none (histone_INPUT) murine embryonic stem cells Others Klf4 Klf4 (kind gift from Dr. Ng from the Genome Institute of Singapore) murine embryonic stem cells Input control Input control none (Klf4_INPUT) murine embryonic stem cells Input control Input control none mouse Ik knockout DP thymocytes Histone H3K27me3 H3K27me3 (Millipore, 07-449) Mouse back skins Histone H3K79me2 H3K79me2 (Abcam, ab3594) Mouse back skins Histone H3K4me3 H3K4me3 (Abcam, ab1012) Mouse back skins Others Ell2 Lin et al. 2010 (Mol. Cell) KH2 Others Ctcf anti-CTCF (SantaCruz #15914) ES_CTCF_ChIPseq Histone H3K9me3 H3K9me3 (Active Motif, cat #39161, lot #170) Embyonic Stem Cell Histone H3K27me3 H3K27me3 Terminally differentiated Neurons (TN) Histone H3K4me1 H3K4me1 Abcam AB8895 ZHBTc4 ES cells Others Stat5b R&D systems, anti-stat 5B serum PA-ST5B Dendritic Cell in Spleen Others Stat3 Invtrogen, monoclonal antibody ST3-5G7 Dendritic Cell in Spleen Others Rest anti-REST (Santa Cruz, #H-290) Neuronal Progenitor (NP) Cells wildtype Input control Input control None Homogenized Mouse Liver Histone H3K27me3 anti-H3K27me3 Terminally differentiated Neurons (TN) Histone H3K27me3 anti-H3K27me3 Neuronal Progenitor (NP) Cells Histone H3K27me3 anti-H3K27me3 Embryonic Stem Cells (ESCs) Others Rela p65 primary bone marrow-derived macrophages Others Bcl6 BCL6 primary bone marrow-derived macrophages Input control Input control no IP Embryonic stem cells Others Rnf2 Ring1B Embryonic stem cells knockout for Eed Others Dmc1 DMC1 (C-20) sc 8973 pups testis Histone H3K4me1 H3K4me1 Abcam AB8895 Embyonic stem cells Unclassified Unclassified E14 TG2A mouse embryonic stem cells Others Smad2 pSmad2 ab16509 E14 TG2A mouse embryonic stem cells Histone H3K4me1 H3K4me1 (ab8895) E2A-/- pre-pro-B cell Histone H3K9ac H3K9ac (Upstate Biotechnologies, 06-942) Chromatin IP against acetylated H3 lysine 9 Histone H3K4me1 H3K4me1 (Vendor: Abcam, cat# ab8895, lot# 721955) PUER cells Others Rag2 RAG2 (rabbit polyclonal antibody raised to RAG2 aa 70-516 (Leu and Schatz, PMID: 7565717)) Total thymocytes Input control Input control native ChIP input control. No antibody. Embryonic stem cells RNA polymerase RNA polymerase II RNA Pol II (Rpb1 N-terminus) ZHBTc4 mES cells Input control Input control native ChIP input control. No antibody. Embryonic stem cells RNA polymerase RNA polymerase II RNA-polymerase II mouse bone marrow-derived macrophages Histone H3K4me3 H3K4me3 Diagenode Unclassified Unclassified source 85924 Unclassified Unclassified source 85921 Unclassified Unclassified source 85923 Unclassified Unclassified source 85920 Unclassified Unclassified source ERS217105 Unclassified Unclassified source ERS217104 Unclassified Unclassified source ERS217103 Unclassified Unclassified source ERS217102 Unclassified Unclassified source ERS217101 Unclassified Unclassified source ERS217100 Unclassified Unclassified source mmuOON489 Unclassified Unclassified source Ter119_pos_E12.5_Fetal_Liver_Cells Unclassified Unclassified source Ter119_neg_E12.5_Fetal_Liver_Cells Unclassified Unclassified source N5 Unclassified Unclassified source 0ON562 Unclassified Unclassified source 2022.4 Unclassified Unclassified source ERS018860 Others Cebpa source CEBPA ChIP 2 Others Hnf1a source HNF1A ChIP 1 Others Foxa2 source FOXA2 ChIP 1 Others Cebpa source CEBPA ChIP 1 Others Onecut1 source HNF6 ChIP 2 Others Onecut1 source HNF6 ChIP 1 Others Mbd3 source Mbd3_null2 Histone H3K4me3 H3K4me3 source ERS002016 Input control Input control source TC1 input 1 Unclassified Unclassified source: C2C12 cells Unclassified Unclassified source: B22 cells were generated previously described in de la Serna et al. (2000) Mol. Cell. Biol. 20, 2839-2851 Input control Input control Input Input control Input control none mouse embryonic fibroblasts Input control Input control none Liver Input control Input control none neural stem cell Input control Input control none hindlimb muscles Others Ctcf CTCF murine primary activated B cells Histone H3K4me3 anti-H3K4me3 Input control Input control none cardiomyocyte Unclassified Unclassified Primary tissue Endothelial in Lung Unclassified Unclassified Primary tissue Endothelial in Heart Others Maf c-Maf Th17 in vitro Others Batf B-ATF Th17 in vitro Input control Input control None Immature B cells Input control Input control N/A mammary gland Input control Input control N/A liver Input control Input control N/A mouse embryonic fibroblasts Histone H3K27me3 H3K27me3 (Diagenode pAb-069-050) TT2 Input control Input control none spermatocytes Histone H3K9me3 a-H3K9me3 miwi2KO_GermCellsTestis_MACS_H3K9me3 Histone H3K9me3 a-H3K9me3 miwi2HET_GermCellsTestis_MACS_H3K9me3 Histone H3K27me3 Millipore, 07-449 KO MEF Histone H3K27me3 Millipore, 07-449 WT MEF Unclassified Unclassified n.a. Pro-B cell Histone H3K27ac H3K27ac male_WT_LF Histone H3K27ac H3K27ac male_WT_HF Input control Input control none Primary B-cells Input control Input control none myoblasts_input Input control Input control none Input_ING1_flag_myotubes Others Wdr5 Wdr5 Wdr5_myoblasts Others Epitope tags anti-FLAG ING1_flag_myotubes Others Spi1 Pu1 FDCPmix Input control Input control None mouse heart Histone H3K27me3 H3K27me3 ES-E14TG2a Others Lhx2 LHX2 Mouse back skins Input control Input control none spleen Input control Input control none shSmyd5_mESC Input control Input control none shLuc_mESC Histone H2A.XS139ph gH2AX Millipore/05-636 Thymus Others Satb1 SATB1 total thymocyte Input control Input control Asynchronous Input Others Kdm6a KDM6A Unclassified Unclassified Primary tissue Endothelial in Embryo Unclassified Unclassified DN3 Unclassified Unclassified ETP Unclassified Unclassified CLP Unclassified Unclassified LMPP Unclassified Unclassified HSC Histone H3K27ac Abcam ab4729 Input control Input control none 3T3-L1 preadipocytes Others Foxp3 Treg Foxp3 ChIP Input control Input control none retina Histone H3K27me3 H3K27me3 (Millipore, 07-449) retina Input control Input control none Thymus Unclassified Unclassified Progenitor B cells Others Ctcf 07-729, Millipore Sperm Histone H3K27me3 H3K27me3 EZH2_Y641F_H3K27_BCELLS_IP Input control Input control EZH2_Y641F_H3K27_BCELLS_Input Histone H3K27me3 H3K27me3 EZH2_WT_H3K27_BCELLS_IP Input control Input control EZH2_WT_H3K27_BCELLS_Input Histone H3K27me3 H3K27me3(Diagnode, pAb-069-050) MII oocyte Others Kmt2d KMT2D Cardiomyocytes Unclassified Unclassified Mammary Input control Input control C2C12_MLXWT-INPUT Input control Input control C2C12_MLXDN-INPUT Input control Input control none (INPUT) retina_input_P12 Input control Input control none (INPUT) retina_input_P0 Histone H3K27me3 H3K27me3-AB3 retina_H3K27me3_P12 Histone H3K27ac H3K27Ac-AB2 retina_H3K27Ac_P12 Histone H3K27me3 H3K27me3 dcKO_E13.5_cortex Histone H3K27me3 H3K27me3 dcKO_P1_cortex RNA polymerase RNA polymerase II PolII 3T3-L1 preadipocytes Input control Input control Input THY1+ spermatogonia Others Sall4 SALL4 THY1+ spermatogonia Others Zbtb16 PLZF THY1+ spermatogonia Others Runx1 Runx1 ab61753 sc-8564 bone marrow Others Rpa1 RPA Spleen Histone H3K4me3 H3K4me3 B1A B cells Histone H3K4me1 H3K4me1 B1A B cells Unclassified Unclassified ESCs_ChIP-seq Others Rag1 RAG1 preB Others Tal1 TAL1 (sc12984) G1E Histone H3K9ac H3K9Ac Liver Input control Input control none whole heart Histone H3K4me2 H3K4me2 mammary gland Others Setdb1 SetDB1 V6.5 mES cells Histone H3K4me3 HEK4me3 Others Ep300 p300 Others Hnf4a HNF4a Others Cebpa CEBPa Others BrdU anti-Br-dUTP source ERS028742 Others BrdU anti-Br-dUTP source ERS028741 Others Brd4 Brd4 (Bethyl A301-985A50, lot 3) K3R3 Brd4 ChIP-seq Others Brd2 Brd2 (Bethyl A302-583A, lot 1) K3R3 Brd2 ChIP-seq Others Brd4 Brd4 (Bethyl A301-985A50, lot 3) WT Brd4 ChIP-seq Others Brd2 Brd2 (Bethyl A302-583A, lot 1) WT Brd2 ChIP-seq Others Brd2 Brd2 (Bethyl A302-583A, lot 1) Brd2 ChIP-seq Others Nr1d1 REV-ERBa (Cell signaling 2124) liver Others Biotin BirAV5-FLBio AB1 ES cells Others Biotin BirAV5-FLBioGcn5 AB1 ES cells Input control Input control none 2o 1B MEFs Others Myc c-Myc antibody (sc-764, Santa Cruz) 2o 1B MEFs Input control Input control Rabbit-IgG (ab37415; GR90135-1; Abcam) mouse embryonic stem cells Others Smc1a Bethyl 300-055A immortalized fibroblast Input control Input control none immortalized fibroblast Others Junb JunB Blast-cultured splenic CD4+ T-cells Others Runx1 Runx1 Blast-cultured splenic CD4+ T-cells Others Brd4 BRD4 Blast-cultured splenic CD4+ T-cells Histone H3K27ac H3K27ac Blast-cultured splenic CD4+ T-cells Others Mecp2 Total MeCP2 antibody (Chen et al. 2003) Frontal Cortex Others Epitope tags Flag, Sigma M2 E9.5 hearts Histone H3S10ph ab14955, abcam Embryonic stem cells Others Pax6 Pax6 (Millipore, ab2237, lot# NG1731333) e12.5 embryonic forebrain, Pax6 ChIP Others Irf8 anti-Irf8 Flt3L cultured dendritic cells Others Batf3 anti-Batf3 Flt3L cultured dendritic cells Input control Input control Whole cell extract mESC Others Ezh2 Ezh2 Cell Signaling #3147 mESC Others Gps2 GPS2 N-terminal (home raised) RAW264.7 cell line (macrophages) Others Gps2 GPS2 N-terminal (home raised) Bone marrow derived macrophages Input control Input control N/A Embryonic stem cells Input control Input control none (input) OKSM reprogramming intermediates from Mouse Embryonic Fibroblasts Others Sox2 goat polyclonal Anti-Sox2 (R&D, catalog# AF2018, lot# KOY0213101) OKSM reprogramming intermediates from Mouse Embryonic Fibroblasts RNA polymerase RNA polymerase II Pol II Antibody (N-20) embryonic fibroblast Others Esr1 anti-estrogen receptor (Santa Cruz Biotechnology sc-8002X) splenic B cells Others Trim33 Trim33 (A301-060A; Bethyl) MLL-AF9/NrasG12D murine cell line Others Trim33 Trim33 (A301-060A; Bethyl) TAL transgenic/HEB heterozygous with Notch truncations (provided by I.Aifantis, NYU) Others Trim33 Trim33 (A301-060A; Bethyl) pro B-Cell Histone H3K4me3 H3K4me3 (07-473; Millipore) Bcr-Abl transformed p19Arf null B-ALL Histone H3K27ac H3K27ac (ab4729; Abcam) Bcr-Abl transformed p19Arf null B-ALL Others Trim33 Trim33 (A301-060A; Bethyl) Bcr-Abl transformed p19Arf null B-ALL Input control Input control none Bcr-Abl transformed p19Arf null B-ALL Histone H3K9K14ac Anti H3 Acetyl K9, K14 (Millipore 06-499) Dendritic cells Input control Input control none (input) Dendritic cells Input control Input control Prdm1/Blimp-1 mutant anti-Irf-1 input Others Irf1 polyclonal rabbit anti-Irf1 antibody (M-20) Prdm1/Blimp-1 mutant anti-Irf-1 ChIP Input control Input control control rabbit IgG wild type IgG ChIP Others Irf1 polyclonal rabbit anti-Irf1 antibody (M-20) wild type anti-Irf-1 ChIP Input control Input control anti-Blimp-1-eGFP input Others Prdm1 GFP Tag Antibody (3E6) anti-Blimp-1-eGFP ChIP Others Notch1 ICN1 (Cell Signaling Technology, 4147s) 8946: ICN1 Chromatin IP Others Myb Myb (sc-7874; Santa Cruz) MLL-AF9/NrasG12D murine cell line Others Cebpa C/EBP (sc-150; Santa Cruz) MLL-AF9/NrasG12D murine cell line Others Cebpa C/EBP (sc-61; Santa Cruz) MLL-AF9/NrasG12D murine cell line Others Erg Erg (sc-354; Santa Cruz) MLL-AF9/NrasG12D murine cell line Others Fli1 Fli1 (ab15289; Abcam) MLL-AF9/NrasG12D murine cell line Others Spi1 Pu.1 (sc-352; Santa Cruz) MLL-AF9/NrasG12D murine cell line Histone H3 Histone H3 (ab1791; Abcam) MLL-AF9/NrasG12D murine cell line Histone H3ac H3AC (acetylated histone H3) ESC differentiated day 6 cells Histone H3ac H3AC (acetylated histone H3) ESC differentiated day 4 cells Histone H3ac H3AC (acetylated histone H3) ESC differentiated day 2 cells Others Hdac1 HDAC1 (3 FLAG-HDAC1) ESC differentiated day 2 cells Unclassified Unclassified Neural stem cells Others Ep300 anti-p300 (EP300) antibody 3134 cells Others Pou2af1 OcaB SantaCruz, catalog# sc-955X CD4 T cells Others Pou2f1 Oct1 SantaCruz, catalog# sc-232X CD4 T cells Input control Input control none ES cells Input control Input control none Embryonic stem cells (ESCs) Others Sirt6 Sirt6 (Cell Signaling Technology, 12486 in a ratio of 1ml/2e7 cells) Embryonic stem cells (ESCs) Others Klf4 GKLF, Santa Cruz Biotechnology, sc-20691, Lot# J1212 Atherosclerosis lesion Histone H3K27me3 H3K27me3(Millipore, #07-449) Haunt knock out in 46C cells Haunt pKO mES cells Histone H3K27me3 H3K27me3(Millipore, #07-449) embryonic stem cells 46C mES cells Histone H3K4me3 H3K4me3 (Abcam, ab8580) Haunt knock out in 46C cells Haunt pKO mES cells Histone H3K4me3 H3K4me3 (Abcam, ab8580) embryonic stem cells 46C mES cells Histone H3K27ac H3K27ac Neuronal Progenitors Others Nr4a1 Nur77(Santa Cruz, SC-5569) Embryonic Stem Cells Others Rxra RXR (Santa Cruz, SC-774) Embryonic Stem Cells Others Tcf4 anti-Tcf4 (Cell signaling, catalog 2569S and lot2) Crypt RNA polymerase RNA polymerase II PolII (Abcam, cat# ab5408, lot# GR106949-6, 5ug) Mammary tissues Others Ezh2 EZH2 (Diagenode, cat# C15410039 and lot# 003) Mammary tissues Others Ezh1 EZH1 (gift from Sartorelli, Mousavi et al. Mol. Cell 2012) Mammary tissues Input control Input control input embryonic stem cells Others Pou5f1 Oct4 embryonic stem cells Input control Input control none (input) 8w Mouse Testis Others Dmrt1 dmrt1 Antibody (PMID: 11040213) 8w Mouse Testis Others Brd2 Bethyl BRD2 A302-583A GATA1 null erythroblasts Input control Input control none Bone marrow derived macrophages Others Creb1 CREB (clone: 48H2) Bone marrow derived macrophages Input control Input control none (input) Naive T cells from spleen and nodes Input control Input control anti-Ig (Dako, catalog# X0936, lot# 73343) Naive T cells from spleen and nodes Others Batf anti-BATF (Cell Signalling, catalog# sc8638, lot# 1) Naive T cells from spleen and nodes Others Irf4 anti-IRF4 (Santa Cruz, catalog# sc6059, lot# B2614) Naive T cells from spleen and nodes Others Nlrp3 anti-NLRP3 (Adipogen, catalog# AG-20B-0014, lot# A22141102) Naive T cells from spleen and nodes Others Stat6 anti-STAT6 (Cell Signalling, catalog# sc9362, lot# 4) Naive T cells from spleen and nodes Others Runx1 RUNX1 myeloid progenitors_expansion cells Others Runx1 RUNX1/ETO Hemogenic endothelium (HE) cells RNA polymerase RNA polymerase II Pol II (Santa Cruz N20) ES cell culture RNA polymerase RNA polymerase II Pol II (Santa Cruz N20) MEF cell culture Others Aff3 Aff3 (Homemade#182) MEF cell culture Unclassified Unclassified AtT20 cells Others Mbd3 Mbd3 (Bethyl, A302-528A) ES cell culture Others Chd4 Chd4 (Abcam, ab70469) ES cell culture Input control Input control none (input) G3-medulloblastoma Others Tet3 mTet3FL (in house) Brain cells Input control Input control IgG (Santa Cruz, SC-2027) Brain cells Input control Input control none Primary culutured mouse cortical neurons (DIV 8) Histone H3K9S10me3 H3K9S10 Millipore (05-809) Primary culutured mouse cortical neurons (DIV 8) Input control Input control none embryonic eye Histone H3K27ac H3K27ac (Millipore, catalog# 05-1334, lot# NG1948294) embryonic eye Histone H3K27ac H3K27ac (Millipore, catalog# 05-1334, lot# NG1948294) embryonic genital tubercle Histone H3K27ac H3K27ac (Millipore, catalog# 05-1334, lot# NG1948294) embryonic hindlimb Histone H3K27ac H3K27ac (Millipore, catalog# 05-1334, lot# NG1948294) embryonic forelimb Others Rad23b RAD23B murine D3 embryonic stem cell line Input control Input control IgG murine D3 embryonic stem cell line Input control Input control none, input Testes Others Pou5f1 sc-5279, Santa Cruz mouse embryonic stem cells E14 Others Prdm16 Made in Lab (Harms et al. 2014. Cell Metab.) Prdm16 Knockout BAT Others Prdm16 Made in Lab (Harms et al. 2014. Cell Metab.) Wildtype BAT Others Atm ATM (Santa Cruz, cat: sc-23922, lot: E3111) Mouse Embryonic Fibroblast (MEF) Histone H2A.XS139ph H2AXS139ph (Millipore, cat: 05-636, lot 2019732) Mouse Embryonic Fibroblast (MEF) Others Hmga2 HMGA2 (Santa cruz, cat. sc-30223, lot: F1407 ) Mouse Embryonic Fibroblast (MEF) Histone H3K4me3 H3K4me3 (millipore #07-473) mouse hippocampus Histone H3K27ac anti H3K27ac Primary proliferating myoblasts Histone H3K4me1 anti H3K4me1 Primary proliferating myoblasts Histone H3 pan-H3 (Sigma I8140) TT2 Others Bach2 Bach2 (SIGMA, cat#: SAB2001201, lot#: QC10599 Nave CD4 T cells Unclassified Unclassified E16.5 sorted germ cells Histone H3K27ac anti-H3K27ac Kupffer cells with CD45.1 mark Histone H3K4me2 anti-H3K4me2 Kupffer cells with CD45.1 mark Histone H3K4me1 anti-H3K4me1 Kupffer cells with CD45.1 mark Histone H3K27ac anti-H3K27ac Spleen red pulp macrophages with CD45.1 mark Histone H3K4me2 anti-H3K4me2 Spleen red pulp macrophages with CD45.1 mark Histone H3K4me1 anti-H3K4me1 Spleen red pulp macrophages with CD45.1 mark Histone H3K27ac anti-H3K27ac Peritoneal cavity macrophages with CD45.1 mark Histone H3K4me2 anti-H3K4me2 Peritoneal cavity macrophages with CD45.1 mark Histone H3K4me1 anti-H3K4me1 Peritoneal cavity macrophages with CD45.1 mark Histone H3K27ac anti-H3K27ac Lung macrophages with CD45.1 mark Histone H3K4me2 anti-H3K4me2 Lung macrophages with CD45.1 mark Histone H3K4me1 anti-H3K4me1 Lung macrophages with CD45.1 mark Histone H3K4me2 anti-H3K4me2 Peritoneal cavity macrophages Histone H3K27ac anti-H3K27ac Peritoneal cavity macrophages Histone H3K4me1 anti-H3K4me1 Peritoneal cavity macrophages Histone H3K27ac anti-H3K27ac Lung macrophages Histone H3K4me1 anti-H3K4me1 Lung macrophages Histone H3K27ac anti-H3K27ac Brain microglia Histone H3K4me1 anti-H3K4me1 Brain microglia Input control Input control none small pre-B cells Histone H3S10phK14ac anti-H3S10pK14Ac Millipore 07-081; Lot 2200929 small pre-B cells Histone H3K9ac anti-H3K9Ac Millipore 06-942; Lot 2279810 small pre-B cells Others Brwd1 anti-Brwd1 E15, sc-83517; Lot J1508 small pre-B cells Histone H3K4me2 Anti- H3K4me2 Millipore (Cat. No. 07-030 ) mouse primary cortical neuron Input control Input control NA RA-treated Mutant ESC Histone H3K9me2 H3K9me2, mAbcam 1220 RA-treated Mutant ESC Input control Input control NA Mutant ESC Histone H3K9me2 H3K9me2, mAbcam 1220 Mutant ESC Input control Input control NA RA-treated WT ESC Histone H3K9me2 H3K9me2, mAbcam 1220 RA-treated WT ESC Input control Input control NA WT ESC Histone H3K27ac Abcam, ab4729 activated B cell Others Epitope tags HA 12CA5 pancreatic beta cell line Others Brd4 BRD4 G1E_BRD4 G1E Others Gata1 GATA-1 Antibody (N6) G1E_GATA1 +JQ1 Others Gata1 GATA-1 Antibody (N6) G1E_GATA1 control Others Runx1 Rabbit polyclonal anti-RUNX1 (non-commercial antibody) EML cells Input control Input control Rabbit Serum IgG (Sigma I5006) EML cells Others Sox2 Sox2 clone 6F1.2 EMD Millipore Cat# 17-656 iMOP cells Others Myc c-Myc (N-262) Santa Cruz Cat# sc-764 iMOP cells RNA polymerase RNA polymerase II RNA polymerase II clone 4H8 (Abcam Cat#ab5408) iMOP cells Histone H3K27ac H3K27ac (Abcam 4729) MLL-AF9-puro transformed murine leukemia cell line RNA polymerase RNA polymerase II Pol II Antibody (H-224) anti-Pol II immunoprecipitated chromatin fragments Adelman_Bl6_macrophage_RNAPolII_ChIP-seq_2hr_LPS RNA polymerase RNA polymerase II Pol II Antibody (H-224) anti-Pol II immunoprecipitated chromatin fragments Adelman_Bl6_macrophage_RNAPolII_ChIP-seq_30min_LPS RNA polymerase RNA polymerase II Pol II Antibody (H-224) anti-Pol II immunoprecipitated chromatin fragments Adelman_Bl6_macrophage_RNAPolII_ChIP-seq_untreated Unclassified Unclassified RA073 Neural progenitor cells Histone H3K4me3 ab8580, abcam Embryonic stem cells Histone H3K9me3 ab8898, abcam Embryonic stem cells Histone H3K36me3 ab9050, abcam Embryonic stem cells Histone H3K4me1 ab8895, abcam Embryonic stem cells Histone H3K9ac ab4441, abcam Embryonic stem cells Histone H3K27ac ab4729, abcam Embryonic stem cells Histone H3K27me3 ab6002, abcam Embryonic stem cells Unclassified Unclassified PP500P Embryonic stem cells Unclassified Unclassified RA073 Embryonic stem cells Input control Input control none NIH3T3 cells, input Histone H3K27ac H3K27ac G1E -ER4 cells, treated with E2 Histone H3K27ac H3K27ac G1E cells, an erythroid progenitor model Histone H3K27ac H3K27ac Splenic conventional dendritic Cells Histone H3K4me1 H3K4me1 Splenic conventional dendritic Cells Histone H3K27me3 H3K27me3 Splenic conventional dendritic Cells Histone H3K4me3 H3K4me3 Splenic conventional dendritic Cells Others Stat3 STAT3 Splenic conventional dendritic Cells Histone H3K27ac H3K27ac Pre-activated CD4+ T cells Histone H3K4me1 H3K4me1 Pre-activated CD4+ T cells Histone H3K27me3 H3K27me3 Pre-activated CD4+ T cells Histone H3K4me3 H3K4me3 Pre-activated CD4+ T cells Others Stat3 STAT3 Pre-activated CD4+ T cells Others Rbpj CSL(RBPSUH) T cell acute lymphocytic leukemia Others Notch1 Notch1 (antisera made in lab) T cell acute lymphocytic leukemia Unclassified Unclassified T cell acute lymphocytic leukemia Others Smc1a Smc1a Anti-Smc1a (Bethyl Laboratories, catalog number A300-055A) CD4+CD8+ double positive thymocytes Histone H3K27me3 H3K27me3 (#17-622, Millipore) Forebrain E10.5 Histone H3K4me1 H3K4me1 (abcam, catalog# ab8895, lot# GR114298-1) Mouse back skins Others Med1 Med1 (Crsp1/Trap220, Bethyl Laboratories, catalog# A300-793A, lot# A300-793A-2) Mouse back skins Histone H3K27ac H3K27ac (abcam, catalog# ab4729, lot# GR132150-1) Mouse back skins Histone H3K4me3 anti-H3K4me3 (Millipore, catalog# 07-473) differentiated cells (ESCs were subjected to Spinal motor Neuron in vitro directed differentiation) Histone H3K4me3 anti-H3K4me3 (Millipore, catalog# 07-473) ES cells RNA polymerase RNA polymerase II RNA polymerase II phosphoS5 antibody Pol II ChIP-Seq Mock 60 min Cort Constant RNA polymerase RNA polymerase II RNA polymerase II phosphoS5 antibody Pol II ChIP-Seq Mock 60 min Cort Pulsed RNA polymerase RNA polymerase II RNA polymerase II phosphoS5 antibody Pol II ChIP-Seq Mock 20 min Cort RNA polymerase RNA polymerase II RNA polymerase II phosphoS5 antibody Pol II ChIP-Seq Mock 0 min Cort Histone H3K27me3 H3K27me3 (Millipore, catalog#07-449, LOT#1154011) lung tumors Histone H3K4me3 H3K4me3 (Homemade #28) ES cell culture Others Zic2 Zic2 (Abcam, ab150404) ES cell culture Unclassified Unclassified Murine MLL-AF9 leukemic cells Input control Input control none Input Others Epitope tags Flag (SIGMA M2 F1804) dCas9-noED + S2 gRNA Others Epitope tags Flag (SIGMA M2 F1804) dCas9-noED + S1 gRNA Others Ctcf CTCF Millipore #07-729 Wehi-231-TFII-I KD Others Ctcf CTCF Millipore #07-729 Wehi-231-CT Input control Input control N/A Mouse e17.5 Embryonic Occipital Cortex Histone H3K4me2 H3K4me2 (Millipore 07-030) Mouse e17.5 Embryonic Occipital Cortex Histone H3K27ac H3K27ac (Abcam ab4729) Mouse e17.5 Embryonic Occipital Cortex Input control Input control N/A Mouse e17.5 Embryonic Frontal Cortex Histone H3K4me2 H3K4me2 (Millipore 07-030) Mouse e17.5 Embryonic Frontal Cortex Histone H3K27ac H3K27ac (Abcam ab4729) Mouse e17.5 Embryonic Frontal Cortex Input control Input control N/A Mouse e14.5 Embryonic Cortex Histone H3K4me2 H3K4me2 (Millipore 07-030) Mouse e14.5 Embryonic Cortex Histone H3K27ac H3K27ac (Abcam ab4729) Mouse e14.5 Embryonic Cortex Input control Input control N/A Mouse e11.5 Embryonic Cortex Histone H3K4me2 H3K4me2 (Millipore 07-030) Mouse e11.5 Embryonic Cortex Histone H3K27ac H3K27ac (Abcam ab4729) Mouse e11.5 Embryonic Cortex Histone H3K27ac H3K27ac (Abcam ab4729) mouse embryonic stem cell Input control Input control Whole cell extract v6.5 mouse embryonic stem cells RNA polymerase RNA polymerase II RNAP2 antibody: Covance MMS-128P v6.5 mouse embryonic stem cells Histone H3K36me3 H3K36me3 antibody: Abcam ab9050 v6.5 mouse embryonic stem cells Histone H3K27ac H3K27ac antibody: Abcam ab4729 v6.5 mouse embryonic stem cells Histone H3K9me3 H3K9me3 antibody: Abcam ab8898 v6.5 mouse embryonic stem cells Histone H3K27me3 H3K27me3 antibody: Upstate 07-449 v6.5 mouse embryonic stem cells Histone H3K4me3 H3K4me3 antibody: Millipore 07-473 v6.5 mouse embryonic stem cells Input control Input control total rabbit IgG, Millipore, Cat. #12-370 whole cerebellum Input control Input control none (input) whole cerebellum Histone H3K27me3 anti-Histone H3K27me3 antibody (ab6002, ChIP grade) induced pluripotent stem cells Histone H3K4me3 anti-Histone H3K4me3 antibody (ab8580, ChIP grade) induced pluripotent stem cells Histone H3 Mnase-ChIP with anti-Histone H3 antibody (ab1791, ChIP grade) induced pluripotent stem cells Histone H3K27me3 anti-Histone H3K27me3 antibody (ab6002, ChIP grade) intermediate stage of somatic cell reprogramming Histone H3K4me3 anti-Histone H3K4me3 antibody (ab8580, ChIP grade) intermediate stage of somatic cell reprogramming Histone H3 Mnase-ChIP with anti-Histone H3 antibody (ab1791, ChIP grade) intermediate stage of somatic cell reprogramming Histone H3K27me3 anti-Histone H3K27me3 antibody (ab6002, ChIP grade) mouse embryo fibroblasts Histone H3K4me3 anti-Histone H3K4me3 antibody (ab8580, ChIP grade) mouse embryo fibroblasts Histone H3 Mnase-ChIP with anti-Histone H3 antibody (ab1791, ChIP grade) mouse embryo fibroblasts Histone H3K4me3 H3K4me3 (Active Motif, 39159, lot 1609004) Embryonic stem cells Histone H3K27me3 H3K27me3 (Millipore, 07-449) mouse embryonic stem cells Others Suz12 Suz12 (Cell Signaling, D39F6) mouse embryonic stem cells Others Jarid2 Jarid2 (Abcam, ab48137) mouse embryonic stem cells Others Hdac3 rabbit antibody to Hdac3 C57BL/6_liver_old_Hdac3 ChIP-seq Others Hdac3 rabbit antibody to Hdac3 C57BL/6_liver_young_Hdac3 ChIP-seq Others Foxa2 Foxa2-specific rabbit antiserum C57BL/6_liver_old_Foxa2_ChIP-seq Others Foxa2 Foxa2-specific rabbit antiserum C57BL/6_liver_young_Foxa2_ChIP-seq Histone H3K4me3 anti-H3K4me3 (Active Motif 39159) primary CD4+ T cells from spleen Histone H3K4me1 anti-H3K4me1 (Active Motif 39287) primary CD4+ T cells from spleen Histone H3K27ac anti-H3k27ac (Active Motif 39133) primary CD4+ T cells from spleen Others Ep300 anti-p300 (Santa Cruz sc551X) primary CD4+ T cells from spleen RNA polymerase RNA polymerase II Pol II Santa Cruz #sc-899 Differentiated motor neuron Others Ezh2 EZH2 in-house Differentiated motor neuron Histone H3K27me3 H3K27me3 Abcam #ab6002 mESC Others Ctcf CTCF Millipore #07-729 Differentiated motor neuron Others Ctcf CTCF Millipore #07-729 mESC Others Myc c-Myc Antibody (N-262) (Santa Cruz, catalog# sc-764, lot# D0413) Primary lymphoma cells Input control Input control none (input) Primary lymphoma cells Histone H3K4me3 H3K4me3 ChIP H3K4me3 (Millipore 07-473, lot#2207275) embryonic stem cells, TC11, ZNF91 plasmid, H3K4me3 ChIP Histone H3K4me3 H3K4me3 ChIP H3K4me3 (Millipore 07-473, lot#2207275) embryonic stem cells, TC11, empty vector, H3K4me3 ChIP Histone H3K4me3 H3K4me3 (Millipre #04-745) H3f3b null testis tissue Histone H3K4me3 H3K4me3 (Millipre #04-745) H3f3b WT/WT testis tissue Input control Input control none H3f3b null testis tissue Input control Input control none H3f3b WT/WT testis tissue RNA polymerase RNA polymerase II RNA Pol II (Abcam, ab817) In-vivo leukemia cells from spleen Histone H3K79me2 H3K79me2 (Abcam, ab3594) In-vivo leukemia cells from spleen Histone H3K36me3 H3K36me3 (Abcam, ab9050) In-vivo leukemia cells from spleen Histone H3K27me3 H3K27me3 (Millipore, 07-449) In-vivo leukemia cells from spleen Histone H3K4me3 H3K4me3 (Abcam, ab8580) In-vivo leukemia cells from spleen Histone H3K4me2 H3K4me2 (Abcam, ab7766) In-vivo leukemia cells from spleen Histone H3K27ac H3K27ac (Abcam, ab4729) In-vivo leukemia cells from spleen Histone H3K18ac H3K18ac (Abcam, ab1191) In-vivo leukemia cells from spleen Others Junb sc46 DIV7 mCTX neurons Others Mecp2 Total MeCP2 antibody (Chen et al. 2003) Cerebellum Histone H3K27me3 H3K27me3 (upstate #07-449) mature B cells Histone H3K4me1 H3K4me1 (abcam ab8895) mature B cells Histone H3K27ac H3K27ac (Cell Signaling 8173) mature B cells Histone H3K27me3 H3K27me3 (upstate #07-449) Pro B Histone H3K27ac H3K27ac (Cell Signaling 8173) Pro B Histone H3K27ac H3K27ac (Cell Signaling 8173) HSC Others Cdk8 cdk8 Santa Cruz SC-1521 Embryonic stem cells Histone H3K27ac H3K27Ac Abcam AB4729 Mouse embryonic fibroblasts Input control Input control None None WCE Mouse embryonic fibroblasts Others Epitope tags mouse monoclonal anti-FLAG , M2 (Sigma, Cat.-No.: F1804) limb buds RNA polymerase RNA polymerase II PolII-S5p, Abcam ab5131 Patski cells RNA polymerase RNA polymerase II RNAPII, sc-899, sc-9001, Santa Cruz Liver tissue Histone H3K4me3 H3K4me3 1000 E6.5 epiblasts RNA polymerase RNA polymerase II PolII: 7C2 RNA Pol II R6_striatum_polII RNA polymerase RNA polymerase II PolII: 7C2 RNA Pol II WT_striatum_polII Others Med1 Med1/TRAP220 Bethyl A300-793A Mouse embryonic fibroblasts Histone H3K27me3 H3K27me3 ChIP (clone 7b11) C2 iMEFs Ezh2 -/- Histone H3K27me3 H3K27me3 ChIP (clone 7b11) C2 iMEFs Ezh2 WT/WT Input control Input control none DP T cells Histone H3K27ac H3K27Ac (Abcam, ab 4729) DP T cells Histone H3.1 crosslink anti-H3.1/2 (antiserum) Embryonic stem cells Histone H3.3 crosslink anti-H3.3 (antiserum) Embryonic stem cells Input control Input control none (input) Embryonic Stem cells Histone H3K27me3 H3K27me3 07-449 Embryonic Stem cells Histone H3K4me3 H3K4me3 07-473 Embryonic Stem cells Histone H3K9me2 H3K9me2 (Abcam ab1220) MC1-ZE7 ES cells Others Suv39h2 ab71683, abcam Neural progenitor cells Others Suv39h1 ab12405, abcam Neural progenitor cells Others Cbx1 1MOD-1A9-AS, euromedex Neural progenitor cells Others Ep300 p300 dY-Foxd3CKO-Tam-p300 ChIP Input control Input control IgG (normal rabbit) dY-Foxd3CKO-Tam-IgG ChIP Histone H3K4me3 H3K4me3 dY-Foxd3CKO-EtOH-H3K27me3 ChIP Input control Input control IgG (normal rabbit) dY-Foxd3CKO-EtOH-IgG ChIP Others Ep300 p300 R-Foxd3CKO-Tam-p300 ChIP Histone H3K27ac H3K27ac R-Foxd3CKO-Tam-H3K27ac ChIP Histone H3K4me3 H3K4me3 R-Foxd3CKO-Tam-H3K4me3 ChIP Histone H3K4me1 H3K4me1 R-Foxd3CKO-Tam-H3K4me1 ChIP Input control Input control IgG (normal rabbit) R-Foxd3CKO-Tam-IgG ChIP Others Ep300 p300 R-Foxd3CKO-EtOH-p300 ChIP Input control Input control IgG (normal rabbit) R-Foxd3CKO-EtOH-IgG ChIP Others Epitope tags M2 anti-Flag dY-Targ-Flag ChIP Others Epitope tags M2 anti-Flag dY-Ctrl-Flag ChIP Others Epitope tags M2 anti-Flag R-Targ-Flag ChIP Others Epitope tags M2 anti-Flag R-Ctrl-Flag ChIP Histone H3K4me3 H3K4m3 KO_Retinoic acid treated ES cells Histone H3K27me3 H3K27me3 KO_Retinoic acid treated ES cells Histone H3K4me3 H3K4m3 WT_Retinoic acid treated ES cells Histone H3K27me3 H3K27me3 WT_Retinoic acid treated ES cells Histone H3K27me3 H3K27me3 KO_ES cells Histone H3K27me3 H3K27me3 WT_ES cells Unclassified Unclassified WT ES cells Input control Input control IgG Santa Cruz, sc-2027 Microdissected developing kidneys Others Wt1 WT1 (C-19) Santa Cruz, sc-192 Microdissected developing kidneys Input control Input control none none input control WEHI-279 mouse lymphoma cells Others Epitope tags SpiB Monoclonal ANTI-FLAG M2 (F3165 SIGMA) ChIP chromatin WEHI-279 mouse lymphoma cells Others Spi1 PU.1 Monoclonal ANTI-FLAG M2 (F3165 SIGMA) ChIP chromatin WEHI-279 mouse lymphoma cells Others Gata6 GATA6 (R&D system, AF1700, lot KWT0112101) mouse embryonic fibroblasts Others Gata4 GATA4 (R&D system, AF2606, lot VAZ0312091) mouse embryonic fibroblasts Others Ctcf CTCF ((Millipore 07-729) P12_Liver Others Hnf4a HNF4A (Santa Cruz sc-8987 X) P12_Liver Others Taf3 TAF3 (IGBMC) P12_Liver Others Gtf2e2 TFIIE (Santa Cruz sc-6935X) P12_Liver Others Gtf2b TFIIB (Santa Cruz sc-225 X) P12_Liver RNA polymerase RNA polymerase II Pol II (Santa Cruz sc-9001X) P12_Liver Others Tbp TBP (Abcam ab28175) P12_Liver Histone H3K9K14ac H3K9/14ac H3K9/14ac WT P6 Histone H3K27ac H3K27ac H3K27ac KO P22 Histone H3K27ac H3K27ac H3K27ac WT P22 Histone H3K9K14ac H3K9/14ac H3K9/14ac KO P22 Histone H3K9K14ac H3K9/14ac H3K9/14ac WT P22 Histone H3K4me3 H3K4me3 H3K4me3 KO P22 Histone H3K4me3 H3K4me3 H3K4me3 WT P22 Others Foxa2 Upstate 07-633 Liver Input control Input control Upstate 12-370 Liver Histone H3K27me3 Polyclonal rabbit-anti-H3K27me3 (10 g/ChIP) Th0.Ezh2KO.ChIP-seq Histone H3K27me3 Polyclonal rabbit-anti-H3K27me3 (10 g/ChIP) Th0.Ezh2ff.ChIP-seq RNA polymerase RNA polymerase II Santa Cruz, sc-899x KO MEF RNA polymerase RNA polymerase II Santa Cruz, sc-899x WT MEF Input control Input control none KO MEF Unclassified Unclassified neuronal progenitor cells, mock treatment Histone H3K27me3 H3K27me3 antibody Immunoprecipitated DNA Ezh2KO Epithelium Histone H3K27me3 H3K27me3 antibody Immunoprecipitated DNA Control Epithelium Others Chd8 CHD8 N terminus mouse E17.5 Cortex Histone H3K9me3 In house anti-H3K9me3 #4861 Mouse Embryonic Fibroblasts Histone H3K9me3 In house anti-H3K9me3 #4861 Neural precursors cells Others Epitope tags -HA (Roche 3F10) and -DYKDDDDK (Biozol) Embryonic Stem cells Histone H3K9me3 In house anti-H3K9me3 #4861 Embryonic Stem cells Input control Input control None Day 7 differentiated mouse embryonic stem cells Others Atrx ATRX Day 7 differentiated mouse embryonic stem cells Input control Input control None Undifferentiated mouse embryonic stem cells Others Atrx ATRX Undifferentiated mouse embryonic stem cells Histone H3K9me3 ab8898 Abcam embryonic stem cells Histone H3K4me3 ab8580 Abcam embryonic stem cells Input control Input control input Mouse embryonic day 11.5 (e11.5) limb Others Arid3a Arid3a Streptavidin-conjugated beads single colony embryonic stem cells Histone H3K4me2 H3K4me2 3T3-L1 pre-adipocytes (4h) Histone H3K4me1 H3K4me1 3T3-L1 pre-adipocytes (4h) Histone H3K27ac H3K27ac 3T3-L1 pre-adipocytes (4h) RNA polymerase RNA polymerase II PolII phospho Ser5 (ab5095, Abcam, Cambridge, MA) uterus Others Esr1 ER (sc-542, Santa Cruz Inc, Santa Cruz CA) uterus Histone H3K4me1 Abcam (ab8895) primary Rag2 -/- thymocytes Others Ets1 Santa Cruz (sc-350x) primary Rag2 -/- thymocytes Others Kdm1a Lsd1 ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells Others Ezh2 Ezh2 ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells Histone H3K4me1 H3K4me1 (Abcam ab8895-50ug) epiblast like cells (EpiLC) Histone H3K27ac H3K27ac (Active Motif 39135) epiblast like cells (EpiLC) Others Otx2 Otx2 (Abcam ab21990-100ug) epiblast like cells (EpiLC) Others Pou5f1 Oct4 (Santa Cruz sc-8628) epiblast like cells (EpiLC) Others Ep300 p300 (Santa Cruz sc-585) epiblast like cells (EpiLC) Histone H3K4me1 H3K4me1 (Abcam ab8895-50ug) embryonic stem cells (ESC) Histone H3K27ac H3K27ac (Active Motif 39135) embryonic stem cells (ESC) Others Ep300 p300 (Santa Cruz sc-585) embryonic stem cells (ESC) Unclassified Unclassified Rabbit IgG (in house purified) Primary proliferating myoblasts Others Jun Rabbit anti c-Jun (sc-1694, Santa Cruz Biotechnology) Primary proliferating myoblasts Input control Input control mouse IgG (278-010, Ancell) Primary myotubes (24hr post differentiation induction) Others Myog Mouse anti MyoG (sc-12732, Santa Cruz Biotechnology) Primary myotubes (24hr post differentiation induction) Others Myod1 Mouse anti MyoD (sc-32758, Santa Cruz Biotechnology) Primary proliferating myoblasts Input control Input control Rabbit non immune serum Primary proliferating myoblasts Others Runx1 Runx1 (in house) Primary proliferating myoblasts Others Epitope tags Anti-Flag, Sigma, F3165 EL4 cells Others Ptf1a Lab generated rabbit anti-Ptf1a E12.5 Neural Tube Input control Input control none (input) E12.5 Neural Tube Input control Input control none limb bud, hearts, branchial arches Others Epitope tags mouse monoclonal anti-FLAG (M2) (Sigma,F1804) limb bud, hearts, branchial arches Histone H3K27me3 H3K27me3 antibody (Upstate 07-449) Foxp3GFPKO (het female) Histone H3K27me3 H3K27me3 antibody (Upstate 07-449) Foxp3GFPKO (male) Histone H3K27me3 H3K27me3 antibody (Upstate 07-449) Tnaive Histone H3K27me3 H3K27me3 antibody (Upstate 07-449) T effector Histone H3K27me3 H3K27me3 antibody (Upstate 07-449) Resting Treg Histone H3K27me3 H3K27me3 antibody (Upstate 07-449) Activated Treg Histone H2A.X H2A.X (Xiao lab) embryo Input control Input control none Py2T breast cancer cells Others Tead2 Tead2 (affinity purified, polyclonal rabbit anti-Tead2 antibody (amino acids 16-32) Py2T breast cancer cells Histone H3K27me3 H3K27me3 (Diagenode C15410069 (pAb-069) RING1A-/-;RING1Bfl/fl Embryonic stem cells, tamoxifen-treated, H3K27me3 ChIP Histone H3K27me3 H3K27me3 (Diagenode C15410069 (pAb-069) RING1A-/-;RING1Bfl/fl Embryonic stem cells, untreated control, H3K27me3 ChIP Others Ezh2 EZH2 Ab (Cell Signaling #5246S) RING1A-/-;RING1Bfl/fl Embryonic stem cells, tamoxifen-treated, EZH2 ChIP Others Ezh2 EZH2 Ab (Cell Signaling #5246S) RING1A-/-;RING1Bfl/fl Embryonic stem cells, untreated control, EZH2 ChIP Others Suz12 SUZ12 Ab (Cell Signaling #3737S) RING1A-/-;RING1Bfl/fl Embryonic stem cells, tamoxifen-treated, SUZ12 ChIP Others Suz12 SUZ12 Ab (Cell Signaling #3737S) RING1A-/-;RING1Bfl/fl Embryonic stem cells, untreated control, SUZ12 ChIP Others Rnf2 RING1B ab (Atsuta et al., 2001; PMID 11289226) RING1A-/-;RING1Bfl/fl Embryonic stem cells, tamoxifen-treated, RING1B ChIP Others Rnf2 RING1B ab (Atsuta et al., 2001; PMID 11289226) RING1A-/-;RING1Bfl/fl Embryonic stem cells, untreated control, RING1B ChIP Input control Input control none RING1A-/-;RING1Bfl/fl Embryonic stem cells, untreated control, sonicated control Histone H3K4me3 H3K4me3 Abcam #ab8580 pro-B cell Histone H3K27ac H3K27ac Abcam #ab4729 pro-B cell Histone H3K4me2 anti-H3K4me2 (Millipore 07-030) Sperm, WT, H3K4me2 ChIP Input control Input control ES cells_input Others Zfp57 Anti-Zfp57 antibody ES cells_Zfp57 ChIP-seq Unclassified Unclassified YAP-ERMS mouse cell line Others Parp1 PARP-1 (rabbit polyclonal anti-PARP, ab6079) Nucleus accumbens tissue Others Ncapd3 CAP-D3 Mouse embryonic fibroblasts Others Rxra RXR N-197 RXR_125_IDGSW3_d35 Others Rxra RXR N-197 RXR_veh_IDGSW3_d35 Others Vdr VDR C-20 VDR_125_IDGSW3_d35 Others Vdr VDR C-20 VDR_Veh_IDGSW3_d35 RNA polymerase RNA polymerase II RNA Pol II fetal liver cells Histone H4K16ac H4K16Ac fetal liver cells Histone H3K79me2 H3K79me2 fetal liver cells Histone H3K36me3 H3K36me3 fetal liver cells Histone H3K27me3 H3K27me3 fetal liver cells Histone H3K9ac H3K9Ac fetal liver cells Histone H3K4me3 H3K4me3 fetal liver cells Histone H3K4me2 H3K4me2 fetal liver cells Unclassified Unclassified Embryonic stem cell Input control Input control none HFSC_input DNA_ChIP-Seq RNA polymerase RNA polymerase II Anti-RNA polymerase II, clone CTD4H8 BMM_LPS_0240_PolII RNA polymerase RNA polymerase II Anti-RNA polymerase II, clone CTD4H8 BMM_LPS_0060_PolII Histone H4ac Acetylated Histone H4 BMM_LPS_0240_AcH4 Histone H4ac Acetylated Histone H4 BMM_LPS_0120_AcH4 Histone H4ac Acetylated Histone H4 BMM_LPS_0060_AcH4 Histone H4ac Acetylated Histone H4 BMM_NoStim_0000_AcH4 Others Srf SRF (Santa Cruz Biotechnology, sc-335, Lot# I2712) cornea Histone H3 Total H3 (Abcam, ab1791, Lot GR82485) In vitro effector CD8+ T cells Histone H3K36me3 H3K36me3 (Abcam, ab9050, Lot GR36719) In vitro effector CD8+ T cells Histone H3K27me3 H3K27me3 (Millipore, 07-449, Lot 2064519) In vitro effector CD8+ T cells Histone H3K27ac H3K27ac (Abcam, ab4729, Lot GR52136) In vitro effector CD8+ T cells Histone H3K4me3 H3K4me3 (Abcam, ab8580, Lot GR33084) In vitro effector CD8+ T cells Histone H3K4me1 H3K4me1 (Abcam, ab8895, Lot GR61280) In vitro effector CD8+ T cells Others Irf4 IRF4 (M-17) (Santa Cruz, sc-6059, Lot C2712) In vitro effector CD8+ T cells Others Batf BATF (Brookwood Biomedical, PAB4003, Lot 004) In vitro effector CD8+ T cells Others GFP GFP (Abcam, Cambridge, UK) Neural Retina Others Cbx8 Cbx8 ES E14 mouse cells Histone H3K36me3 H3K36me3 mouse embryonic fibroblasts Histone H3K9me3 H3K9me3 mouse embryonic fibroblasts Others Kdm4c Jmjd2c mouse embryonic fibroblasts Others Kdm4c Jmjd2c Conditional Jmjd2c knockout ESCs Histone H3K36me3 H3K36me3 (Abcam, ab9050, lot# GR52625-1) MC3T3-E1 cells differentiated for 15 days Histone H3K4me3 H3K4me3 (Abcam, ab1012, lot# GR10853-1) MC3T3-E1 cells differentiated for 15 days Histone H3K4me1 H3K4me1 (Abcam, ab8895, lot# GR43807-1) MC3T3-E1 cells differentiated for 15 days Histone H3K9ac H3K9Ac (Millipore, 06-942, lot#31636) MC3T3-E1 cells differentiated for 15 days Histone H4K5ac H4K5Ac (Millipore, 07-327, lot# DAM1794310) MC3T3-E1 cells differentiated for 15 days Others Runx2 RUNX2 (Santa Cruz, M-70, sc10758, lot# D1411) MC3T3-E1 cells differentiated for 15 days Others Cebpb C/EBP (Santa Cruz, C-19, sc-150, lot# F3011) MC3T3-E1 cells differentiated for 15 days Others Rxra RXR (Santa Cruz, N-197, sc-774, lot# G2310) MC3T3-E1 cells differentiated for 15 days Others Vdr VDR (Santa Cruz, C-20, sc-1008, lot# A0912) MC3T3-E1 cells differentiated for 15 days Histone H3K36me3 H3K36me3 (Abcam, ab9050, lot# GR52625-1) MC3T3-E1 cells Histone H3K4me3 H3K4me3 (Abcam, ab1012, lot# GR10853-1) MC3T3-E1 cells Histone H3K4me1 H3K4me1 (Abcam, ab8895, lot# GR43807-1) MC3T3-E1 cells Histone H3K9ac H3K9Ac (Millipore, 06-942, lot#31636) MC3T3-E1 cells Histone H4K5ac H4K5Ac (Millipore, 07-327, lot# DAM1794310) MC3T3-E1 cells Others Runx2 RUNX2 (Santa Cruz, M-70, sc10758, lot# D1411) MC3T3-E1 cells Others Cebpb C/EBP (Santa Cruz, C-19, sc-150, lot# F3011) MC3T3-E1 cells Others Rxra RXR (Santa Cruz, N-197, sc-774, lot# G2310) MC3T3-E1 cells Others Vdr VDR (Santa Cruz, C-20, sc-1008, lot# A0912) MC3T3-E1 cells Histone H3K27me3 H3K27me3 naive CD4 T cells Histone H3K27ac H3K27ac naive CD4 T cells Histone H3K4me3 H3K4me3 naive CD4 T cells Others Utf1 Utf1 (Abcam, ab24273) KH2 mouse embryonic stem cells Input control Input control none mammary tissues, p13, no treatment, input Others Chd4 Anti-CHD4 (clone 3F2/4), Abcam AB70469, lot: GR104037-2 Pro-B cell Input control Input control NA 3134 cells Others Chd4 CHD4 3134 cells Input control Input control NA Embryonic stem cells Input control Input control none ESC-derived endoderm Others Tcf12 HEB (Santa Cruz, sc-357, lot G0209) ESC-derived endoderm Others Tcf12 HEB (Santa Cruz, sc-357, lot G0209) Embryonic stem cells Others GFP Abcam:Ab290 ES cells Input control Input control none, input thymus Input control Input control NULL shKdm5b LSD1i ES cells Input control Input control NULL shLuc LSD1i ES cells Histone H3K4me1 Anti-H3K4me1 antibody (Abcam; ab8895) shKdm5b LSD1i ES cells Histone H3K4me2 Anti-H3K4me2 antibody (Abcam; ab32356) shKdm5b LSD1i ES cells Histone H3K4me3 Anti-H3K4me3 antibody (Millipore; CS200580) shKdm5b LSD1i ES cells Histone H3K4me1 Anti-H3K4me1 antibody (Abcam; ab8895) shLuc LSD1i ES cells Histone H3K4me2 Anti-H3K4me2 antibody (Abcam; ab32356) shLuc LSD1i ES cells Histone H3K4me3 Anti-H3K4me3 antibody (Millipore; CS200580) shLuc LSD1i ES cells Histone H3K4me2 Anti-H3K4me2 antibody (Abcam; ab32356) shKdm5b ES cells Histone H3K4me3 Anti-H3K4me3 antibody (Millipore; CS200580) shKdm5b ES cells Histone H3K4me2 Anti-H3K4me2 antibody (Abcam; ab32356) shLuc ES cells Histone H3K4me3 Anti-H3K4me3 antibody (Millipore; CS200580) shLuc ES cells Histone H3K4me1 Anti-H3K4me1 antibody (Abcam; ab8895) shKdm5b ES cells Input control Input control none (input) Liver Histone H2AK119Ub Millipore, 07-146 mouse embryoid bodies Histone H2Aub Millipore, 05-678 mouse embryoid bodies Others Usp16 Usp16 purified antibody (Non commercial, available upon request) mouse embryoid bodies Histone H2AK119Ub Millipore, 07-146 mouse embryonic stem cell Histone H2Aub Millipore, 05-678 mouse embryonic stem cell Others Usp16 Usp16 purified antibody (Non commercial, available upon request) mouse embryonic stem cell Histone H3K27me3 H3K27me3 (Cat# 07-449, Millipore, lot# JBC1873477) CD4+ T cells Histone H3K4me3 H3K4me3 (Cat# 07-473, Millipore, lot# 2289139) CD4+ T cells Others Ascl2 Ascl2 mAb (clone, 7E2, Millipore, lot# 2066321) CD4+ T cells Others Grhl3 Grhl3 (custom made) adult mouse epidermis Others Grhl3 Grhl3 (custom made) whole embryonic mouse skin Others Suz12 SUZ12 Ab (Cell Signaling #3737S) Embryonic stem cells, tamoxifen treated, SUZ12 ChIP Others Suz12 SUZ12 Ab (Cell Signaling #3737S) Embryonic stem cells, untreated control, SUZ12 ChIP Others Ep400 p400 (Bethyl, A300-541A) mouse embryonic stem cells Input control Input control NA main olfactory epithelium Histone H3K27ac Millipore, cma309 main olfactory epithelium Histone H3K4me1 Abcam, ab8895 main olfactory epithelium Others Hnf4a HNF4A (ab41898, Abcam, lot # GR4841-13) colonic epithelial cells Input control Input control Input chromatin liver Input control Input control Input chromatin aorta Others Esr1 anti mouse ER-alpha liver Others Esr1 anti mouse ER-alpha aorta Histone H3K4me3 H3K4me3 Embryonic Stem Cells RNA polymerase Polr2b anti-POLR2B (mouse and humans), Santa Cruz Cat N. SC-67318 (H-201) Mouse Liver Others Kansl3 KANSL3 (SIGMA, HPA035018) Neuronal progenitor cells Others Msl2 MSL2 (SIGMA, HPA003413) Neuronal progenitor cells Others Kat8 MYST1 (BETHYL, A3000992A) Neuronal progenitor cells Input control Input control none Neuronal progenitor cells Others Kansl3 KANSL3 (SIGMA, HPA035018) Embryonic stem cells Others Msl2 MSL2 (SIGMA, HPA003413) Embryonic stem cells Others Msl1 MSL1 (in-house, Rabbit Polyclonal, Final Bleed) Embryonic stem cells Others Kat8 MYST1 (BETHYL, A3000992A) Embryonic stem cells Histone H2A.Z H2AZ Embryonic fibroblasts Input control Input control Input Embryonic fibroblasts Histone H3K4me2 H3K4me2 (Millipore 07-030) Intestinal crypt enterocyte progenitors Histone H3K4me2 H3K4me2 (Millipore 07-030) Intestinal crypt secretory progenitors Others Epitope tags Monoclonal ANTI-FLAG M2 Antibody, Sigma C2C12 myotubes, IP flag PGC-1alpha Input control Input control rIgG (sc-2027, SantaCruz) rIgG Others Ar AR (Sahu et al. 2011) AR_SPARKI Others Ar AR (Sahu et al. 2011) AR_wt Others Med1 Med1 cell line Others Klf4 Klf4 cell line Others Pou5f1 Oct4 cell line Unclassified Unclassified E36 Ebs cells Unclassified Unclassified E36 Ebs cells EED KO Unclassified Unclassified E14 ES cells Histone H3K27ac H3K27ac (Abcam, catalog# ab4729, lot# GR45851-1) embryonic fibroblasts, E13.5 Histone H3K4me1 H3K4me1 (Abcam, catalog# ab8895, lot# GR46388-1) embryonic fibroblasts, E13.5 Histone H3K4me3 H3K4me3 (Active Motif, catalog# 39159, lot# 1609004) embryonic fibroblasts, E13.5 Others Myc c-Myc N262 (Santa Cruz , catalog# sc764, lot#G0111) embryonic fibroblasts, E13.5 RNA polymerase RNA polymerase II RNAPII (Santa Cruz, catalog# sc-899, lot# F0112) embryonic fibroblasts, E13.5 Others Stat6 STAT6 (Santa Cruz, M-20, sc-981) Th9 cells, 72h, STAT6 ChIP Others Stat5b STAT5B (R&D Systems, Sta5B) Th9 cells, 72h, STAT5B ChIP Others Bcl6 BCL6 (Santa Cruz, N-3, sc-858) Th9 cells, 72h, BCL6 ChIP Others Spi1 Anti-PU.1 (in-house rabbit polyclonal against the N-Terminal (aa. 1-100)) In vitro reconstituted chromatin (genomic DNA from primary bone marrow-derived macrophages) RNA polymerase RNA polymerase II anti-pol II CTD (abcam ab5095) whole heart Input control Input control None Input chromatin Trophoblast giant cells - cultured Histone H3K27me3 H3K27me3 (ActiveMotif, 39535, lot 33310009) Trophoblast giant cells - cultured Histone H3K4me1 H3K4me1 (Abcam, ab8895, lot 962583) Trophoblast giant cells - cultured Histone H3K9me3 H3K9me3 (Abcam, ab8898, lot GR110001) Trophoblast giant cells - cultured Histone H3K4me3 H3K4me3 (ActiveMotif, 39159, lot 1609004) Trophoblast giant cells - cultured Histone H3K27ac H3K27ac (Abcam, ab4729, lot 730178) Trophoblast giant cells - cultured Histone H4 Histone H4 calvaria Histone H3K4me3 H3K4me3 mouse embryonic stem cell Histone H3K4me2 H3K4me2 mouse embryonic stem cell Unclassified Unclassified na intestinal epithelial cells Histone H3K4me2 H3K4me2 mouse brown preadipocytes, MLL4 KO, H3K4me2 ChIP Histone H3K4me2 H3K4me2 mouse brown preadipocytes, WT, H3K4me2 ChIP RNA polymerase RNA polymerase II Pol II mouse brown preadipocytes, MLL4 KO, Pol II ChIP RNA polymerase RNA polymerase II Pol II mouse brown preadipocytes, WT, Pol II ChIP Others Pparg PPARgamma mouse brown preadipocytes, WT, PPARgamma ChIP Others Cebpb C/EBPbeta mouse brown preadipocytes, WT, C/EBPbeta ChIP Others Cebpa C/EBPalpha mouse brown preadipocytes, WT, C/EBPalpha ChIP Histone H3K4me1 Monoclonal anti-H3K4me1 Splenic NK cells Input control Input control IgG (Santa Cruz Biotechnology, Sc-2027) Undifferentiated mouse ES cells Others Kdm6b anti-Jmjd3 (rabbit polyclonal) Embryonic stem cells Others Kdm6a anti-UTX (Ab84190) Embryonic stem cells Others Hira anti-Hira (WC15/WC119) Embryonic stem cells Others Suz12 SUZ12 Cell signaling, cat# 3737 E14 Histone H3K27me3 H3K27me3 Millipore #07-449 E14 Others Klf4 Klf4 (SC-20691, Santa Cruz) Normal murine mammary epithelial (NMuMG) cells Input control Input control none 3T3-L1 adipocytes (Day 7) Others Crebbp anti-CBP (sc-369; Santa Cruz) 3T3-L1 adipocytes (Day 7) Others Cebpa anti-C/EBP (sc-61; Santa Cruz) 3T3-L1 adipocytes (Day 7) Others Med1 anti-MED1 (sc-8998; Santa Cruz) 3T3-L1 adipocytes (Day 7) Others Myc Myc (Invitrogen 46-0603, Lot no. 1141786) mouse corneal epithelium Histone H3K4me1 H3K4me1 (ab8895, Abcam) C2C12 Others Myod1 MyoD (C-20, Santa Cruz) C2C12 Input control Input control none Undifferentiated mouse embryonic stem cell line Input control Input control Input Pancreatic acinar cells Histone H3K4me3 H3K4Me3 (cat#04-745 Millipore) Pancreatic acinar cells Histone H3K4me1 (rb) -H3K4me1 (#524; Ali Shilatifard) ES cell culture Input control Input control none, input control Forelimb Others Ascl1 Ascl1 (ab74065) embryonic fibroblasts treated with BAM factors Others Cebpa Cebpa: Santa Cruz 14-AA GMP_CebpaWT Input control Input control input DNA CD4+ CD8+ Double Positive Thymocytes Others Nanog Nanog (A300-397A), Bethyl Laboratories Jmjd2b KD mESCs Histone H3K27ac H3K27ac (Abcam ab4729) Primary thioglycollate-elicited peritoneal macrophages Others Cebpa C/EBPa (Santa Cruz sc-61) Primary thioglycollate-elicited peritoneal macrophages RNA polymerase RNA polymerase II RNA polymerase II CTD phsophoSerine 2 (Abcam 5095) Primary thioglycollate-elicited peritoneal macrophages Others Nr0b1 bioDax1 ChIP DNA from ES cells Others Myc bioMyc ChIP DNA from ES cells Input control Input control Input control Splenic CD4+ dendritic cells Others Runx3 Runx3poly clonal home made Splenic CD4+ dendritic cells Input control Input control normal rabbit IgG liver tissue Histone H3K27me3 H3K27me3 Cell Signaling Technologies #9773 pro-B cell Histone H3K27me3 H3K27me3 (Active, Motif, lot AM) ES cells Histone H3K9me3 H3K9me3 (Abcam, Ab8898, lot GR88132-1) ES cells Histone H3K27me3 H3K27me3 (Active, Motif, lot 39155) ES cells Histone H3K27me3 H3K27Me3 (Active, Motif, lot 39155) ES cells Histone H3K27ac H3K27Ac (Active, Motif, lot 39133) ES cells Histone H3K9me3 H3K9me3 (Abcam, Ab8898, lot 699671) ES cells Histone H2BK5ac H2BK5Ac mouse plasmacytoma PCT4961 Histone H3K9ac H3K9Ac mouse plasmacytoma PCT4961 Histone H3K27ac H3K27Ac mouse plasmacytoma PCT4961 Histone H3K4me3 H3K4me3 mouse plasmacytoma PCT4961 Histone H4K91ac H4K91Ac mouse plasmacytoma PCT4961 Histone H3K36me2 H3K36me2 mouse plasmacytoma PCT4961 Histone H2A.Z H2AZ mouse plasmacytoma PCT4961 Histone H4K8ac H4K8Ac mouse plasmacytoma PCT4961 Histone H2BK120ac H2BK120Ac mouse plasmacytoma PCT4961 Histone H4K8ac H4K8Ac mouse, in vitro activated B cells Histone H2A.Z H2AZ mouse, in vitro activated B cells Histone H3K36me2 H3K36me2 mouse, in vitro activated B cells Unclassified Unclassified in house antibody Embryonic stem cells Others Spi1 anti-PU.1 (Santa Cruz; sc-352) purified primary B cells from Bi-8i mice; stimulated for 1 Days; anti-PU.1 ChIP Input control Input control normal mouse IgG Prdm4-EGFP_ESCs_B6_mIgG_ChIP Input control Input control normal mouse IgG Prdm4-EGFP_ESCs_B1_mIgG_ChIP Others GFP GFP (clone 3E6) Mouse IgG2a, Monoclonal Antibody Prdm4-EGFP_ESCs_B6_GFP_ChIP Others GFP GFP (clone 3E6) Mouse IgG2a, Monoclonal Antibody Prdm4-EGFP_ESCs_B1_GFP_ChIP Input control Input control No Antibody Neural progenitor cells Histone H3K27me3 anti-H3K27me3 (Cell Signaling 9733 (C36B11) rabbit monoclonal antibody) Embryonic stem cell culture Others Stat3 anti-Stat3 Pooled gastric tumor tissue from 3 individual IL11-treated gp130F/F mice, Stat3 ChIP Others Stat3 anti-Stat3 Pooled gastric tumor tissue from 3 individual IL6-treated gp130F/F mice, Stat3 ChIP Others Stat3 anti-Stat3 Pooled gastric tumor tissue from 3 individual PBS-treated gp130F/F mice, Stat3 ChIP Others Biotin Dynabeads MyOneTM Streptavidin T1 ESC E14 Others Suz12 rabbit anti-SUZ12 (Cell signaling) Mouse embryotic stem cells Others Rnf2 rabbit anti-RNF2/Ring1B (NAST; antigen sequence: NASTHSNQEAGPSNKRTKT) Mouse embryotic stem cells Others Rest rabbit anti-REST (Millipore, 07-579) Mouse embryotic stem cells Histone H3K27me3 rabbit anti-H3K27Me3 (Cell Signalling, C36B11) Mouse embryotic stem cells Others Jarid2 rabbit anti-Jarid2 (Novus Biologicals) Mouse embryotic stem cells Input control Input control Rabbit IgG (DAKO) Mouse embryotic stem cells Histone H2AK119Ub H2AK119ubq (05-678) CD43 negative mouse resting B cells Histone H3S28ph H3S28ph CD43 negative mouse resting B cells Others Kdm5c Kdm5C (Iwase et al., 2016) hipocampal tissue from adult mice Others Ebf2 EBF2 immortalized brown adipocytes Input control Input control none (input) Fetal Liver Others Epitope tags HA (Santa Cruz Biotechnology, sc-7329X, F-7) Fetal Liver Histone H3K27me3 anti H3K27me3 antibody (Cell Signaling #9733) DPdouble positive thymocytes derived from in vitro expanded bone marrow cells transduced with Nup98-HoxB4, grown with IL7 and DLL4 (Notch signaling) and injected into Rag2-/- mouse Histone H3K4me3 anti H3K4me3 antibody (Abcam ab8580) DPdouble positive thymocytes derived from in vitro expanded bone marrow cells transduced with Nup98-HoxB4, grown with IL7 and DLL4 (Notch signaling) and injected into Rag2-/- mouse Histone H3K27me3 anti H3K27me3 antibody (Cell Signaling #9733) ProT in vitro expanded bone marrow cells transduced with Nup98-HoxB4 and grown with IL7 and DLL4 (Notch signaling) Histone H3K4me3 anti H3K4me3 antibody (Abcam ab8580) ProT in vitro expanded bone marrow cells transduced with Nup98-HoxB4 and grown with IL7 and DLL4 (Notch signaling) Histone H3K27me3 anti H3K27me3 antibody (Cell Signaling #9733) HSC in vitro expanded bone marrow cells transduced with Nup98-HoxB4 Histone H3K4me3 anti H3K4me3 antibody (Abcam ab8580) HSC in vitro expanded bone marrow cells transduced with Nup98-HoxB4 Input control Input control IgG C57Black mouse maintained on a high fat diet Input control Input control IgG C57Black mouse maintained on a calorie restricted diet Others Ppara PPAR C57Black mouse maintained on a high fat diet Others Rxra RXR C57Black mouse maintained on a high fat diet Others Ppara PPAR C57Black mouse maintained on a calorie restricted diet Others Rxra RXR C57Black mouse maintained on a calorie restricted diet Input control Input control None (Whole cell extract) CM stage cultures, Whole cell extract Input control Input control None (Whole cell extract) CP stage cultures, Whole cell extract Input control Input control None (Whole cell extract) MES stage cultures, Whole cell extract Input control Input control None (Whole cell extract) ESC stage cultures, Whole cell extract RNA polymerase RNA polymerase II RNA Polymerase II (phospho S5) (Abcam ab5131) CM stage cultures, RNA Polymerase II RNA polymerase RNA polymerase II RNA Polymerase II (phospho S5) (Abcam ab5131) CP stage cultures, RNA Polymerase II RNA polymerase RNA polymerase II RNA Polymerase II (phospho S5) (Abcam ab5131) MES stage cultures, RNA Polymerase II Histone H3K4me3 H3K4me3 (Millipore 07-473) CM stage cultures, H3K4me3 Histone H3K4me3 H3K4me3 (Millipore 07-473) CP stage cultures, H3K4me3 Histone H3K4me3 H3K4me3 (Millipore 07-473) MES stage cultures, H3K4me3 Histone H3K4me3 H3K4me3 (Millipore 07-473) ESC stage cultures, H3K4me3 Histone H3K27me3 H3K27me3 (Millipore 07-449) ESC stage cultures, H3K27me3 Histone H3K27ac H3K27ac (Abcam ab4729) CM stage cultures, H3K27ac Histone H3K27ac H3K27ac (Abcam ab4729) CP stage cultures, H3K27ac Histone H3K27ac H3K27ac (Abcam ab4729) MES stage cultures, H3K27ac Histone H3K27ac H3K27ac (Abcam ab4729) ESC stage cultures, H3K27ac Histone H3K9me3 H3K9me3 (Abcam, 8898, lot 699671) mouse embryonic stem cells Histone H3K9me3 H3K9me3 (Diagenode. Cat no. pAb-056-050, Lot# A93-0041) mouse embryonic stem cells RNA polymerase Polr3gl anti-mouse POLR3GL ZCH10079-1434 Ab, raised against peptide RPPKSTDDKEETIQK Hepa 1-6 cells RNA polymerase Polr3g anti-mouse POLR3G ZCH10075-1430 Ab, raised against peptide VGFSRGEKLPDVVLK Hepa 1-6 cells RNA polymerase Polr3d anti-POLR3D (mouse and human) CS681 Ab, raised against peptide CSPDFESLLDHKHR {Chong, 2001 #96} Hepa 1-6 cells RNA polymerase Polr3gl anti-mouse POLR3GL ZCH10079-1434 Ab, raised against peptide RPPKSTDDKEETIQK Liver RNA polymerase Polr3g anti-mouse POLR3G ZCH10075-1430 Ab, raised against peptide VGFSRGEKLPDVVLK Liver RNA polymerase Polr3d anti-POLR3D (mouse and human) CS681 Ab, raised against peptide CSPDFESLLDHKHR {Chong, 2001 #96} Liver Input control Input control none (input) Neural tube Input control Input control None Connective tissue Others Smarca4 Brg1 (from anki.ostlund Farrant (Stockholm University)) Connective tissue Histone H3K9me3 H3K9Me3 (abcam ab8898) Connective tissue Others Dr1 Anti NC2 beta antibody from Abcam (ab50783) ESC cells Others Ino80 Anti Ino80 antibody from Proteintech (18810-1-AP) ESC cells Others Btaf1 Anti murine Mot1 antibody from Abcam (ab72285) ESC cells Input control Input control None OLP_Stat3 Input Others Stat3 p-STAT3 (Y705) (Cell Signaling D3A7 Rb mAb 9145S Lot 26) OLP_Stat3 ChIP Others Maf c-Maf (Santa Cruz, M-153) Primary CD4+ Th cells Histone H3K27me3 H3K27me3 (Millipore, 07-449) Primary CD4+ Th cells Others Jarid2 Jarid2 (Abcam, ab48137) Primary CD4+ Th cells Input control Input control none Primary CD4+ Th cells Others Foxa2 Goat anti-Foxa2 (Santa cruz;Hnf3b M-20 #6554) E17.5 Pancreas Others Rbpjl Lab generated rabbit anti-Rbpjl (AN2165/2166) E17.5 Pancreas Others Rbpj Lab generated rabbit anti-Rbpj(Tx857) E12.5 Neural Tube Others Ptf1a Lab generated rabbit anti-Ptf1a (AN255/256) E17.5 Pancreas Others Ptf1a Lab generated rabbit anti-Ptf1a (AN255/256) E12.5 Neural Tube Unclassified Unclassified Mouse embryonic stem cells (E14) Histone H3K36me3 H3K36me3 (Abcam 9050) hindlimb muscles Input control Input control rIgG (sc-2027, SantaCruz) rIgG1 Others Ar AR (Sahu et al. 2011) AR_Cast1 Others Tfap2a AP2a (ab52222, Abcam) AP2a_Cast+T Others Hnf4a HNF4a (ab41898, Abcam) Hnf4a_Cast+T Others Ctcf Rabbit anti-Ctcf antibody (07-729, Millipore, unpurified) Pro-B cell Others Men1 Menin (bethyl: A300-105A) Three-week cultured Th2 cells generated from primary splenic CD4_T cells Others Men1 Menin (bethyl: A300-105A) Five-day cultured Th2 cells generated from primary splenic CD4_T cells Others Cebpa Cebpa: Santa Cruz 14-AA Haematopoietic progenitor cells Others Jund JunD (329; sc-74x) Junbfl/flCD4cre Th17 cells Others Jund JunD (329; sc-74x) Junb+/+CD4cre Th17 cells Input control Input control none WT Th17 cells Input control Input control anti-IgG Murine erythroleukemia (MEL) cells Histone H4K16ac E14 ES cells, CHX, H4K16ac ChIP Histone H4K16ac E14 ES cells, control, H4K16ac ChIP Others Rad21 Anti-Rad21, Abcam ChIP Grade (ab992) Ter119+ Erythroid cells Others Smyd2 anti-Smyd2 (Santa Cruz, Catalog# sc-79084, Lot# H2014) epithelial cells Histone H3K27me3 Anti-H3K27me3 (Upstate, 07-449) mESC Histone H3K4me3 H3K4me3 (07-473, Millipore), lot# DAM1798683 spleen Histone H3K27me3 H3K27me3 (Millipore, Cat. No. 07-449, Lot No. DAM1588246) Embryonic cortex Others Egr2 EGR2 (PRB-236P,Covance) CD4+ T cells_treatment with immobilized anti-CD3 mAb_Egr2_IP Others Pparg PPARy H100 (sc-7196X) Brown adipose tissue RNA polymerase RNA polymerase II Pol II (Santa Cruz sc-899 or sc-9001) Brown adipose tissue Others Ebf2 EBF2 (R+D AF 7006) Brown adipose tissue Others Myc Myc (Cell Signaling, 2272) Embryonic stem cells Histone H3K27me3 H3K27me3 (Millipore, 07-449) Embryonic stem cells Histone H3K4me3 H3K4me3 (Millipore, 07-473) Embryonic stem cells Others Rbpj T6719; Institute of Immunology, Kyoto ; lot: 901119 T29 cells Input control Input control none T29 cells Others Cebpb CEBPbeta immortalized brown adipocytes Input control Input control none iPax7 myogenic progenitors -dox 3d Histone H3K4me1 anti-H3K4m1, ab8895, AbCam CD4+ T cells Others Spi1 anti-PU.1 (Santa Cruz, SC-352) RAW macrophages Histone H3K4me1 anti-H3K4me1 (Abcam, 8895) RAW macrophages Histone H3K9ac anti-H3K9ac (Millipore, 07-352) RAW macrophages Input control Input control input control F9_RBPJ_input Others Yy1 YY1 C2C12 myoblasts Unclassified Unclassified mouse peritoneal macrophage Others Med1 Anti Med1 antibody (SC-5334x) ESC cells Others Mecp2 MeCP2; Cell Signaling; D4F3; lot # 2 Cerebellar Granule Cells Histone H3K4me3 H3K4me2 antibody, Cat#9726; RRID:AB_915839 3T3-L1 preadipocytes Histone H3K4me1 H3K4me1 antibody, Cat#ab8895; RRID:AB_306847 3T3-L1 preadipocytes Histone H3K27ac H3K27ac antibody, Cat#ab4729; RRID:AB_2118291 3T3-L1 preadipocytes Histone H3K27me3 H3K27me3 (ab6002; Abcam) spermatogenic cells, Ezh2 mutant, H3k27me3 ChIP Histone H3K27me3 H3K27me3 (ab6002; Abcam) spermatogenic cells, control, H3k27me3 ChIP Histone H3K27me3 H3K27me3 NMuMG cells, TGF, day 20 Histone H3K27me3 H3K27me3 NMuMG cells, TGF, day 10 Histone H3K27me3 H3K27me3 NMuMG cells, TGF, day 7 Histone H3K27me3 H3K27me3 NMuMG cells, TGF, day 4 Histone H3K27me3 H3K27me3 NMuMG cells, TGF, day 1 Histone H3K27me3 H3K27me3 NMuMG cells, TGF, day 0 Others Stat5a STAT5A (Santa Cruz Biotechnology, sc-1081) Mammary RNA polymerase RNA polymerase II RNA polymerase II (Abcam, ab5408) Mammary Histone H3K27me3 H3K27me3 (#07-449, Millipore, Billerica, MA, USA) VEGF_minus_48h_H3K27me3 Histone H3K4me3 H3K4me3 (non-commercial, gifted by Dr. Hiroshi Kimura, Tokyo Institute Technology, Japan) VEGF_minus_48h_H3K4me3 Histone H3K27me3 H3K27me3 (#07-449, Millipore, Billerica, MA, USA) VEGF_plus_48h_H3K27me3 Histone H3K4me3 H3K4me3 (non-commercial, gifted by Dr. Hiroshi Kimura, Tokyo Institute Technology, Japan) VEGF_plus_48h_H3K4me3 Histone H3K27me3 H3K27me3 (#07-449, Millipore, Billerica, MA, USA) VEGF_minus_6h_H3K27me3 Histone H3K4me3 H3K4me3 (non-commercial, gifted by Dr. Hiroshi Kimura, Tokyo Institute Technology, Japan) VEGF_minus_6h_H3K4me3 Histone H3K27me3 H3K27me3 (#07-449, Millipore, Billerica, MA, USA) VEGF_plus_6h_H3K27me3 Histone H3K4me3 H3K4me3 (non-commercial, gifted by Dr. Hiroshi Kimura, Tokyo Institute Technology, Japan) VEGF_plus_6h_H3K4me3 Histone H3K27me3 H3K27me3 (#07-449, Millipore, Billerica, MA, USA) Flk_H3K27me3 Histone H3K4me3 H3K4me3 (non-commercial, gifted by Dr. Hiroshi Kimura, Tokyo Institute Technology, Japan) Flk_H3K4me3 Input control Input control none R1 ES cells, shKdm5b, input Input control Input control none R1 ES cells, shLuc, input Input control Input control none uterus Others Trim28 KAP1 (custom rabbit polyclonal) mESCs_KAP1_ChIP-seq Histone H3K9me3 H3K9me3 (Diagenode, pAb-056-050) mESCs_Trim28 shRNA_H3K9_ChIP-seq Input control Input control mESCs_control shRNA_input Histone H3K9me3 H3K9me3 (Diagenode, pAb-056-050) mESCs_control shRNA_H3K9_ChIP-seq Histone H3K4me1 H3K4Me1 CD8 T cells Others Myc anti-MYC (ab32072, Abcam) E-Myc lymphoma #1 cell line Input control Input control N/A E-Myc lymphoma #1 cell line RNA polymerase RNA polymerase II anti-RNA polymerase II (CTD4H8, Millipore) E-Myc lymphoma #1 cell line Others Brd4 anti-Brd4 (ab128874, Abcam) E-Myc lymphoma #1 cell line Histone H3K36me3 anti-H3K36me3 (Diagenode, Premium, C15410192) B6spo11ko_H3K36me3_ChIPseq Histone H3K36me3 anti-H3K36me3 (Diagenode, Premium, C15410192) RJ2_H3K36me3_ChIPseq Histone H3K36me3 anti-H3K36me3 (Diagenode, Premium, C15410192) B6_H3K36me3_Input Histone H3K36me3 anti-H3K36me3 (Diagenode, Premium, C15410192) B6_H3K36me3_ChIPseq Others Dmc1 anti-DMC1 (Santa Cruz, C-20) RJ2_DMC1_ChIPseq Others Dmc1 anti-DMC1 (Santa Cruz, C-20) B6_DMC1_ChIPseq Others Prdm9 anti-PRDM9 (BdM) B6spo11ko_PRDM9_Input Others Prdm9 anti-PRDM9 (BdM) B6spo11ko_PRDM9_ChIPseq Others Top2b Top2b (Santa Cruz) Cerebellar granule neuron Others Chd7 Chd7 (Cell Siganling) Cerebellar granule neuron progenitor Others Bcl11b anti-Bcl11b Abs, a mixture of A300-383A (Bethyl), A300-385A (Bethyl), ab18465 (Abcam) and 12120 (CST) BM_DN3_aBcl11b-ChIP Others Creb1 a.a. 5-24 of human CREB 17-600 (Millipore) 3T3-L1 cells (ATCC #CL-173) Others Duxbl1 MO488, MO489 (anti-hDUX4) cultured mouse myoblasts (C2C12) Unclassified Unclassified NIH3T3 cells Others Nkx2-5 E11.5 heart, Nkx2-5 ChIP Histone H3K27ac H3K27ac (Active Motif, 39133) epididymal WAT Unclassified Unclassified Pool of epididymal and inguinal WAT Histone H3K27ac H3K27ac (Active Motif, 39133) BAT Others Ctcf CTCF (Abcam ab70303 / Millipore 07-729) delC-L1-CTCF Others Stag1 STAT5A (Santa Cruz Biotechnology, sc-1081) delA-L1-STAT5A RNA polymerase RNA polymerase II RNA polymerase II (Abcam, ab5408) delA-L1-Pol2 Histone H3K27ac H3K27ac (Abcam ab4729) delA-L1-H3K27ac Others Nr3c1 GR (Thermo Scientific, PA1-511A) delA-L1-GR Others Ctcf CTCF (Abcam ab70303 / Millipore 07-729) delA-L1-CTCF Others Ctcf CTCF (Abcam ab70303 / Millipore 07-729) Mammary-WT-L1-CTCF Histone H3K27ac H3K27ac (Abcam ab4729) Mammary-delE-L1-H3K27ac Histone H3K27ac H3K27ac (Abcam ab4729) Mammary-delD-L1-CTCF Histone H3K27ac H3K27ac (Abcam ab4729) Mammary-delC-L1-H3K27ac Others Jarid2 anti JARID2 rabbit Novus NB100-2214 Undifferentiated ES cells Histone H3K27ac H3K27Ac primary T cells Histone H3K4me1 H3K4me1 primary T cells Input control Input control none mouse embryonic fibroblasts (MEFs) Histone H3K4me1 H3K4me1 (Millipore, 08-034, lot 112345) mouse embryonic fibroblasts (MEFs) Histone H3K4me2 H3K4me2 (Millipore, 07-030, lot 122116) mouse embryonic fibroblasts (MEFs) Histone H3K4me3 H3K4me3 (Abcam ab8580, 10ug per IP) Cortex, H3K4me3 ChIP Unclassified Unclassified d6 PGCLC Unclassified Unclassified d2 PGCLC Others Ctcf CTCF (Abcam ab128873) embryonic stem cells Others Rad21 Rad21 (Abcam ab154769) embryonic stem cells Unclassified Unclassified MEFs expressing Sox2,Klf4 from pMX vector for 48h Unclassified Unclassified MEFs expressing Oct4,Klf4 from pMX vector for 48h Unclassified Unclassified MEFs expressing Sox2 from pMX vector for 48h Unclassified Unclassified MEFs expressing Oct4 from inducible system for 48h Unclassified Unclassified MEFs expressing Klf4 from inducible system for 48h Histone H3K4me1 H3K4me1 (39297, Active Motif) mESC Histone H3K27ac H3K27ac (39133, Active Motif) AntNPC (anterior neural progenitors derived from mESC) Others Brd2 Brd2 (Bethyl; IHC-00612) Sample_JQ1_Brd2 Others Brd4 Brd4 (Bethyl; IHC-00396) Sample_JQ1_Brd4 Others Brd4 Brd4 (Bethyl; IHC-00396) Sample_Th17_Brd4 Others Brd2 Brd2 (Bethyl; IHC-00612) Sample_Th17_Brd2 Histone H3K27me3 anti-H3K27me3 (Cell Signaling, 9733S, C36B11, Lot 8) Mmu N H3K27me3 Histone H3K27me3 anti-H3K27me3 (Cell Signaling, 9733S, C36B11, Lot 8) Mmu bRG H3K27me3 Histone H3K27me3 anti-H3K27me3 (Cell Signaling, 9733S, C36B11, Lot 8) Mmu aRG-N H3K27me3 tech Histone H3K27me3 anti-H3K27me3 (Cell Signaling, 9733S, C36B11, Lot 8) Mmu aRG-P H3K27me3 Histone H3K27me3 anti-H3K27me3 (Cell Signaling, 9733S, C36B11, Lot 8) Mmu NEC H3K27me3 Histone H3K4me3 anti-H3K4me3 (Cell Signaling, 9751S, LC42,D8, Lot 7) Mmu N H3K4me3 Histone H3K4me3 anti-H3K4me3 (Cell Signaling, 9751S, LC42,D8, Lot 7) Mmu bRG H3K4me3 Histone H3K4me3 anti-H3K4me3 (Cell Signaling, 9751S, LC42,D8, Lot 7) Mmu aRG-N H3K4me3 Histone H3K4me3 anti-H3K4me3 (Cell Signaling, 9751S, LC42,D8, Lot 7) Mmu aRG-P H3K4me3 Histone H3K4me3 anti-H3K4me3 (Cell Signaling, 9751S, LC42,D8, Lot 7) Mmu NEC H3K4me3 Others Prm1 sc-30174, Santa Cruz Sperm Others Smc1a A300-055A, Bethyl laboratories Sperm Histone H3K4me3 ab8580, Abcam Sperm Histone H3K4me1 ab8895, Abcam Sperm Histone H3K9me3 ab8898, Abcam Sperm Histone H3K27ac ab4729, Abcam Sperm Input control Input control none Jejunal intestinal epithelial cells Histone H3K9me2 H3K9me2 Phf8 KO_cortical neuronal chromatin_H3K9me2 Histone H3K27me2 H3K27me2 Phf8 KO_cortical neuronal chromatin_H3K27me2 Histone H3K4me3 H3K4me3 Phf8 KO_cortical neuronal chromatin_H3K4me3 Histone H3K4me1 H3K4me1 Phf8 KO_cortical neuronal chromatin_H3K4me1 Input control Input control None Phf8 KO_cortical neuronal chromatin_None Histone H3K27me2 H3K27me2 wild type_cortical neuronal chromatin_H3K27me2 Histone H3K4me1 H3K4me1 wild type_cortical neuronal chromatin_H3K4me1 Input control Input control None wild type_cortical neuronal chromatin_None Input control Input control none derived from J1 ESC Input control Input control none J1 ESC Others Kdm5c JARID1C/Kdm5C Antibody (A301-034A; Bethyl lab) 3T3-L1_Kdm5C Day 2 Others Kdm5a KDM5A antibody (ab70892; Abcam) 3T3-L1_Kdm5A Day 2 Others Kdm5a KDM5A antibody (ab70892; Abcam) 3T3-L1_Kdm5A 4 hour Others Kdm5a KDM5A antibody (ab70892; Abcam) 3T3-L1_Kdm5A Day 0 Others Drosha Drosha V6.5 embryonic stem cells Others Dgcr8 DGCR8 V6.5 embryonic stem cells Histone H3K27me3 H3K27me3: Millipore #17-622 Lgr5+ intestinal stem cells from adult mice Histone H3K27me3 H3K27me3: Millipore #17-622 enterocyte from adult mice Histone H3K27ac H3K27Ac: Abcam 4729 Lgr5+ intestinal stem cells from adult mice Histone H3K27ac H3K27Ac: Abcam 4729 enterocyte from adult mice Histone H3K4me3 H3K4me3: Millipore #07-473 Lgr5+ intestinal stem cells from adult mice Histone H3K4me3 H3K4me3: Millipore #07-473 enterocyte from adult mice Histone H2A.Z H2A.Z: Active Motif, #39113 Lgr5+ intestinal stem cells from adult mice Histone H2A.Z H2A.Z: Active Motif, #39113 enterocyte from adult mice Input control Input control none (input) Cell line_input_Cbx3_siRNA Input control Input control none (input) Cell line_input_control_siRNA Input control Input control none (input) Cell line_input_no treatment Histone H3K27ac anti-H3K27Ac (Active Motif, catalog number 39133) Primary tissue Heart RNA polymerase RNA polymerase II Pol II antibody from Santa Cruz (sc-899) Raw 264.7 Others Spi1 PU.1 home made antibody Primary bone marrow-derived macrophages (BMDM); 7th day of differentiation Input control Input control Total input mESC E3 Others Trim28 antiKAP1 (Trono laboratory, rabbit polyclonal S23470) KAP1 ChIP-Seq in mESC E3 Histone H3K9me3 antiH3K9me3 (Diagenode, C15410056) H3K9me3 ChIP-Seq of Liver Kap1 KO cells (female), MNase digested Histone H3K9me3 antiH3K9me3 (Diagenode, C15410056) H3K9me3 ChIP-Seq of Liver WT cells (female), MNase digested Others Sox9 rabbit polyclonal anti-mouse Sox9 antibody (Abcam, UK) Intestinal epithelium stem cells Input control Input control none Min6 cells Input control Input control none pre-pro B cells Others Bach2 Bach2 (Bach2N2) pre-pro B cells Others Rnf2 Ring1b antibody (Clone#3) Embryonic stem cell Others Sp9 Sp9 (homemade antibody) olfactory bulb Input control Input control none pro-B cells Others Spi1 Rabbit polyclonal anti-mouse PU.1 (T-21) (Santa Cruz Biotechnology) pro-B cells Others Ctcf CTCF (Millipore ref: 07-729 lot: DAM1772428) CD43- B cells extracted from spleen Input control Input control Rabbit IgG (Bethyl, ref: P120-101 lot: P120-101-8) CD43- B cells extracted from spleen Others Smc3 Smc3 (Abcam ref: ab9263 lot: GR81379-1) CD43- B cells extracted from spleen Others Smc1a Smc1 (Bethyl ref: A300-055A lot: A300-055A-3) CD43- B cells extracted from spleen Others Biotin Streptavidin mouse embryonic stem cells RNA polymerase RNA polymerase II Anti-PolII N20 (Santa Cruz, sc-899) cultured cortical neurons Histone H3K9ac ab4441 (lot#GR105501-1) C3H10T1/2 cells Histone H3K27me3 07-449 (lot#2064519) C3H10T1/2 cells Histone H3K4me3 ab8580 (lot#GR95388-1) C3H10T1/2 cells Histone H3K27ac ab4729 (lot#GR103379-1) C3H10T1/2 cells Others BrdU Brdu GE Healthcare, RPN-202 and BD Biosciences, 347580 Splenic B Cells Histone H2A.XS139ph gH2AX Millipore, 05-636 Splenic B Cells Unclassified Unclassified wild type mouse ES cells derived from C57Bl/6 blastocysts Others Irf4 Santa Cruz Biotech/sc-6059x stromal adherent WT pre-B cell progenitors derived from WT mice Others Tcf3 Santa Cruz Biotech/sc-349x stromal adherent IKDN pre-B cell progenitors derived from IKDN CD2 Cre mice Histone H3K4me1 Active Motif/AM39297 stromal adherent IKDN pre-B cell progenitors derived from IKDN CD2 Cre mice Others Hdac2 HDAC2 (Abcam, ab7029) Heart Others Eed EED (Millipore, 17-10034,17-663 ) Heart Histone H3K27me3 H3K27me3 macrophage from aorta Histone H3K9ac H3K9ac macrophage from aorta Histone H3K4me1 H3K4me1 (Homemade, #024) mouse embryonic stem cells Others Hif1a HIF1A (#AF1935) melan-Ink4a-Arf-null Input control Input control IgG in vitro-generated TH17 cells Others Batf BATF in vitro-generated TH17 cells Others Irf4 IRF4 in vitro-generated TH17 cells Others Junb JUNB in vitro-generated TH17 cells Histone H3K27me3 K27me3 CST #9733 Mouse embryonic stem cells Histone H3K4me3 K4me3 CST #9751 Mouse embryonic stem cells Input control Input control none none KH2 ES cells RNA polymerase RNA polymerase II Polymerase II antibody polII ChIP-seq Others Wdr5 Wdr5 antibody wdr5 ChIP-seq Others Phf20 PHF20 antibody phf20 ChIP-seq Unclassified Unclassified control sample Histone H3K9me2 Histone H3 dimethyl Lys9 mammary gland Others Erf S17S anti-Erf rabbit polyclonal antibody Mouse Embryonic Fibroblasts Input control Input control none Mammary glands of 10-week-old wildtype mice treated with E+EP6h, input Others Pgr anti-PR (Santa Cruz, sc-7208) Mammary glands of 10-week-old wildtype mice treated with E+EP6h, PR ChIP Histone H3 H3 Day2 differentiating rtta ESCs, H3 ChIP Histone H3K27ac H3K27Ac Day2 differentiating rtta ESCs, H3K27Ac ChIP Histone H3 H3 Day2 differentiating Teto-Brn2 ESCs, H3 ChIP Input control Input control none Day2 differentiating rtta ESCs, WCE Others Sox2 Sox2 Day2 differentiating rtta ESCs, Sox2 ChIP Others Pou3f2 Brn2 Day2 differentiating rtta ESCs, Brn2 ChIP Input control Input control none Day2 differentiating Teto-Brn2 ESCs, WCE Others Sox2 Sox2 Day2 differentiating Teto-Brn2 ESCs, Sox2 ChIP Others Pou3f2 Brn2 Day2 differentiating Teto-Brn2 ESCs, Brn2 ChIP Input control Input control none Embryonic stem cells, WCE Others Sox2 Sox2 ES-derived neural progenitor cells, Sox2 ChIP Others Pou3f2 Brn2 ES-derived neural progenitor cells, Brn2 ChIP Histone H3K4me3 mouse ES cells, shMLL4, H3K4me3 ChIP Others Pou5f1 mouse ES cells, shH2A.Z, Oct4-ChIP Others Suz12 mouse ES cells, shH2A.Z, Suz12 ChIP Others Rbbp5 mouse ES cells, shH2A.Z, RbBP5 ChIP Histone H3K27me3 mouse ES cells, shH2A.Z, H3K27me3 ChIP Histone H3K4me3 mouse ES cells, shH2A.Z, H3K4me3 ChIP Others Pou5f1 mouse ES cells, shluc control, Oct4-ChIP Others Suz12 mouse ES cells, shluc control, Suz12 ChIP Others Rbbp5 mouse ES cells, shluc control, RbBP5 ChIP Histone H3K27me3 mouse ES cells, shluc control, H3K27me3 ChIP Histone H3K27me3 Millipore 07-449 Round spermatids Histone H3K4me3 Millipore 17-614 Round spermatids Unclassified Unclassified Van Der Heijden et al. Nature Genetics, 2007, pubmed ID:17237782 Sperm Others Ptf1a PTF1A antiboby from JE Johnson pancreas Others Ptf1a PTF1A antiboby from RJ MacDonald pancreas Others Cdc73 Cdc73 antibody, serum purified ESC shPhf5a WITH LIF Others Leo1 Leo1 antibody, serum purified ESC shPhf5a WITH LIF Others Cdc73 Cdc73 antibody, serum purified ESC shControl WITH LIF Others Leo1 Leo1 antibody, serum purified ESC shControl WITH LIF Others Hdac3 HDAC3 (Abcam, catalog# 7030) Liver tissue Input control Input control Rabbit IgG- ab37415 Embryonic stem cells (E14) Others Med1 Med1/TRAP220 (Bethyl, Catalog No.A300-793A) ZHBTc4 ES cells Input control Input control None primary pre-B cell Others Ikzf1 Rabbit anti-C-terminal Ikaros from Stephen Smale Lab primary pre-B cell Unclassified Unclassified normal liver Input control Input control none Reconstitute Flag tag MEF cell Input control Input control none MEF cell Input control Input control none iPS cell from TTF cell Input control Input control none iPS cell from PF cell Histone H2A.X H2A.X MEF cell Histone H2A.X H2A.X iPS cell from TTF cell Histone H2A.X H2A.X iPS cell from PF cell Others Rad51 anti-RAD51(H-92) Santa Cruz sc-8349, lot#H1810 Primary B cells Others Prdm16 PRDM16 (Made in Lab, Harms et al. 2014. Cell Metab.) Brown fat precursor cell Histone H3K27ac H3K27ac (Abcam ab4729) Brown fat precursor cell Others Smc1a Smc1a (Bethyl, Cat. No. A300-055A, Lot No. A300-055A-3) Limb bud Others Elf5 Elf5 (Santa Cruz, sc-9645x, lot D2109) Trophoblast stem cells Others Eomes Eomes (Abcam, ab23345-100, lot 798757) Trophoblast stem cells Histone H3K27me3 H3K27me3 (ActiveMotif, 39535, lot 33310009) Trophoblast stem cells Histone H3K9me3 H3K9me3 (Abcam, ab8898, lot GR110001) Trophoblast stem cells Histone H3K27ac H3K27ac (Abcam, ab4729, lot 730178) Trophoblast stem cells Unclassified Unclassified Mouse liver Others Epitope tags Anti-HA, A2095, Sigma-Aldrich Mouse liver Others Aff3 AFF3 murine embryonic stem cells Histone H3 anti-H3gen (Ab1791) Embryonic stem cells Histone H3K27ac anti-H3K27ac (Ab4729) Embryonic stem cells Histone H3K27me3 anti-H3K27me3 (Millipore 07-449) Embryonic stem cells Histone H3K4me3 anti-H3K4me3 (AM39159) Embryonic stem cells Histone H3K27me2 H3K27me2 (Cell signaling, 9728S, lot unknown) C2C12 cell line Others Trim28 Tronolab, rabbit polyclonal SY 3267-68 Histone H3K27ac H3K27ac (Abcam: ab4729) Histone H3K9me3 H3K9me3 (Abcam: ab8898) Histone H3K4me3 H3K4me3 (Abcam #ab8580 RRID:AB_306649) Medial ganglionic eminence Histone H3K27ac H3K427ac (Abcam #ab4729 RRID:AB_2118291) Medial ganglionic eminence Histone H3K27me3 H3K27me3 (Active Motif #39155 RRID:AB_2561020) Medial ganglionic eminence Histone H3K4me1 H3K4me1 (Abcam #ab8895 RRID:AB_306847) Medial ganglionic eminence Input control Input control Rabbit IgG control (Santa Cruz Biotechnology #sc-2027 RRID:AB_737197) Medial ganglionic eminence Input control Input control none (input) input_DNA Others Epitope tags anti-Myc tag antibody 9B11 (Cell Signaling Technology #2276, lot #24) PPFP_ChIPseq Histone H3K27me3 H3K27me3 (Active Motif Cat39155 Lot 07711009) MLL-AF9 leukemic cells Unclassified Unclassified Rag1 -/- pro-B cells Input control Input control no antibody cultured TH2 cells Histone H3K27ac H3K27Ac (Abcam, ab4729, Lot:GR200563-1) Liver tumor cell line, sgMll3/Cas9, H3K27Ac ChIP Histone H3K4me3 H3K4me3 (Abcam, ab8580, Lot:GR164706-1) Liver tumor cell line, sgp53/Cas9, H3K4me3 ChIP Others Zscan5b Zscan5b Mouse Fetal Placenta Unclassified Unclassified Streptavidin lymph node Others Pcgf6 Pcgf6 (Abcam, ab48010) Embryonic stem cells Others Pcgf6 Pcgf6 (Santa Cruz, sc-160649) Embryonic stem cells Input control Input control genomic DNA 3T3-L1 cell line Others Pparg PPARG (Cell Signaling Technologies SC-7196X) genomic DNA 3T3-L1 cell line Others Rad21 RAD21 (Abcam: ab992) Embryonic Midbrain Others Ctcf CTCF (Active motif: 613111) Embryonic Midbrain Input control Input control Input mouse tumor cells Histone H3K4me3 H3K4me3 Abcam cat #: Ab8580 mouse tumor cells Histone H3K27me3 H3K27me3 Ali Shilatifards lab cat #: 9733S mouse tumor cells Histone H3K4me1 anti-H3K4me1 Primary bone marrow-derived macrophages, IL4 for 24hrs, H3K4me1 ChIP Histone H3K4me1 anti-H3K4me1 Primary bone marrow-derived macrophages, IFNg for 24hrs, H3K4me1 ChIP Others Stat1 anti-Stat1 Primary bone marrow-derived macrophages, no treatment, Stat1 ChIP Histone H3K27ac anti-H3K27ac Primary bone marrow-derived macrophages, IFNg for 4hrs, H3K27ac ChIP Others Spi1 anti-PU.1 (rabbit polyclonal against the N-terminus (aa. 1-100)) Primary bone marrow-derived macrophages, IFNg for 4hrs, PU.1 ChIP Histone H3K4me1 anti-H3K4me1 Primary bone marrow-derived macrophages, IFNg for 4hrs, H3K4me1 ChIP Others Spi1 anti-PU.1 (rabbit polyclonal against the N-terminus (aa. 1-100)) Primary bone marrow-derived macrophages, IL4 for 4hrs, PU.1 ChIP Unclassified Unclassified ES cells. HV+S- FACs sorted population Others Ctcf rabbit anti-CTCF mouse embryonic fibroblasts Others Pitx1 Pitx1 (Santa Cruz, sc-18922, lot # G0105 ) embryonic hindlimb Input control Input control IgG; Abcam, #46540 IgG_ChIPSeq Others Phf19 Phf19 - OpenBiosystems, costum made Phf19_ChIPSeq Histone H3K4me3 Anti-Histone H3 (tri methyl K4) antibody (ab8580, Abcam) 3T3-L1_H3K4tri shKdm5ABC Day 2 Histone H3K4me3 Anti-Histone H3 (tri methyl K4) antibody (ab8580, Abcam) 3T3-L1_H3K4tri shKdm5ABC 4 hour Histone H3K4me3 Anti-Histone H3 (tri methyl K4) antibody (ab8580, Abcam) 3T3-L1_H3K4tri shKdm5ABC Day 0 Histone H3K4me3 Anti-Histone H3 (tri methyl K4) antibody (ab8580, Abcam) 3T3-L1_H3K4tri shLuc Day 2 Histone H3K4me3 Anti-Histone H3 (tri methyl K4) antibody (ab8580, Abcam) 3T3-L1_H3K4tri shLuc 4 hour Histone H3K4me3 Anti-Histone H3 (tri methyl K4) antibody (ab8580, Abcam) 3T3-L1_H3K4tri shLuc Day 0 RNA polymerase RNA polymerase II S2ph pol2 (Abcam, ab5095) S2ph pol2_ChIPSeq RNA polymerase RNA polymerase II S5ph pol2 (Abcam, ab5131) S5ph pol2_ChIPSeq Histone H3K36me3 H3K36me3 (Abcam, ab9050) H3K36me3_ChIPSeq Histone H3K27me3 H3K27me3 3T3-L1 preadipocytes Input control Input control hippocampus_CTCF input Others Ctcf CTCF millipore antibody (07-729) hippocampus_CTCF ChIP Histone H3K27me3 H3K27me3 (Cell Signaling, D18C8) E8.5 head Histone H3K4me3 H3K4me3 (Cell Signaling, C42D8) E8.5 head Others Sox2 goat anti-SOX2 (AF2018, R&D). Stomach Others Hdac3 Anti-HDAC3 ABCAM, Cat# 7030, Lot# GR121157-6 Brown adipose tissue Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. ES-E14 Others Gata1 GATA-1 GATA-1 GATA-1 is a transcriptional activator which probably serves as a general switch factor for erythroid development. It binds to DNA sites with the consensus sequence ATGATAAG} within regulatory regions of globin genes and of other genes expressed in erythroid cells. Anti-GATA-1 rabbit polyclonal antibody was generated by using a purified GST fusion to amino acids 1-89 of mouse GATA-1. Antibody Target: GATA1 MEL Others Mafk MafK_(ab50322) ab50322 NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. Rabbit polyclonal. Raised against synthetic peptide: TTNPKPNKALKVKKEA conjugated to KLH by a C-terminal Cysteine residue linker, corresponding to amino acids 2-17 of Human MAFK. Antibody Target: MafK MEL Others Usf2 USF2 ab60931 Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). Mouse monoclonal. Immunogen corresponds to amino acids 1-101 of Human USF2. Antibody Target: USF2 MEL Others Ctcf CTCF_(SC-15914) sc-15914 Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. Goat polyclonal, epitope mapping near the C-terminus of CTCF of human origin. Antibody Target: CTCF MEL Others Ets1 Ets1 (Santa Cruz, Sc-350X) Spleen Unclassified Unclassified Lck-Dlx5 T-cell lymphoma Others Epitope tags FLAG M2 C2C12 myoblasts Others Nfia NFI immortalized brown adipocytes Histone H3K4me3 histone H3K4me3 Mammary tissues RNA polymerase RNA polymerase II RNA polymerase II Mammary tissues Others Stat5b STAT5B Mammary tissues Others Stat5a STAT5A Mammary tissues Others Stat3 Stat3 Th17 in vitro Others Ep300 p300 Th0 in vitro Others Etv6 Etv6 Th17 in vitro Others Ctcf CTCF Th17 in vitro Others Ctcf CTCF Th0 in vitro Others Batf B-ATF Th0 in vitro Histone H3K9me3 H3K9me3 ab8898 Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. rabbit polyclonal, ChIP grade. Antibody Target: H3K9me3 MEL Histone H3K4me3 H3K4me3 ab8580; 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal. Antibody Target: H3K4me3 MEL Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal. Antibody Target: H3K4me1 ES-E14 Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. Placenta Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. BMDM Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. OlfactBulb Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. Thymus Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. Testis Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. Limb Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. BAT Histone H3K27ac H3K27ac ab4729 Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K27ac Liver Histone H3K27ac H3K27ac ab4729 Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K27ac Heart Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal. Antibody Target: H3K4me1 CH12 Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal. Antibody Target: H3K4me3 CH12 Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. WholeBrain Histone H3K36me3 H3K36me3 ab9050 Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts. rabbit polyclonal. Antibody Target: H3K36me3 CH12 Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. SmIntestine Histone H3K27me3 anti-H3K27me3 (Millipore; Cat #: 07-449; Lot: 2382150) mTr_H3K27me3 Histone H3K27me3 anti-H3K27me3 (Millipore; Cat #: 07-449; Lot: 2382150) aTr_H3K27me3 Histone H3K27me3 anti-H3K27me3 (Millipore; Cat #: 07-449; Lot: 2382150) rTr_H3K27me3 Others Ctcf CTCF (Pugacheva et. al. 2005 Hum Mol Genet 14, 953-965) F1 C/B trophoblast stem cells Input control Input control none cultured N-NUP98 transduced mouse bone marrow LSK cells Input control Input control none cultured NUP98-TOP1 transformed mouse bone marrow LSK cells Histone H3K27me3 H3K27me3 conditional KO Rb MEF Histone H3K9me3 H3K9me3 conditional KO Rb MEF Histone H3K4me3 H3K4me3 conditional KO Rb MEF Histone H3ac H3Ac conditional KO Rb MEF Others Rb1 Rb 4.1 conditional KO Rb MEF Others Suz12 anti-SUZ12 (Cell Signalling, catalog# 3737) ESCs Others Aebp2 anti-AEBP2 (generated in this study) ESCs RNA polymerase RNA polymerase II PolI, Abcam, ab817 Mouse embryonic stem cells RNA polymerase RNA polymerase II PolIIS5P, Abcam, ab5131 Mouse embryonic stem cells Input control Input control ESC time-ChIP input (for replicate 1) Input control Input control none Post-H/S Input_ChIPSeq RNA polymerase RNA polymerase II Pol II S2P panel (Abcam, catalog# ab103968, lot# 139798-3) B2LNA Pol II S2P_ChIPSeq RNA polymerase RNA polymerase II Pol II S2P panel (Abcam, catalog# ab103968, lot# 139798-3) Post-H/S Pol II S2P_ChIPSeq Histone H3K27me3 H3K27me3 (Active Motif, catalog# 39155, lot# 23813016) Post-H/S H3K27me3_ChIPSeq Others Ezh2 Ezh2 (D2C9) (Cell Signaling Technology, catalog# 5246S, lot# 6) Post-H/S Ezh2_ChIPSeq RNA polymerase RNA polymerase II Pol II S2P panel (Abcam, catalog# ab103968, lot# 139798-3) Pre-H/S Pol II S2P_ChIPSeq Histone H3K27me3 H3K27me3 (Active Motif, catalog# 39155, lot# 23813016) Pre-H/S H3K27me3_ChIPSeq Others Ezh2 Ezh2 (D2C9) (Cell Signaling Technology, catalog# 5246S, lot# 6) Pre-H/S Ezh2_ChIPSeq Input control Input control none Gr1dim Mac1+ granulocytic progenitor cells Histone H3K27ac H3K27ac Gr1dim Mac1+ granulocytic progenitor cells Histone H3K4me1 H3K4me1 Gr1dim Mac1+ granulocytic progenitor cells Others Tead1 TEAD1 BD Biosciences C2C12 cells Others Tead4 TEAD4 Aviva C2C12 cells Input control Input control No antibody C2C12 cells Histone H3K27me3 H3K27me3 closed chromatin Mouse Others Hdac1 abcam, ab7028 resting B cell Others Hdac1 abcam, ab7028 activated B cell Histone H3K27me2 abcam, ab24684-25 resting B cell Histone H3K9ac H3 K9Ac differentiating murine hematopoietic cells Others Tal1 SCL differentiating murine hematopoietic cells Others Fli1 FLI1-1 differentiating murine hematopoietic cells Others Epitope tags Anti-HA differentiating murine hematopoietic cells Histone H3K27me3 anti-H3K27me3: Millipore, cat.# 07-449, lot #1154011 crypts-WT-H3K27me3 Histone H3K27ac anti-H3K27Ac; Abcam, cat.# ab4729, lot #254707-01 crypts-WT-H3K27ac Others Sox9 rabbit anti SOX9 homemade (ref Gasca et al, PNAS 2002, vol 99, 11199-11204) fetal testis Histone H3 H3 Abcam/No 1791/GR50122-1 E36 ES cells Others Mybl1 Rabbit anti-A-MYB (Sigma-Aldrich, HPA008791) testes Unclassified Unclassified Rat anti-mCherry (ThermoFisher Scientific, M11217) testes Others Epitope tags Mouse anti-FLAG (Sigma-Aldrich, F3165) testes Others GFP Anti-GFP (Abcam:Ab290) ES cells Histone H3K27me3 anti-H3K27me3 (Millipore, 07-449) embryonic forelmb bud, H3K27me3 ChIP Histone H3K27ac anti-H3K27ac (Abcam, ab4729) embryonic forelmb bud, H3K27ac ChIP Others Kdm4c anti-Jmjd2c, ktwl L-GMP transformed with MLL-AF9 Others Kdm4a anti-Jmjd2a (Cell Signaling Technology, #5328) L-GMP transformed with MLL-AF9 Others Nfib Nfib antibody (Sigma, #HPA003956) Nfib pulldown KP22_PD Others Nfib Nfib antibody (Sigma, #HPA003956) Nfib pulldown 16T_PD Input control Input control None Input DNA Others Rai1 anti-FLAG M2 (Sigma, catalog# F1804) Cortex-Rai-ChIP Histone H3K4me3 Abcam, ab8580 EpiSCs Histone H3K36me3 anti-H3K36me3 (D5A7) (Cell Signaling #4909 Lot 1) ESCs, Jmjd2abc, OHT, H3K36me3 ChIP Histone H3K36me3 anti-H3K36me3 (D5A7) (Cell Signaling #4909 Lot 1) ESCs, Jmjd2abc, Control, H3K36me3 ChIP Histone H3K36me3 anti-H3K36me3 (D5A7) (Cell Signaling #4909 Lot 1) ESCs, Jmjd2ac, OHT, H3K36me3 ChIP Histone H3K36me3 anti-H3K36me3 (D5A7) (Cell Signaling #4909 Lot 1) ESCs, Jmjd2ac, Control, H3K36me3 ChIP Histone H3K9me3 anti-H3K9me3 (Abcam ab8898 Lot GR102573) ESCs, Jmjd2abc, OHT, H3K9me3 ChIP Histone H3K9me3 anti-H3K9me3 (Abcam ab8898 Lot GR102573) ESCs, Jmjd2abc, Control, H3K9me3 ChIP Histone H3K9me3 anti-H3K9me3 (Abcam ab8898 Lot GR102573) ESCs, Jmjd2ac, OHT, H3K9me3 ChIP Histone H3K9me3 anti-H3K9me3 (Abcam ab8898 Lot GR102573) ESCs, Jmjd2ac, Control, H3K9me3 ChIP Others Esrra SC-66882, Santa Cruz Biotechnology Frontal Cortex Histone H3K4me3 H3K4me3 (Cell Signaling, 9751) OldLens_H3K4me2 Histone H3K4me3 H3K4me3 (Cell Signaling, 9751) YoungLens_H3K4me2 Histone H3K4me1 Abcam ab8895 Thymus Histone H3K27ac Abcam ab4729 Thymus Input control Input control rabbit igg fresh Six2-expressing cells Input control Input control none (input control) fresh Six2-expressing cells Input control Input control none (input control) BIO-treated Six2-expressing cells Others Ctnnb1 beta-catenin BIO-treated Six2-expressing cells RNA polymerase RNA polymerase II Pol II : Santa-Cruz (Sc9001) liver Histone H2A.XS139ph Anti-gamma H2A.X (phospho S139) (ab2893, Abcam) C-MYC expressing primary B cell precursors (D7-9 post transduction) Histone H2A.XS139ph Anti-gamma H2A.X (phospho S139) (ab2893, Abcam) BCR-ABL1 expressing primary B cell precursors (D7-9 post transduction) Unclassified Unclassified Splenic B cells activated in vitro Histone H3K27ac Anti-H3K27ac (Abcam ab4729) Splenic B cells activated in vitro Others Biotin streptavidin beads Invitrogen 656-01 Dynabeads MyOne? Streptavidin T1 Embryonic Stem Cell Others Stat1 STAT3 (Invitrogen, 13-7000) CD4+ T Cells Others Irf8 IRF8 (from Keiko Ozato, not commercial available) CD4+ T Cells Others Irf4 IRF4 (Santa Cruz, sc-6059) B cells Others Onecut2 Onecut2 anti-Onecut2 (R&D Systems AF294) ES-derived embryoid bodies with induced transcription factors Others Ebf2 Ebf2 anti-Ebf2 (Abcam ab156999) ES-derived embryoid bodies with induced transcription factors Histone H3K4me3 H3K4me3 (0.5 ug/ml, Cell Signaling 9751S) Olfactory Epithelium Histone H3K4me3 antibody: diagenode (pAb003-050) mESCs Histone H3K36me3 antibody: abcam (ab9050-100) mESCs Histone H3K27ac anti-H3K27Ac (Abcam ab4729, lot number GR211895-1) CD19+IgD-B220+IgM-CD25+ckit- pre-B cells Histone H3K27ac anti-H3K27Ac (Abcam ab4729, lot number GR211895-1) CD19+IgD-B220+IgM+ immature B cells Histone H3K27ac anti-H3K27Ac (Abcam ab4729, lot number GR211895-1) CD4-CD8- double negative (CD25+CD44-/+) T cells Histone H3K27ac H3K27ac (abcam, ab4729) Rag KO Primary Thymocytes Others Spi1 PU1 Bone Marrow Input control Input control none Bone Marrow Others Kdm6a KDM6A (Sigma, HPA002111) Mammary Input control Input control None P15 oocyte Histone H3K4me3 H3K4me3 (Merck Millipore, catalogue number 04-745) P15 oocyte Input control Input control None P12 oocyte Histone H3K4me3 H3K4me3 (Merck Millipore, catalogue number 04-745) P12 oocyte RNA polymerase RNA polymerase II RNA Pol II (Abcam, ab5408) Mammary Others Elob abcam 168836 GR160741-2 Undifferentiated ES cells Others Elob bethyl A304-008A Lot -1 Undifferentiated ES cells Histone H3K27me3 Active Motif 39155 Lot 23813016 Undifferentiated ES cells Unclassified Unclassified home-made against aa 1-240 Lot2 Undifferentiated ES cells Unclassified Unclassified home-made against aa 1-240 Lot1 Undifferentiated ES cells Histone H3K27ac H3K27ac (Abcam, catalog# ab4729, lot# GR00563-2) Motor neurons progenitors day 4 Others Isl1 Isl1 (gifts from T. Jessell) Postmitotic motor neurons day 6 Others Isl1 Isl1 (gifts from T. Jessell) Postmitotic motor neurons day 5 Unclassified Unclassified E14 mouse embryonic stem cells Others Hdac3 HDAC3 (Santa Cruz, sc11417X) pro-B Ba/F3_ChIP_HDAC3plus Others Hdac3 HDAC3 (Santa Cruz, sc11417X) pro-B Ba/F3_ChIP_HDAC3minus Others Kdm1a LSD1 (Abcam, ab17721) pro-B Ba/F3_ChIP_LSD1plus Others Kdm1a LSD1 (Abcam, ab17721) pro-B Ba/F3_ChIP_LSD1minus Others Stat5a STAT5a (Santa Cruz, sc1081X) pro-B Ba/F3_ChIP_STAT5Aplus Others Stat5a STAT5a (Santa Cruz, sc1081X) pro-B Ba/F3_ChIP_STAT5Aminus Unclassified Unclassified activated CD8 T cells Others Epop EPOP (Ab2) Embryonic stem cells Others Klf6 Klf6 (Santa Cruz, SC-7158X, Lot: F1212) Immature oligodendrocytes Input control Input control none Immature oligodendrocytes Others Klf6 Klf6 (Santa Cruz, SC-7158X, Lot: F1212) Oligodendrocyte progenitor cells Others Spi1 Rabbit polyclonal anti-mouse PU.1 (T-21) (Santa Cruz Biotechnology) ChIP-seq for PU.1 on control, non-induced iBN cells Others Spi1 Rabbit polyclonal anti-mouse PU.1 (T-21) (Santa Cruz Biotechnology) ChIP-seq for PU.1 on iBN cells induced for 72 hours with doxycyclin Histone H3K4me3 H3K4me3(Cell signaling Technology, #9727) mouse embryonic stem cells Others Jund JunD (sc-74, Santa Cruz) Pre-activated CD8+ T cells Histone H3K4me3 H3K4me3 (Active Motif, catNo:39159, Lot: 01609004) E36 ES cells Histone H3K4me1 H3K4me1 (Abcam, catNo:8895, Lot: 962543) E36 ES cells Histone H3K27me1 H3K27me1 (Active Motif, cat No:61015, Lot: 08711001) E36 ES cells Input control Input control none E36 ES cells Histone H3K27me3 H3K27 trimethyl (Millipore 07-449) ESCs Histone H3K4me3 H3K4 trimethyl (Millipore 07-473) ESCs Histone H3K27me3 H3K27 trimethyl (Millipore 07-449) RA-treated ESCs Histone H3K4me3 H3K4 trimethyl (Millipore 07-473) RA-treated ESCs Others Nfe2l2 anti-Nrf2 antibody C2C12 myotubes_ChIP Input control Input control - Small intestine; duodenum Histone H3K27me3 H3K27me3 ab6002 Small intestine; duodenum Histone H3K27me3 anti-H3K27me3 (Abcam, ab6002) motor neurons (Day 5) Others Epitope tags anti-V5 (Abcam, ab15828) progenitor motor neurons (Day 4) Histone macroH2A1 MacroH2A (Buschbeck et al., 2009) C2C12 cell line Histone H3K27me3 H3K27me3 (Abcam ab6002) haematopoietic stem and progenitor cell (HSC) Histone H3K4me3 H3K4me3 (Abcam ab8580) haematopoietic stem and progenitor cell (HSC) Histone H3K27me3 H3K27me3 (Abcam ab6002) induced pluripotent stem (iPS) cell Histone H3K4me3 H3K4me3 (Abcam ab8580) induced pluripotent stem (iPS) cell Others Zfp143 ZNF143, rabbit polyclonal raised against a C-terminal epitope of ZNF143 (Myslinski et al JBC 2006) Mouse embryonic fibroblast cell line Others Ezh2 Ezh2 (Cell signalling, 5264) embryonic fibroblast chromatin Others Foxf1 FOXF1, R&D Biosystems, AF4798, Lot#B1508 Whole lung Histone H3K27ac H3K27ac (Abcam ab4729, Lot. GR184558-1) Forelimb Histone H3K9me3 Anti-H3K9me3 mAb (Active Motif, 39161) Native chromatin ES cells Input control Input control input DNA Native chromatin ES cells Histone H3K9me3 Anti-H3K9me3 mAb (MBL, MABI0318) Crosslinked chromatin ES cells Histone H3K27ac H3K27ac (abcam) Act B cell Others Tcf3 Tcf3 FO B cell Histone H3K27me3 Anti H3K27me3 - Millipore (cat # 07-449) Mouse Liver Tissue Unclassified Unclassified Natural killer cells Histone H3K27ac AbCam ab4729 Natural killer cells Others Ep300 Santa Cruz sc585 Natural killer cells Histone H3K27ac H3K27ac (Abcam ab4729, GR254707-1) 46c_H3K27ac Histone H3K64ac anti-H3K64ac (Di Cerbo et al 2014, PMID: 24668167) 46c_H3K64ac Histone H3K122ac anti-H3K122ac (Tropberger et al 2013, PMID: 23415232) 46c_H3K122ac Unclassified Unclassified Invitrogen prot A dynabeads p19 cells Unclassified Unclassified Growing C1C12 myoblasts Others Jun c-Jun, SantaCruz: sc-1694x Growing C1C12 myoblasts Histone H3K27me3 H3K27me3 (07-449, Upstate) Th1 Histone H3K4me1 H3K4me1 (ab8895, Abcam) Th1 Others Cdk9 CDK9 (H-169)X, Santa Scruz, Cat # sc-8338x, Lot #:J2813 Macrophages Others Hes1 HES1 (H-140), Santa Cruz? Cat # sc-25392, Lot # : I2413 Macrophages Input control Input control Santa Cruz SC-2025 Quiescent B cells, lipopolysaccharide (LPS) and 10058-F4 treatments for 4hrs Unclassified Unclassified Clontech, 632460 Quiescent B cells, lipopolysaccharide (LPS) treatment for 4hrs Others Gmnn Gmnn Mouse embriyonic stem cell Others Zic1 Zic1 Mouse neural progenitor cells Others Gmnn Gmnn Mouse neural progenitor cells Histone H3K9ac H3K9ac, Active Motif, Cat# 39917, Lot# 23913004 leukemic spleen cells Others Satb1 Satb1 (AbCam ab109122) thymus Histone H3K27me3 H3K27Me3 E6.5 epiblast Histone H3K27me3 H3K27Me3 Inner cell mass Histone H3K27me3 H3K27Me3 Growing oocyte Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. Erythrobl Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. Megakaryo Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. G1E Histone H3K4me2 H3K4Me2 - Abcam, ab32356 H3K4Me2.FC/FC Unclassified Unclassified immunoprecipitated DNA lung tumors Others Brd4 Brd4 (Abcam 128874) EB Others Brd4 Brd4 (Abcam 128874) mESC Histone H4ac anti-acetyl-H4 (Millipore 06-866) EB Histone H4ac anti-acetyl-H4 (Millipore 06-866) mESC Others Crebbp CBP (D6C5) Rabbit mAb Brown preadipocyte cell Histone H3K4me1 H3K4me1 Antibody Brown preadipocyte cell Input control Input control none Total thymocytes, input Others Mllt3 AF9 (Sigma HPA001824) RAW264.7 Input control Input control none (input) Embryonic stem cells Others Epop EPOP (Ab1) Embryonic stem cells Input control Input control none Cerebral cortex, day P5 Histone H3K27me3 H3K27me3 (Cell signaling, cat n. 9733BF) Cerebral cortex, day P5 Input control Input control none neural stem cells Others Epitope tags HA antibody (ab9110; Abcam) MEF Input control Input control None Input data from Wildtype B3 Cells Others Ikzf1 Anti-haemagglutinin (HA) (Covance). ChIP-Seq data from HA-Ikaros transduced B3 cells using Anti-haemagglutinin (HA) Others Ikzf1 Rabbit anti-C-terminal Ikaros ChIP-Seq data from Wildtype B3 Cells using Rabbit anti-C-terminal Ikaros antibody Histone H2BK20ac H2BK20ac (ab52988, Abcam) FACS-purified Pou5f1-GFP-positive germ cells Histone H3K27me3 H3K27me3 embryonic fibroblasts RNA polymerase RNA polymerase II PolII murine embryonic stem cells Histone H3K27me3 H3K27me3 Ab (gift from T.Jenuwein) Mature B Histone H3K4me2 H3K4me2 Ab (Upstate 07-030, Lot# DAM1474881) Mature B Others Med12 Med12 (bethyl-A300-774A, lot 1) HPC7 Input control Input control none (input) none (input) HSPCs Others Hsf1 HSF-1 STHdhQ111/Q111 striatal cells Others Hsf1 HSF-1 STHdhQ7/Q7 striatal cells Input control Input control none (input) C2C12 cell line Histone macroH2A1.2 mH2A1.2 (Cell signaling, Cat# 4827S, Lot# 1) C2C12 cell line Others Pparg CS2443 (lot#2) C3H10T1/2 cells Histone H3K27ac H3K27ac (Abcam,ab4729, lot GA104852-2) Visceral yolk sac endoderm Histone H3K4me3 H3K4me3 (Millipore, 07-473, lot 2384705) Liver Others Kdm2b Fbxl10 (custom-made) embryonic stem cells Others Kdm5c KDM5c 333 ChIP-DNA KDM5c_Spikein_SMCX_333_ChIP_KO_CN Others Kdm5c KDM5c 333 ChIP-DNA KDM5c_Spikein_SMCX_333_ChIP_WT_CN Others Ep300 Bethyl A300-358A mESC Input control Input control input whole cell lysate mouse primary CD4+ T cells Others Ep300 p300 (Santa Cruz sc-585) mouse primary CD4+ T cells Others Prdm1 Blimp1 (Cell Signaling #9115) mouse primary CD4+ T cells Input control Input control none Mouse V19-OSKM Fibroblast, Utx-/Y Histone H3K4me3 H3K4me3; ChIP grade, ab8580, abcam Mouse V19-OSKM Fibroblast, Utx-/Y Histone H3K27me3 H3K27me3; ChIP grade, 07-449, Millipore Mouse V19-OSKM Fibroblast, Utx-/Y Others Kdm6a UTX Ab-UTX 5/1, PID 17178841 Mouse V19-OSKM Fibroblast Histone H3K4me3 H3K4me3; ChIP grade, ab8580, abcam Mouse V19-OSKM Fibroblast Histone H3K27me3 H3K27me3; ChIP grade, 07-449, Millipore Mouse V19-OSKM Fibroblast RNA polymerase RNA polymerase II RNA pol II rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000) M12 B Lymphomas Histone H3K4me3 H3K4me3 H3K4me3 3.2N Menin-null Embryonic Stem Cells Histone H3K4me3 H3K4me3 H3K4me3 TC1 Embryonic Stem Cells Input control Input control input 3.2N Menin-null Embryonic Stem Cells Input control Input control input TC1 Embryonic Stem Cells Histone H3K9me2 H3K9me2 Jmjd1c f/f MLL-AF9-GFP CRE Mouse bone marrow cells Histone H3K9me2 H3K9me2 Jmjd1c f/f MLL-AF9-GFP MIT Mouse bone marrow cells Others Irf3 IRF3 primary bone marrow-derived macrophages Histone H3K4me3 H3K4me3 (Abcam ab8580, lot# GR111321-2) H1 TKO embryonic stem cells, H3K4me3 ChIP Histone H3K4me3 H3K4me3 (Abcam ab8580, lot# GR111321-2) WT embryonic stem cells, H3K4me3 ChIP Input control Input control none H1 TKO embryonic stem cells, H3K4me1 H3K4me3 input Histone H3K4me1 H3K4me1 (Abcam ab8895, lot# GR61306-1) H1 TKO embryonic stem cells, H3K4me1 ChIP Input control Input control none WT embryonic stem cells, H3K4me1 H3K4me3 input Histone H3K4me1 H3K4me1 (Abcam ab8895, lot# GR61306-1) WT embryonic stem cells, H3K4me1 ChIP Others Ctcf CTCF 07-729 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. rabbit polyclonal. Antibody Target: CTCF MEL Histone H3K27ac H3K27Ac, Abcam: Ab4729 C1C12 myotubes differentiated for 96h Histone H3K27ac H3K27Ac, Abcam: Ab4729 Growing C1C12 myoblasts Unclassified Unclassified Thymic epithelial cells Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. Spleen Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. ES-Bruce4 Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. MEF Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. Lung Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. Cerebellum Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. Cortex Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. BoneMarrow Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. Kidney Histone H3K9K14ac H3ac_(06-599) 06-599 missing rabbit polyclonal antibody raised against a KLH-conjugated peptide corresponding to amino acids 1-20 of Tetrahymena histone H3 (ARTKQTARK*STGGK*APRKQLC) where K* is acetylated. Antibody Target: H3ac C2C12 Histone H3K36me3 H3K36me3 ab9050 Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts. rabbit polyclonal. Antibody Target: H3K36me3 C2C12 Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal. Antibody Target: H3K4me3 C2C12 Histone H3K27me3 H3K27me3 07-449 Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. rabbit polyclonal. Antibody Target: H3K27me3 C2C12 Histone H3K79me2 H3K79me2_(ab3594) ab3594 H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3) Rabbit polyclonal. Antibody Target: H3K79me2 C2C12 Histone H3K4me1 H3K4me1 neural stem cell RNA polymerase RNA polymerase II Pol2 Wild Type MEF Others Kmt2c Mll3 Wild Type MEF Histone H3K4me3 H3K4Me3 Wild Type MEF Input control Input control No Mouse back skin Others Cebpb CEBPB sc-150 epitope mapping at the C-terminus of C/EBP-beta of rat origin Rabbit polyclonal IgG. Antibody Target: CEBPB C2C12 Others Max Max sc-197 The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). Rabbit polyclonal IgG, epitope mapping at the C-terminus of Max of human origin. Antibody Target: Max C2C12 Others Usf1 USF-1 sc-229 The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. Rabbit polyclonal, USF-1 (C-20). Antibody Target: USF1 C2C12 Others Trim28 KAP1 (Abcam, ab10483) Embryonic stem cells Others Zfp57 ZFP57 (Abcam, ab45341) Embryonic stem cells Others Kat8 Mof Embryonic stem cells Unclassified Unclassified cerebral cortex Others Rad21 Rad21 ab992 Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 Rabbit polyclonal. Antibody Target: RAD21 MEL Others Rbpj anti-RBP-J 1F1 rat monoclonal C2C12, DAPT 24h, RBP-J 1F1 ChIP Others Rbpj anti-RBP-J 1F1 rat monoclonal C2C12, Delta 24h, RBP-J 1F1 ChIP Others Rbpj anti-RBP-J 1F1 rat monoclonal C2C12, DAPT 6h, RBP-J 1F1 ChIP Others Rbpj anti-RBP-J 1F1 rat monoclonal C2C12, Delta 6h, RBP-J 1F1 ChIP Histone H3K4me3 H3K4me3 (Cat. 9751, Cell Signaling) Dendritic cells Others Stat3 STAT3 (Cat. 9132, Cell Signaling) Dendritic cells Others Ep300 p300 Antibody (C-20) Brown preadipocyte cell_p300_ChIPSeq Others Kmt2d Anti-MLL4 #3 Brown preadipocyte cell_MLL4_ChIPSeq Others Parp1 PARP-1 (Active Motif; 39561) embryonic stem cells Histone H3K4me3 H3K4me3 (Active Motif; 3915) embryonic stem cells Histone H3K27me3 H3K27me3 (Millipore; 170622) embryonic stem cells Input control Input control IgG (Santa Cruz) C2C12 myoblasts Histone H3K27me3 H3K27me3 (Milipore) C2C12 myoblasts Others Eed Eed (Milipore) C2C12 myoblasts Others Ezh2 Ezh2 (Active Motif) C2C12 myoblasts Histone H3K4me3 Abcam (ab8580) P5424 thymic cell line Histone H3K4me1 Abcam (ab8895) P5424 thymic cell line Input control Input control N/A In vitro Th17 Others Ddx5 goat anti-DDX5 In vitro Th17 Others Cebpe CEBPe SC-158 (Santa Cruz Biotechnology) bone marrow Input control Input control Input Control bone marrow Others Cebpe CEBPe GTX109155 (GeneTex) bone marrow Others Men1 Menin (Bethyl, catalog# A300-105A, lot# A300-105A-1) Five-day cultured Th2 cells generated from primary splenic CD4_T cells Others Men1 Menin (Bethyl, catalog# A300-105A, lot# A300-105A-1) Primary CD4_T cells isolated from 6-8 week old mice (C57BL/6) Others Ezh2 Ezh2 (Diagenode, catalog# pAb-039-050, lot# 001) Primary CD4_T cells isolated from 6-8 week old mice (C57BL/6) Others Men1 Menin (Bethyl, catalog# A300-105A, lot# A300-105A-1) B6N-22 ES cells Others Ezh2 Ezh2 (Diagenode, catalog# pAb-039-050, lot# 001) B6N-22 ES cells Input control Input control none B6N-22 ES cells Input control Input control Mouse IgG1 Isotype Control Ab (Southern Biotech, catalog# 0102-01, lot# JC044-V877) Primary CD4_T cells isolated from 6-8 week old mice (C57BL/6) Input control Input control Mouse IgG1 Isotype Control Ab (Southern Biotech, catalog# 0102-01, lot# JC044-V877) Primary B220_B cells isolated from 6-8 week old mice (C57BL/6) Input control Input control none Primary B220_B cells isolated from 6-8 week old mice (C57BL/6) Input control Input control none (input) genomic DNA from mixed samples of WT and CKO Histone H3K27me3 H3K27me3 (Millipore, 17-622) H3K27me3_CKO Histone H3K27me3 H3K27me3 (Millipore, 07-449) H3K27me3_CKO_luc_P5 Histone H3K27me3 H3K27me3 (Millipore, 07-449) H3K27me3_CKO_EED_P5 Histone H3K27me3 H3K27me3 (Millipore, 07-449) H3K27me3_CKO_EED_P25 Histone H3K27me3 H3K27me3 (Millipore, 07-449) H3K27me3_CKO_EED_P14 Histone H3K27ac H3K27ac (Abcam, ab4729) H3K27ac_CKO Histone H3K27ac H3K27ac (Active Motif, 39133) H3K27ac_CKO_luc_P5 Histone H3K27ac H3K27ac (Active Motif, 39133) H3K27ac_CKO_EED_P5 Histone H3K27ac H3K27ac (Active Motif, 39133) H3K27ac_CKO_EED_P25 Histone H3K27ac H3K27ac (Active Motif, 39133) H3K27ac_CKO_EED_P14 Others Nr1d1 REV-ERBa (Cell Signaling, E1Y6D, #13418) REV-ERBa_ChIPSeq Others GFP anti-GFP Whole Brain Histone H3K4me3 H3K4me3 Abcam AB8580 Chromatin IP against H3K4me3 Histone H2BK119ub H2BK119ub1 Moshe Oren MOSHE OREN LABORATOR Chromatin IP against H2Bub RNA polymerase RNA polymerase II RNA polymerase II (ab5095, lot# GR32890-1, Abcam) uterus Others Esr1 ER alpha (sc-542, lot# D1310, Santa Cruz) uterus Input control Input control anti-IgG (Santa Cruz; catalog# sc-2028; lot# J2114) BMiFLT3 (15-3) cells Others Mef2c anti-Mef2c (Santa Cruz; catalog# sc-13266X; lot# C2309) BMiFLT3 (15-3) cells Input control Input control Input (none) ESC shPhf5a WITH LIF Others Epitope tags mouse monoclonal anti-FLAG , M2 (Sigma, Cat.-No.: F1804) heart Input control Input control none (input) neuronal progenitors Others Nrf1 NRF1 (Abcam, ab55744) neuronal progenitors Input control Input control none (input) embryonic stem cells Histone H3K4me2 H3K4me2 HPC-iPSC H3K4me2 ChIPseq Histone H3K4me2 H3K4me2 MEF-iPSC H3K4me2 ChIPseq Histone H3K4me3 H3K4me3 HPC-iPSC H3K4me3 ChIPseq Histone H3K4me3 H3K4me3 MEF-iPSC H3K4me3 ChIPseq Histone H3K27me3 H3K27me3 APC H3K27me3 ChIPseq Histone H3K27me3 H3K27me3 HPC-iPSC H3K27me3 ChIPseq Histone H3K27me3 H3K27me3 MEF-iPSC H3K27me3 ChIPseq Unclassified Unclassified APC input DNA Input control Input control HPC input DNA Input control Input control HPC-iPSC input DNA Input control Input control MEF-iPSC input DNA Others Tcf7 Tcf1 CD8 T cells Histone H3K27ac H3K27ac (abcam-ab4729) Plasmacytoid dendritic cell (pDC) Histone H3K27ac H3K27ac (abcam-ab4729) Classical dendritic cell (cDC) Histone H3K27ac H3K27ac (abcam-ab4729) Common dendritic cell progenitor (CDP) Histone H3K27ac H3K27ac (abcam-ab4729) Multipotent progenitor (MPP) Input control Input control none (input) In vitro activated CD4+ Treg Input control Input control none embryonic stem cells_Day 3 differentiation, Input Others Epitope tags M2 (Sigma, catalog# F3165, lot# SLBF1225). Used 4ug of antibody per ChIP embryonic stem cells_Day 3 differentiation, Sp5 Others Relb Relb bone marrow Others Rel Rel bone marrow Histone H3 H3 C-terminal (H3CT) antibody Primary mouse OCP cells (Anet al. 2014 J Biol Chem 289: 24366-24373) Histone H3K14ac H3K14ac-specific antibody Primary mouse OCP cells (Anet al. 2014 J Biol Chem 289: 24366-24373) Input control Input control none E11.5 Mouse forebrain Others Tet3 mTet3FL (in house) Neural progenitor cells Others Suz12 anti-Suz12 Suz12 ChIP in RESTko NP cells Others Suz12 anti-Suz12 Suz12 ChIP in wildtype NP cells Others Nkx3-1 anti-Nkx3.1 (Santa Cruz Biotechnology, sc-15022) Nkx3-1_HET_ChIP-Seq Others Nkx3-1 anti-Nkx3.1 (Santa Cruz Biotechnology, sc-15022) Nkx3-1_WT_ChIP-Seq Others Suz12 anti-Suz12 (3737, Cell Signaling) ILC87 cell line derived from a thymic T cell tumor Histone H3K27ac H3K27ac antibody (Active Motif, catalogue number AM39133) 8-cell embryos Histone H3K4me3 H3K4me3 (Merck Millipore, catalogue number 04-745) 8-cell embryos Histone H3K27ac H3K27ac antibody (Active Motif, catalogue number AM39133) 2-cell embryos Histone H3K4me3 H3K4me3 (Merck Millipore, catalogue number 04-745) 2-cell embryos Histone H3K27ac H3K27ac antibody (Active Motif, catalogue number AM39133) oocytes Histone H3K4me3 H3K4me3 (Merck Millipore, catalogue number 04-745) oocytes Histone H3K27ac H3K27ac antibody (Active Motif, catalogue number AM39133) E14 Others Ebf1 anti EBF1 #0647 homemade FO B Others Ebf1 anti EBF1 #0647 homemade Pro-B Others Stag1 SA1 Chromatin IP against SA1 Others Smc3 SMC3 Chromatin IP against SMC3 Others Atf4 anti-ATF4 Mouse embronic fibroblast Others Ddit3 anti-CHOP Mouse embronic fibroblast Others Epitope tags HA-tag antibody (Santa Crruz Biotechnology, sc-7392) G1ME cells Histone H3K4me3 Anti-H3K4me3 Millipore (#07-473) Anti-H3K4me3 B6_testis_ChIP-Seq Others Dmc1 Anti-DMC1 (C-20) Anti-DMC1 Prdm9-/-_testis_SSDS Input control Input control Input DNA with Kinetic Enrichment_testis_SSDS Others Dmc1 Anti-DMC1 (C-20) Anti-DMC1 F1_testis_SSDS Others Yy1 anti-YY1 Cardiac progenitor cells, YYI ChIP Histone H3 H3 ChIP-seq, siNS Histone H3K4me3 H3K4me3 ChIP-seq, siNS Histone H3K36me3 H3K36me3 ChIP-seq, siNS Others Stat5a anti-STAT5/R & D Systems, #PA-ST5A, lot #RU07 CD8 T cell Histone H3K4me3 rabbit anti-H3K4me3 (Abcam ab8580) Rods from WT mouse retina Histone H3K4me1 rabbit anti-H3K4me1 (Abcam ab8895) Rods from WT mouse retina Histone H3K27me3 rabbit anti-H3K27me3 (Millipore 07-449) Rods from WT mouse retina Histone H3K27ac rabbit anti-H3K27ac (Abcam ab4729) Rods from WT mouse retina Input control Input control none, input E13.5 preSertoli cells Histone H3K27ac Rabbit-anti-H3K27ac; Abcam ab4729 E13.5 preSertoli cells Input control Input control none (input) Bcell Histone H3K4me3 K4me3 GST #9751 Mouse embryonic stem cells Histone H3K27me3 K27me3 GST #9733 Mouse embryonic stem cells Others 5-mC 5mC Active Motif, #39649 Mouse embryonic stem cells Others 5-hmC 5hmC Active Motif, #39769 Mouse embryonic stem cells Others Smad2 anti-Smad2/3 mouse pancreatic cancer cell line Histone H2Bub H2Bub1 (Cell signaling, 5546) Mouse embryonic fibroblasts Input control Input control Input control Low fat diet Input control Input control Input control High fat diet Histone H3 rabbit H3 antibody (Abcam, ab1791) Low fat diet Histone H3 rabbit H3 antibody (Abcam, ab1791) High fat diet Histone H3K27ac H3K27ac (Anti-H3K27ac, C15410196-10, Diagenode) Embryonic stem cells Histone H3K4me1 H3K4me1 (Anti-H3K4me1, CS-037-100, Diagenode) Embryonic stem cells Input control Input control None bone marrow Others Hdac1 HDAC Abcam #ab7028 (rabbit) TauEGFP MEFs Others Sin3b Sin3b Santa Cruz #sc-996 (rabbit) TauEGFP MEFs Others Myt1l Myt1la (rabbit) TauEGFP MEFs Others Myt1l Myt1lb (rabbit) E13.5 Mouse Brain Unclassified Unclassified E13.5 Mouse Brain Histone H3K4me3 H3K4me3 embryonic stem cells Histone H3K4me1 H3K4me1 embryonic stem cells Others Biotin streptavidin neuronal progenitor cells Others Biotin streptavidin embryonic stem cells Input control Input control none (input) T-ALL mnase input Histone H3K4me3 H3K4me3 T-ALL H3K4me3 Histone H3K27me3 H3K27me3 T-ALL H3K27me3 Input control Input control none (input) DP mnase input Histone H3K9ac H3K9ac DP H3K9ac Others Pgr PR Mouse uterus Others Gata3 GATA3 CD4+CD25CD62L+ T cells Histone H3K4me1 H3K4me1 Germinal Center B cells Histone H3K4me3 H3K4me3 Marginal Zone B cells Histone H3K4me3 H3K4me3 Follicular B cells Histone H3K4me3 H3K4me3 Mature B cells Histone H3K4me1 H3K4me1 Mature B cells Histone H3K4me3 H3K4me3 Immature B cells Histone H3K4me1 H3K4me1 Immature B cells Histone H3K4me3 H3K4me3 Pro B cells Histone H3K4me1 H3K4me1 Pro B cells Others Tcf4 Tcf4 (C48H11) (Cell signaling, catalog# 2569S, lot# 2) ISC Input control Input control none D1 epiblast-like cells 3h after Nanog induction +Dox (200ng/ml) Input control Input control none D2 epiblast-like cells 3h after Nanog induction +Dox (200ng/ml) Input control Input control none Embryonic stem cells with Dox-inducible Nanog transgene Others Nanog NANOG (RCAB0001P) D1 epiblast-like cells 3h after Nanog induction +Dox (200ng/ml) Others Nanog NANOG (RCAB0001P) D2 epiblast-like cells 3h after Nanog induction +Dox (200ng/ml) Others Nanog NANOG (RCAB0001P) Embryonic stem cells with Dox-inducible Nanog transgene Histone H3K4me3 custom-made H3K4Me3 antibody (Abmart) Inner cell mass Histone H3K4me3 custom-made H3K4Me3 antibody (Abmart) MII oocyte Others Grip1 GRIP1 primary bone marrow-derived macrophages Histone H3K27me3 H3K27me3 cell signaling H3K27me3 Pre-PB Histone H3K27me3 H3K27me3 cell signaling H3K27me3 Act B cell Others Prdm1 Streptavidin Bio-ChIP-seq Blimp1 PB Histone H3K27me3 Antibody H3K27me3 (Millipore 07-449, DAM-1588246) Embryonic Stem cells Input control Input control na Lin-Sca1-cKit+ cells Others Cdx2 Bethyl BL3194, lotA300-691A-1 CDX2 ChIP-Seq in WT mouse villus cells Histone H3K4me1 H3K4me1 (Abcam, ab8895) MEF_Smarca4-KO Histone H3K4me1 H3K4me1 (Abcam, ab8895) MEF_Smarcb1-KO Histone H3K4me1 H3K4me1 (Abcam, ab8895) MEF_WT Histone H3K27ac H3K27ac (Cell Signaling Technology, D5E4, 8173) MEF_Smarca4-KO Histone H3K27ac H3K27ac (Cell Signaling Technology, D5E4, 8173) MEF_Smarcb1-KO Histone H3K27ac H3K27ac (Cell Signaling Technology, D5E4, 8173) MEF_WT Input control Input control none regenerating liver harvested 12 h after PH Histone H3K79me2 H3K79me2 (Abcam, catalog# ab3594, lot# GR201271-1) Primary HSPC Cells RNA polymerase RNA polymerase II RNAPII S5P CTD4H8 (MMS-128P, Covance) Undifferentiated ES cells Others E2f1 anti-E2F1 (Santa Cruz, catalog# sc-193x, lot# B0615) mouse embryonic fibroblasts Others Whsc1l1 NSD3 (polyclonal antibody made in house raised against the peptide: PTDYYHSEIPNTRPHEC) MLL-AF9/NrasG12D murine cell line Others Chd8 CHD8 (#A301-224A; Bethyl) MLL-AF9/NrasG12D murine cell line Unclassified Unclassified Primary non-B cells Others Mecp2 MeCP2 antibody MeCP2_ChIP_WT Unclassified Unclassified Tip5-knockdown E14 cells Histone H3K27ac anti-H3K27ac (Abcam, catalog# ab4729, lot# GR183919-2) MMTV-Myc cells Histone H3K27me3 anti-H3K27me3 (Millipore, catalog# 07-449, lot# 2194165) MMTV-Myc cells Histone H3K4me3 anti-H3K4me3 (Abcam, catalog# ab1012, lot# GR187380-1) MMTV-Myc cells Input control Input control Rabbit IgG (Santa Cruz: sc2027) NS5 Neural Stem Cell Others Epitope tags mouse anti-V5 Agarose affinity gel antibody (sigma A7345) NS5 Neural Stem Cell Others Epitope tags HA-probe sc-7392 (Santa Cruz Biotechnology) ESD3 Others Epitope tags HA-probe sc-7392 (Santa Cruz Biotechnology) F9 Cells Histone H3K27me3 anti-H3K27me3 (Millipore, catalog# 07-449, lot# 2475696) Multipotent progenitors Histone H3K4me3 anti-H3K4me3 (Cell Signaling, catalog# 9751S, 11/2014, lot# 8) Multipotent progenitors Histone H3K27me3 anti-H3K27me3 (Millipore, catalog# 07-449, lot# 2475696) Short-term Hematopoietic stem cells Histone H3K4me3 anti-H3K4me3 (Cell Signaling, catalog# 9751S, 11/2014, lot# 8) Short-term Hematopoietic stem cells Histone H3K27me3 anti-H3K27me3 (Millipore, catalog# 07-449, lot# 2475696) Long-term Hematopoietic stem cells Histone H3K4me3 anti-H3K4me3 (Cell Signaling, catalog# 9751S, 11/2014, lot# 8) Long-term Hematopoietic stem cells Histone H3K4me3 anti-H3K4me3 (Cell Signaling, catalog# 9751S, 11/2014, lot# 8) Embryonic stem cells Others Irf8 anti-IRF8 (Santa Cruz, C-19) LPS actived B cells Others Irf4 anti-IRF4 (Santa Curz, M-17) LPS actived B cells Histone H3K9me3 H3K9me3 WT H3K9me3 ChIP-seq Histone H3K9me3 H3K9me3 NT Kdm4b H3K9me3 ChIP-seq Others Trp53 anti-p53(FL-393) and anti-p53(M19) Santa Cruz Biotechnology/sc-6243X and sc-1312 mouse embroid bodies Histone H3K4me3 H3K4me3 (Millipore, CS200580) Mammary gland Histone H3K9me2 H3K9me2 (Abcam, ab1220) ESC Histone H3K9me2 H3K9me2 (Abcam, ab1220) EpiLC Histone H3K9me2 H3K9me2 (Abcam, ab1220) Epiblast E6.25 Histone H3K9me2 H3K9me2 (Abcam, ab1220) EpiSC Histone H3K27ac ab4729 (Abcam) liver Others Foxa2 Antibody Mix: clone 3C10 (Millipore) + ab23630 (Abcam) liver Others Epitope tags Anti-HA and anti-Flag 46C ES cells Others Epitope tags Anti-HA 46C ES cells Histone H3K4me2 H3K4me2 Diagenode pAb-035-050 Bone Marrow Histone H2A.X anti-H2A.X (Xiaolab_Maked) iTSC_4_factor Histone H2A.X anti-H2A.X (Xiaolab_Maked) iTSC_3_factor Histone H2A.X anti-H2A.X (Xiaolab_Maked) TS cell Others Rnf2 RING1B (Activ Motif 39664, Lot. 23012002) forelimb buds Histone H3K27me3 H3K27me3 (Millipore 07-449) Ring1B I53A/I53A mESCs Histone H3K27me3 H3K27me3 (Millipore 07-449) E14Tg2a mESCs Others Rnf2 Ring1B (MBL D139-3) Ring1B I53A/I53A mESCs Input control Input control none Ring1B I53A/I53A mESCs Input control Input control none melan-Ink4a-Arf-1 (melan-a) Others Sox10 SOX10 (sc-17342X; Santa Cruz Biotechnology) melan-Ink4a-Arf-1 (melan-a) Histone H3K27me3 H3K27me3 (ab6002; Abcam) melan-Ink4a-Arf-1 (melan-a) Histone H3K27ac H3K27ac (ab4729; Abcam) melan-Ink4a-Arf-1 (melan-a) Unclassified Unclassified rabbit polyclonals ES-derived NS5 cells_ChIP Others Epitope tags anti-FLAG (Sigma F3165) KSL Unclassified Unclassified Adult Hippocampal NeuN- Cells (~7 weeks postnatal) Histone H3.3 H3.3 Embryonic Cortical NeuN+ Cells (E16.5) Unclassified Unclassified MEF Cell Line Histone H3K9me3 H3K9me3 (Active Motif: 39161) H3K9me3_ChIPSeq_noTam Input control Input control Normal Goat IgG (SC, catalog# 2028, lot# F1411) Basal Ganglia and Septum Histone H3K27me3 H3K27me3 Embryonic stem cells Histone H3K4me3 H3K4me3 (Abcam, ab8580, lot GR164534-1) liver Histone H3K9ac H3K9ac (Abcam, ab4441, lot GR159800-1) liver Others Epitope tags FLAG M2 (Sigma F1805) fS248A-Tg mESC, short, ChIP Others Epitope tags FLAG M2 (Sigma F1805) fS248A-Tg mESC, long, ChIP Others Epitope tags FLAG M2 (Sigma F1805) fSOX2-Tg mESC, short, ChIP Others Epitope tags FLAG M2 (Sigma F1805) fSOX2-Tg mESC, long, ChIP Others Rad21 Rad21 Bethyl A300-080A Embryonic stem cells Others Ncapg CapG Tatsuya Hirano AFR310-4L Embryonic stem cells Others Ncapd3 CapD3 Tatsuya Hirano AFR319-3L Embryonic stem cells Input control Input control none none Mouse liver cells RNA polymerase Polr2b RPB2 sc-67318 Mouse liver cells Histone H3K36me3 H3K36me3 ab9050 Mouse liver cells RNA polymerase Polr3d RPC4 CS681, raised against the C-terminus of RPC4, peptide CSPDFESLLDHKHR (same peptide as CS682, see (Chong, Hu et al. 2001)) Mouse liver cells RNA polymerase Polr3a RPC1 CS377, raised against the C-terminus of RPC1, peptide PKRPLIFDTNEFHIPLVT, see (Sepehri and Hernandez 1997)), Mouse liver cells Histone H3K27me3 H3K27me3 antibody (Cell Signaling, catalog # 9733, lot # 10) C3H10T1/2 cells & S2 cells Histone H3K36me2 H3K36me2 antibody (Millipore, catalog # 07-369-I, lot # 2475921) C3H10T1/2 cells & S2 cells Histone H3K36me3 H3K36me3 antibody (active motif, catalog # 61101, lot # 32412003) C3H10T1/2 cells & S2 cells Input control Input control none C3H10T1/2 cells & S2 cells Others Rnf2 Ring1b antibody (Active Motif, catalog # 39663, lot # 23012002) C3H10T1/2 cells Input control Input control none C3H10T1/2 cells Histone H3K27ac H3K27ac (ab4729, Abcam) Naive CD4 T cells Others Kmt2d MLL4 (PMCID: PMC3869375) Naive CD4 T cells Histone H3K27me3 H3K27me3, 07-449, upstate Pancreatic Beta Cells Histone H3K4me1 H3K4me1, ab8895, Abcam Pancreatic Beta Cells Unclassified Unclassified p1 mouse rib chondrocytes Unclassified Unclassified Ileal epithelial cells Others Kmt2a MLL (anti-rabbit antibody made by our lab) Bone marrow Histone H3K9me3 crosslink anti-H3.3 (09-838); H3K9me3 (ab8898) Embryonic stem cells Input control Input control NA no antibody Embryonic stem cells Others Cbx7 CBX7 Embryonic stem cells WT Histone H3K27me3 H3K27me3 (Millipore) C2C12 muscle progenitor cells Histone H3K4me3 H3K4me3 (Abcam) C2C12 muscle progenitor cells RNA polymerase RNA polymerase II PolII 8WG16 C2C12 myoblasts RNA polymerase RNA polymerase II POL2 (Santa Cruz, sc-899) MEF cells Histone H3K4me3 H3K4me3 (Abcam, AB8580) MEF cells Histone H3K27ac H3K27ac (Active Motif, 39133) MEF cells Histone H3K27ac anti-H3K27ac (ab4729, Abcam) Tet2-/-: AML1-ETO_anti-H3K27ac Histone H3K4me3 anti-H3K4me3 (9751S, Cell signalling) Tet2-/-: AML1-ETO_anti-H3K4me3 Input control Input control IgG control (Gamma-globulin (10760815, Pierce)) Tet2-/-: AML1-ETO_IgG control Histone H3K4me1 anti-H3K4me1 (39635, Active Motif) Tet2fl/fl; AML1-ETO_anti-H3K4me1 Input control Input control IgG control (Gamma-globulin (10760815, Pierce)) Tet2fl/fl; AML1-ETO_IgG control Others Rfx2 RFX2 antibody from Santa Cruz Biotechnology Catalog # sc-10657 Lot # L0413 Decapsulated testis Input control Input control none, input Decapsulated testis Histone H3K27ac H3K27ac (ab4729, Abcam, Cambridge, MA, USA) Mouse Embryonic day 14.5 Fetal Liver Histone H3K4me3 H3K4me3 (07-473, Millipore,Billerica, MA, USA) Mouse Embryonic day 14.5 Fetal Liver Input control Input control Isotype antibody mouse Tumor intitating stem cells Others Nanog Nanog, Abcam ab21624 mouse Tumor intitating stem cells Input control Input control none (Whole cell extract) Neural stem cells RNA polymerase RNA polymerase II Pol II primary myotubes Histone H3K36me3 H3K36me3 Neuronal progenitor (NP) cells derived from mouse embryonic stem cells Histone H3K36me3 H3K36me3 Embryonic Stem (ES) Cells Histone H3K36me3 H3K36me3 ab9050 mouse Ik knockout DP thymocytes Histone H3K9ac H3K9ac2 06-599 mouse Ik knockout DP thymocytes Histone H3K27me3 H3K27me3 07-449 mouse Ik knockout DP thymocytes Histone H3K4me3 H3K4me3 ab8580 and 07-473 mouse Ik knockout DP thymocytes Input control Input control none input_stim_3T3 Input control Input control none input_unstim_3T3 Input control Input control none input_stim_DC Input control Input control none input_unstim_DC Others Stag2 SA2 Chromatin IP against SA2 Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal MEL Histone H3K4me3 H3K4me3 Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb embryonic stem cells Others Kdm5b Jarid1b-DAIN embryonic stem cells Others Mbd3 Mbd3 Mbd3 ChIP Histone H3K4me2 dimethyl-Histone H3 (Lys4) Lin-Sca1-cKit+ cells Input control Input control none Megakaryocyte Progenitor Cell Line (G1ME) Input control Input control none EML cells Others Runx1 anti-AML(RUNX1) rabbit polyclonal antibody PC284 EML cells Histone H3K4me2 H3K4me2 (Millipore 07-030) ThyDP Histone H3K4me2 H3K4me2 (Millipore 07-030) ThyDN3 Histone H3K4me2 H3K4me2 (Millipore 07-030) FLDN2b Histone H3K4me2 H3K4me2 (Millipore 07-030) FLDN1 Histone H3K9K14ac H3K(9,14)Ac (Millipore 06-599) ThyDP Histone H3K9K14ac H3K(9,14)Ac (Millipore 06-599) ThyDN3 Histone H3K9K14ac H3K(9,14)Ac (Millipore 06-599) FLDN2b Histone H3K9K14ac H3K(9,14)Ac (Millipore 06-599) FLDN1 Others Mapk8 anti-JNK13 Terminally differentiated neurons (TN) Others Smc1a Smc1 Bethyl A301-779A Embryonic stem cells Histone H3K4me1 H3K4me1 Id2-HPC cells induced under myeloid conditions, H3K4me1 ChIP Histone H3K4me1 H3K4me1 Id2-HPC cells induced under B-cell conditions, Cd19+, 120h, H3K4me1 ChIP Histone H3K4me1 H3K4me1 Id2-HPC cells induced under B-cell conditions, 48h, H3K4me1 ChIP Histone H3K4me1 H3K4me1 Uninduced Id2-HPC cells, 0h, H3K4me1 ChIP Others Epitope tags anti-V5 (Abcam, ab15828) Chromatin IP against V5 RNA polymerase RNA polymerase II RNA Pol II Embryonic Stem cells Histone H3K27me3 anti-H3K27me3 embryonic hindlimb bud, H3K27me3 ChIP Histone H3K27ac anti-H3K27ac embryonic hindlimb bud, H3K27ac ChIP Histone H3K27me3 anti-H3K27me3 embryonic forelimb bud, H3K27me3 ChIP Histone H3K27ac anti-H3K27ac embryonic forelimb bud, H3K27ac ChIP Histone H3K27ac H3K27ac Frontal cortex Histone H3K4me3 H3K4me3 Frontal cortex RNA polymerase RNA polymerase II Pol II 8WG16 Covance (Mono) KH2 Others Ctcf anti-CTCF (SantaCruz #15914) TKO_CTCF_ChIPseq Others Tal1 TAL1 sc-12984 Ter119+ cells Histone H3K9me3 H3K9me3 ab8898 G1E cells Histone H3K4me1 H3K4me1 ab8895 G1E cells Others Gata2 GATA2 SC-9008 G1E cells Others Tal1 TAL1 sc-12984 G1E cells Others Gata3 anti-Gata3 (558686, BD bioscience) CD8 cells Others Gata3 anti-Gata3 (558686, BD bioscience) Double positive cells Histone H4K16ac anti-H4K16Ac E14.5 embryo head Input control Input control none (Input) None Mouse spleen Histone H3K4me3 H3K4me3 Millipore, 05-745 Mouse spleen Histone H3K4me1 H3K4me1 Abcam, ab8895 Mouse spleen Input control Input control none C2C12 myotubes differentiated for 96h Input control Input control none Growing C2C12 myoblasts Input control Input control none ES cells, input Others Pparg PPARgamma Preadipocyte cell line Others Kdm5a 1416 (Benevolenskaya et al.,Mol Cell 18, 623-635) Kdm5a f/f ES cells Histone H3K27me3 anti-H3K27me3 (Upstate, 07-449) mouse embryonic stem cells RNA polymerase RNA polymerase II RNA Pol II Preadipocyte cell line Others Cebpd C/EBPdelta Preadipocyte cell line Others Chd4 Mi-2b Abcam AB72418 Embyonic stem cells Others Kdm1a Lsd1 Abcam AB17721 Embyonic stem cells Others Hdac2 HDAC2 Abcam AB7029 Embyonic stem cells Others Hdac1 HDAC1 Abcam AB7028 Embyonic stem cells Histone H3K27me3 anti-H3K27me3 (Millipore,#07-449) Neuronal Progenitor (NP) Cells RESTko Histone H3K27me3 anti-H3K27me3 (Millipore,#07-449) Embryonic Stem Cells (ESCs) RESTko Others Stat5b STAT5B T cell Others Stat5a STAT5A T cell Histone H3K4me2 anti-H3K4me2 T-helper 2 cells Histone H3K27me3 anti-H3K27me3 T-helper 2 cells Others Fli1 Fli1 (santa cruz, cat#sc356X, Lot#L0407) CD8 cells Input control Input control Rabbit IgG Mouse ES cells Input control Input control none Doxycycline-induced MEFs Others Mapk8 anti-JNK13 Terminally differentiated Neurons (TN) Others Nfya anti-NFYA Neuronal Progenitor (NP) Cells Others Mapk8 anti-JNK13 Neuronal Progenitor (NP) Cells Others Nfya anti-NFYA Embryonic Stem Cells (ESCs) Others Mapk8 anti-JNK13 Embryonic Stem Cells (ESCs) Others GFP goat-anti-eGFP, raised against His-tagged full-length eGFP and affinity-purified with GST-tagged full-length eGFP ESC Others Epitope tags HA: mouse monoclonal anti-HA (clone HA-7), Sigma, Catalog A2095 (lot N/A) mouse ES cells Input control Input control N/A mammary epithelial cells Histone H3K27me3 H3K27Me3 mammary gland Others Tet1 Tet1-N embryonic stem cells Others Tet1 Tet1-C embryonic stem cells Input control Input control None Mouse Embryonic Fibroblasts with Dox-inducible Klf4, Sox2 and Oct4 (KSO) Others Ep300 p300 Santa Cruz s.c. 585 Embyonic stem cells Input control Input control none Embyonic stem cells Histone H3K27ac H3K27ac Abcam AB4729 Embyonic stem cells Others Supt5 Spt5 Santa Cruz Biotechnology anti-Spt5 (H300) ActivatedBCell_Spt5 Histone H4K12ac H4K12ac (Millipore 07-595 Lot 1676174) thioglycollate-elicited peritoneal macrophages Histone H4K8ac H4K8ac (Millipore 07-328 Lot 1655221) thioglycollate-elicited peritoneal macrophages Histone H4K5ac H4K5ac (Millipore 07-327, Lot 1682153) thioglycollate-elicited peritoneal macrophages Others Suz12 Suz12 Embryonic Stem cells Histone H3 anti-H3 AB1791 Embyonic stem cells Histone H4K8ac H4K8ac mouse B cells Histone H3K9ac H3K9ac mouse B cells Histone H3K27ac H3K27ac mouse B cells Histone H3K36me3 H3K36me3 mouse B cells RNA polymerase RNA polymerase II Pol II (4H8) mouse B cells Others Smc1a Smc1 Bethyl A300-055A Mouse embryonic fibroblasts Others Nipbl Nipbl Bethyl A301-779A Embyonic stem cells Others Med1 Med1/TRAP220 Bethyl A300-793A Embyonic stem cells Others Med12 Med12 Bethyl A300-774A Embyonic stem cells Unclassified Unclassified embryonic stem cells E14 Histone H3K36me3 H3K36me3 ab9050 Hematopoietic stem and progenitor cells Histone H3K27me3 H3K27me3 07-449 Hematopoietic stem and progenitor cells Histone H3K4me3 H3K4me3 07-474 Hematopoietic stem and progenitor cells Others Tbp TBP Abcam AB818 Embyonic stem cells Histone H3K79me2 H3K79me2 Abcam AB3594 Mouse embryonic fibroblasts Histone H3K4me1 H3K4me1 (ab8895) A12 (E2A-/- T cell) Others Tcf3 E2A.E12(V-18) (sc-349) E2A-/- pre-pro-B cell Others Stat6 STAT6<SantaCruz#sc981> primary CD4+ T cells from spleen and lymph nodes Others Stat4 STAT4<SantaCruz#sc486> primary CD4+ T cells from spleen and lymph nodes Input control Input control IgG1 Conditional Myb transformed myeloid cell line Input control Input control N/A ES-cell derived erythroid progenitors Others Cebpb CEBP (Santa Cruz Biotechnologies, sc-150) Chromatin IP against CEBPb Histone H3K4me3 H3K4me3 8580 in vitro polarized Th17 T cells Histone H3K4me1 H3K4me1 (Vendor: Abcam, cat# ab8895, lot# 721955) bone marrow-derived macrophages Others Spi1 PU.1 (Vendor: Santa Cruz, cat# sc-352, lot# F1808) bone marrow-derived macrophages Histone H3K27me3 H3K27me3 Mouse embryonic fibroblast Histone H3K4me3 H3K4me3 Mouse embryonic fibroblast Histone H3K27me3 anti-H3K27me3 Chromatin IP against H3K27me3 Histone H3K9me3 anti-H3K9me3 Chromatin IP against H3K9me3 Histone H3K4me3 H3K4me3 (#07-473, Millipore) Total thymocytes Input control Input control IgG Retina, Nrl ko, IgG ChIP Others Crx Crx Retina, Nrl ko, Crx ChIP Others Crx Crx Retina, wt, Crx ChIP Histone H3K4me3 H3K4me3 R1 embryonic stem cells Histone H3K27me3 H3K27me3 Extraembryonic endoderm stem cell Histone H3K4me3 H3K4me3 Extraembryonic endoderm stem cell Histone H3K27me3 H3K27me3 Trophoblast stem cells Histone H3K4me3 H3K4me3 Trophoblast stem cells Histone H3K27me3 H3K27me3 R1 embryonic stem cells Histone H3K4me1 H3K4me1 mouse B cells Histone H3K27me3 anti-H3K27me3 Double positive cells Histone H3K4me3 H3K4me3 (Abcam ab8580) Embryonic stem cells Others Nfic NFI (H300): sc-5567, SantaCruz Biotechnology mouse embryonic fibroblasts (MEF) Histone H3K4me1 H3K4me1 (Abcam ab8895) Embryonic stem cells Input control Input control x-link ChIP input control. No antibody. Embryonic stem cells Others Epitope tags anti-HA (12CA5) Neural progenitor cells Histone H3K36me3 anti-H3K36me3 Embryonic stem cells Others Suz12 Suz12 Embyonic stem cells Others Jarid2 Jarid2 Embyonic stem cells Others Irf4 IRF4 murine Irf4 deficient CD4+ T Unclassified Unclassified Embyonic stem cells Unclassified Unclassified V6.5 embryonic stem cells Histone H3K9me3 H3K9me3 (Up07222) V6.5 mES cells Histone H3K27me3 H3K27me3 mouse bone marrow-derived macrophages Histone H3K4me3 H3K4me3 mouse bone marrow-derived macrophages Input control Input control none, whole cell extract Histone H3K4me3 source H3K4me3_control_2 Histone H3K4me3 source H3K4me3_Salt_2 Unclassified Unclassified source mouse 15 pancreas Unclassified Unclassified source ERS433271 Unclassified Unclassified source ERS433270 Unclassified Unclassified source ERS433269 Unclassified Unclassified source ERS433268 Unclassified Unclassified source ERS433267 Unclassified Unclassified source ERS433266 Histone H3K27ac source 1 Diff-K27ac-1 Histone H3K27ac source 6 Diff-K27ac-6 Unclassified Unclassified source ERS022702 Unclassified Unclassified source ERS002989 Unclassified Unclassified source ERS005004 Others Mecp2 Chromotek GFP trap Agarose source ERS327677 Others Mecp2 Chromotek GFP trap Agarose source ERS327676 Others Mecp2 Chromotek GFP trap Agarose source ERS327675 Others Mecp2 Chromotek GFP trap Agarose source ERS327674 Others Mecp2 Chromotek GFP trap Agarose source ERS327673 Others Mecp2 Chromotek GFP trap Agarose source ERS327672 Others Mecp2 Chromotek GFP trap Agarose source ERS327671 Others Mecp2 Chromotek GFP trap Agarose source ERS327670 Others Mecp2 Chromotek GFP trap Agarose source ERS327669 Others Mecp2 Chromotek GFP trap Agarose source ERS327668 Unclassified Unclassified source ERS184474 Unclassified Unclassified source ERS184473 Unclassified Unclassified source ERS184472 Unclassified Unclassified source ERS184471 Unclassified Unclassified source ERS184470 Unclassified Unclassified source ERS184469 Unclassified Unclassified source ERS184468 Unclassified Unclassified source ERS184467 Unclassified Unclassified source Transfection_1 Unclassified Unclassified source Transfection_2 Others Foxo1 anti-foxo1 source ERS177122 Others Foxo1 anti-foxo1 source ERS177121 Others Foxo1 anti-foxo1 source ERS177120 Others Foxo1 anti-foxo1 source ERS177124 Others Foxo1 anti-foxo1 source ERS177118 Others Foxo1 anti-foxo1 source ERS177117 Others Foxo1 anti-foxo1 source ERS177123 Others Foxo1 anti-foxo1 source ERS177115 Unclassified Unclassified source mmuBL60ON562 Unclassified Unclassified source mmu0h490+491 Unclassified Unclassified source 0SQ17 Unclassified Unclassified source 2022.3 Unclassified Unclassified source 0ON490+491 Unclassified Unclassified source tc152039_brain Unclassified Unclassified source tc152038_brain Unclassified Unclassified source tc144737 Unclassified Unclassified source tc152038_liver Unclassified Unclassified source ERS026036 Unclassified Unclassified source ERS017525 Unclassified Unclassified source ERS017524 Unclassified Unclassified source ERS017521 Unclassified Unclassified source ERS017520 Unclassified Unclassified source ERS017523 Unclassified Unclassified source ERS017519 Unclassified Unclassified source ERS017518 Unclassified Unclassified source ERS017517 Unclassified Unclassified source ERS017516 Unclassified Unclassified source ERS017515 Unclassified Unclassified source ERS017514 Unclassified Unclassified source ERS017513 Unclassified Unclassified source ERS017512 Unclassified Unclassified source ERS017511 Unclassified Unclassified source ERS017510 Unclassified Unclassified source ERS017509 Unclassified Unclassified source ERS017508 Unclassified Unclassified source ERS017507 Unclassified Unclassified source ERS017506 Unclassified Unclassified source ERS017505 Unclassified Unclassified source ERS017504 Unclassified Unclassified source ERS017503 Unclassified Unclassified source ERS017502 Unclassified Unclassified source ERS017501 Unclassified Unclassified source ERS023702 Unclassified Unclassified source ERS023696 Unclassified Unclassified source ERS023700 Unclassified Unclassified source ERS023699 Unclassified Unclassified source ERS023697 Unclassified Unclassified source ERS023698 Unclassified Unclassified source ERS023693 Unclassified Unclassified source ERS023695 Unclassified Unclassified source ERS023701 Unclassified Unclassified source ERS023694 Unclassified Unclassified source ERS018864 Unclassified Unclassified source ERS018863 Unclassified Unclassified source ERS018862 Unclassified Unclassified source ERS018861 Unclassified Unclassified source ERS005085 Unclassified Unclassified source ERS005090 Unclassified Unclassified source ERS005082 Unclassified Unclassified source ERS005083 Unclassified Unclassified source ERS005086 Unclassified Unclassified source ERS005088 Histone H3K4me3 H3K4me3 source ERS071964 Histone H3K4me3 H3K4me3 source ERS071972 Histone H3K4me3 H3K4me3 source ERS071958 Histone H3K4me3 H3K4me3 source ERS071970 Histone H3K4me3 H3K4me3 source ERS071956 Histone H3K4me3 H3K4me3 source ERS071969 Histone H3K4me3 H3K4me3 source ERS071953 Others Hnf4a source HNF4A ChIP 1 Others Stag1 source STAG1 ChIP 1 Others Gabpa source GABPA ChIP 1 Unclassified Unclassified source tc1_28.1_m9_AND_28.2_m10_testes Unclassified Unclassified source tc1_138.1 Others Ncor2 source Cell culture 4 SMRT Others Ncor2 source Cell culture 2 SMRT Others Ncor2 source Cell culture 3 SMRT Others Ncor2 source Cell culture 1 SMRT Others Sp2 source MEF_deltaSp2 Unclassified Unclassified source MEF_wt Input control Input control input_DNA source ERS002486 Unclassified Unclassified source Treated-Male Unclassified Unclassified source Treated-Female Unclassified Unclassified source Untreated-Male Histone H2AK5sc source mouse H2AK5sc ChIP 1 Unclassified Unclassified source mmu491_testes Unclassified Unclassified source mmu491_muscle Unclassified Unclassified ERS011162 Input control Input control source mouse input 1 Histone H3K9me2 EpiSC cells were cultured on murine fibroblast feeders in DMEM/F12 supplemented with 20% KSR, bFGF, nonessential amino acids, b-mercaptoethanol, L-glutamax, penicillin, and streptomycin.ChIP experiment with anti-H3K9me2 antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Histone H3K9me3 EpiSC cells were cultured on murine fibroblast feeders in DMEM/F12 supplemented with 20% KSR, bFGF, nonessential amino acids, b-mercaptoethanol, L-glutamax, penicillin, and streptomycin.ChIP experiment with anti-H3K9me3 antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Histone H3K27me3 EpiSC cells were cultured on murine fibroblast feeders in DMEM/F12 supplemented with 20% KSR, bFGF, nonessential amino acids, b-mercaptoethanol, L-glutamax, penicillin, and streptomycin.ChIP experiment with anti-H3K27me3 antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Histone H3K4me3 EpiSC cells were cultured on murine fibroblast feeders in DMEM/F12 supplemented with 20% KSR, bFGF, nonessential amino acids, b-mercaptoethanol, L-glutamax, penicillin, and streptomycin.ChIP experiment with anti-H3K4me3 antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Histone H3K4me1 EpiSC cells were cultured on murine fibroblast feeders in DMEM/F12 supplemented with 20% KSR, bFGF, nonessential amino acids, b-mercaptoethanol, L-glutamax, penicillin, and streptomycin.ChIP experiment with anti-H3K4me1 antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Others Kdm1a EpiSC cells were cultured on murine fibroblast feeders in DMEM/F12 supplemented with 20% KSR, bFGF, nonessential amino acids, b-mercaptoethanol, L-glutamax, penicillin, and streptomycin.ChIP experiment with anti-Lsd1 antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Input control Input control EpiSC cells were cultured on murine fibroblast feeders in DMEM/F12 supplemented with 20% KSR, bFGF, nonessential amino acids, b-mercaptoethanol, L-glutamax, penicillin, and streptomycin.ChIP experiment with whole cell extract was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Others Nr5a1 Ad4BP ChIP product from adult Leydig cells Input control Input control The embryonic kidneys (at E16.5) of the wild type mouse were fixed for 30min, sonicated, and mixed with no antibody at 4C overnight, followed by precipitation by using Dynabeads M-280 conjugated with anti-rabbit IgG (Invitrogen). Input control Input control The embryonic kidneys (at E16.5) of the wild type mouse were fixed for 30min, sonicated, and mixed with anti-rabbit IgG (Invitrogen) at 4C overnight, followed by precipitation by using Dynabeads M-280 conjugated with anti-rabbit IgG (Invitrogen). Others Nr5a1 ChIP-seq for Ad4BP Others Chd2 source:C2C12 cells transfected mir3139 targeted Chd2 Others Rorc RORgamma liver Others Nr1d1 Rev-erbalpha eWAT Input control Input control input NA spermatocytes Input control Input control Input E9.5 hearts Input control Input control none C2C12 cells Others Six4 anti-Six4 C2C12 cells Others Epitope tags anti-Flag C2C12 cells Unclassified Unclassified hypothalamus Input control Input control wild type anti-Irf-1 input Input control Input control none 8946: Input Histone H3K27ac H3K27ac Day10 Neurons Histone H3K27ac H3K27ac Day1 Neurons Histone H3K4me1 H3K4me1 Mnase-dY-Tam-K4me1 Histone H3K4me1 H3K4me1 Mnase-dY-EtOH-K4me1 Histone H3K4me1 H3K4me1 Mnase-R-Tam-K4me1 Histone H3K4me1 H3K4me1 Mnase-R-EtOH-K4me1 Others Smarca4 Brg1 dY-Tam-Brg1 Others Hdac1 HDAC1 dY-Tam-HDAC1 Others Smarca4 Brg1 dY-EtOH-Brg1 Others Hdac1 HDAC1 dY-EtOH-HDAC1 Others Smarca4 Brg1 R-Tam-Brg1 Others Hdac1 HDAC1 R-Tam-HDAC1 Others Smarca4 Brg1 R-EtOH-Brg1 Others Hdac1 HDAC1 R-EtOH-HDAC1 Others Pparg anti-PPAR? antibody F1_eWAT_chow Others Pparg anti-PPAR? antibody 129_eWAT_chow Others Pparg anti-PPAR? antibody B6_eWAT_chow Others Pparg anti-PPAR? antibody 129_eWAT_12wLFD Others Pparg anti-PPAR? antibody B6_eWAT_12wLFD Unclassified Unclassified 10E2 G3-medulloblastoma Histone H3K27me3 H3K27me3 Testis Histone H3K4me3 H3K4me3 Testis Unclassified Unclassified Testis Input control Input control none Mouse Embryonic Fibroblast (MEF) Histone H3K27me3 Millipore, #07-449 E14 Histone H3K4me3 Millipore, #04-745 E14 Others Epop C17orf96 E14 Histone H3K4me1 anti-H3K4me1 Spleen red pulp macrophages Histone H3K27ac anti-H3K27ac Neutrophils Histone H3K4me1 anti-H3K4me1 Neutrophils Histone H3K27ac anti-H3K27ac Monocytes Histone H3K4me1 anti-H3K4me1 Monocytes Histone H3K27ac anti-H3K27ac Small intestine macrophages Histone H3K4me1 anti-H3K4me1 Small intestine macrophages Histone H3K27ac anti-H3K27ac Large intestine macrophages Histone H3K4me1 anti-H3K4me1 Large intestine macrophages Histone H3K27ac anti-H3K27ac Kupffer cells Histone H3K4me1 anti-H3K4me1 Kupffer cells Others Tal1 Scl/Tal1 ES cells Others Brd4 BRD4 G1E_BRD4 +GATA1 Input control Input control none G1ME_GATA1s_ChIP_input Input control Input control none G1ME_GATA1fl_ChIP_input Others Epitope tags anti-HA G1ME_GATA1s_ChIP Others Epitope tags anti-HA G1ME_GATA1fl_ChIP Input control Input control Input Spermatocytes Histone H3K4me3 ab8580, abcam Neural progenitor cells Histone H3K4me1 ab8895, abcam Neural progenitor cells Histone H3K9ac ab4441, abcam Neural progenitor cells Histone H3K27ac ab4729, abcam Neural progenitor cells Histone H3K27me3 ab6002, abcam Neural progenitor cells Histone H3K9me2 H3K9me2 spermatocytes Others Hif1a anti-HIF1a embryonic heart Histone H3K27me3 anti-H3K27me3 IkL/L_LSK_H3K27me3 Histone H3K27me3 anti-H3K27me3 WT_LSK_H3K27me3 Input control Input control none WT_DP_input Input control Input control none WT_DN4_input Input control Input control none WT_DN3_input Histone H3K27me3 anti-H3K27me3 WT_DP_H3K27me3 Histone H3K27me3 anti-H3K27me3 WT_DN4_H3K27me3 Histone H3K27me3 anti-H3K27me3 WT_DN3_H3K27me3 Input control Input control none IkL/L_DPe_input Histone H3K27me3 anti-H3K27me3 IkL/L_DPe_H3K27me3 Input control Input control none WT_DPe_input Histone H3K27me3 anti-H3K27me3 WT_DPe_H3K27me3 Input control Input control none Cerebellum Unclassified Unclassified mESCs Histone H3K4me3 H3K4me3 1000 mEpiSCs Histone H3K4me3 H3K4me3 1000 mESCs Histone H3K27ac H3k27ac R6_striatum_H3k27ac Histone H3K27ac H3k27ac WT_striatum_H3k27ac Histone H3K36me3 ab9050, abcam Neural progenitor cells Histone H3K9me3 ab8898, abcam Neural progenitor cells Histone H3K9me3 a-H3K9me3 miwi2HET_SomaticCellsTestis_MACS_H3K9me3 Input control Input control miwi2HET_SomaticCellsTestis_MACS_inputDNA Histone H3K4me3 H3K4me3 dY-Foxd3CKO-Tam-H3K27me3 ChIP Histone H3K27ac H3K27ac dY-Foxd3CKO-Tam-H3K27ac ChIP Histone H3K4me3 H3K4me3 dY-Foxd3CKO-Tam-H3K4me3 ChIP Histone H3K4me1 H3K4me1 dY-Foxd3CKO-Tam-H3K4me1 ChIP Others Ep300 p300 dY-Foxd3CKO-EtOH-p300 ChIP Histone H3K27ac H3K27ac dY-Foxd3CKO-EtOH-H3K27ac ChIP Histone H3K4me3 H3K4me3 dY-Foxd3CKO-EtOH-H3K4me3 ChIP Histone H3K4me1 H3K4me1 dY-Foxd3CKO-EtOH-H3K4me1 ChIP Histone H3K4me3 H3K4me3 R-Foxd3CKO-Tam-H3K27me3 ChIP Histone H3K4me3 H3K4me3 R-Foxd3CKO-EtOH-H3K27me3 ChIP Histone H3K27ac H3K27ac R-Foxd3CKO-EtOH-H3K27ac ChIP Histone H3K4me3 H3K4me3 R-Foxd3CKO-EtOH-H3K4me3 ChIP Histone H3K4me1 H3K4me1 R-Foxd3CKO-EtOH-H3K4me1 ChIP Others Kdm4a anti-KMD4A antibody 3T3-L1 Others Gps2 Anti-GPS2 3T3-L1_GPS2 Histone H3K4me3 H3K4me3 H3K4me3 WT P6 Unclassified Unclassified Heart Histone H3 anti-H3; Company:Abcam, Catalog#:ab1791, Lot#:GR135165-1 Liver Histone H2B anti-H2B; Company:Abcam, Catalog#:ab1790, Lot#:GR47273-1 Liver Input control Input control none (Input) Mouse Embryonic Fibroblasts Input control Input control input mouse hippocampus Unclassified Unclassified VYS Histone H3K79me3 Anti-H3K79me3 olfactory epithelium_ChIP-seq Others Arntl BMAL1 Liver Others Clock CLOCK Liver Others Smarca5 Snf2h 3134 cells Others Smarca4 monoclonal Brg1 3134 cells Input control Input control wildtype-input Histone H3K4me3 anti-H3K4me3 wildtype-h3k4me3 Histone H3K27me3 anti-H3K27me3 wildtype-h3k27me3 Histone H3K27ac H3K27ac (Ab4729; Lot # GR28147-1) colonic epithelial cells Input control Input control none C2C12 myotubes, WCE Others Ncor2 SMRT liver RNA polymerase RNA polymerase II Pol 2 cell line Unclassified Unclassified cell line Unclassified Unclassified TT2 Input control Input control none myotubes_input Input control Input control none Input_ING1_flag_myoblasts Others Sin3a Sin3A Sin3A_myotubes Others Kmt2a MLL1 Menin_myoblasts Others Men1 Menin Menin_myoblasts Others Epitope tags anti-FLAG ING1_flag_myoblasts Others Klf5 Klf5 mouse ESCs Others Klf4 Klf4 mouse ESCs Others Ezh2 EZH2 in-house E14 Input control Input control None None WCE pro-B cell Others Ezh2 Ezh12 ES-E14TG2a Others Supt6 Spt6 ES-E14TG2a Input control Input control none female_input Histone H3K27ac H3K27ac female_NAG1_LF Histone H3K27ac H3K27ac female_NAG1_HF Histone H3K27ac H3K27ac female_WT_LF Histone H3K27ac H3K27ac female_WT_HF Input control Input control None None WCE mouse heart Others Tcf7 Tcf1 thymus Input control Input control input Heart Histone H3K27ac Anti-H3K27ac (Abcam, ab4729) mESC Histone H3K4me1 Anti-H3K4me1 (Abcam, ab8895) mESC Others Nr2f2 NR2F2 atria Input control Input control none Mouse Embryonic Fbroblast Unclassified Unclassified 7438 cells Others Cebpa CEBPalpha immortalized brown adipocytes Histone H3K27ac H3K27Ac immortalized brown adipocytes Input control Input control none iPax7 myogenic progenitors +dox Unclassified Unclassified Hippocampus Histone H3K9ac anti-H3K9ac (Millipore, 07-352) bone marrow dervied macrophages RNA polymerase RNA polymerase II H14 NIH3T3_POLIIS5P_UO RNA polymerase RNA polymerase II H14 NIH3T3_POLIIS5P_LAT RNA polymerase RNA polymerase II H14 NIH3T3_POLIIS5P_15 RNA polymerase RNA polymerase II H14 NIH3T3_POLIIS5P_03 RNA polymerase RNA polymerase II H5 NIH3T3_POLIIS2P_UO RNA polymerase RNA polymerase II H5 NIH3T3_POLIIS2P_LAT RNA polymerase RNA polymerase II H5 NIH3T3_POLIIS2P_15 RNA polymerase RNA polymerase II H5 NIH3T3_POLIIS2P_03 RNA polymerase RNA polymerase II 8WG16 NIH3T3_8WG16_LAT RNA polymerase RNA polymerase II 8WG16 NIH3T3_8WG16_15 Others Srf SRF NIH3T3_SRF_15 Others Srf SRF NIH3T3_SRF_03 Histone H3K9me2 H3K9me2 ES cells RNA polymerase RNA polymerase II POL2 Others Kdm1a LSD1 Others Sfmbt1 SFMBT1 Input control Input control none (input) Input control Input control mESCs_input Input control Input control mESCs_Trim28 shRNA_input Histone H3K4me1 anti-H3K4me1 Histone H3K27ac anti-H3K27ac Others Prdm9 anti-PRDM9 (BdM) RJ2_PRDM9_Input Others Prdm9 anti-PRDM9 (BdM) RJ2_PRDM9_ChIPseq Others Prdm9 anti-PRDM9 (BdM) B6_PRDM9_Input Others Prdm9 anti-PRDM9 (BdM) B6_PRDM9_ChIPseq Unclassified Unclassified BM_DN3_1%_input RNA polymerase RNA polymerase II PolII Covance/MMS-128P Thymus Histone H3K27me3 H3K27me3 Abcam/ab6002 Thymus Unclassified Unclassified BAT Others Mettl3 mettl3_clone2_IP Others Mettl3 mettl3_clone1_IP Unclassified Unclassified PB Unclassified Unclassified PRP Unclassified Unclassified E12.5_PGC Others Bcl11b anti-Bcl11b antibody (Bethyl Laboratories, A300383A) total thymocyte Unclassified Unclassified MEFs Input control Input control none Sample_JQ1_input Input control Input control none Sample_Th17_input Input control Input control Mmu Input Input control Input control input total thymocyte Histone H3K9me2 H3K9me2 wild type_cortical neuronal chromatin_H3K9me2 Histone H3K4me3 H3K4me3 wild type_cortical neuronal chromatin_H3K4me3 Others Supt6 Spt6 Input control Input control none Mouse embryonic fibrobrasts Unclassified Unclassified WT_brain_116HG_ChIRP-seq Unclassified Unclassified stem cell Others Sox17 Sox17 V5 KH2 ES cells Others Nkx2-1 Bethyl BL4000 Histone H3K4me3 Histone H3 trimethyl Lys4 Others Nfib NFIB HfSCs_NFIB_ChIPSeq Input control Input control none HfSCs_input DNA Histone H3K27ac H3K27Ac Day2 differentiating Teto-Brn2 ESCs, H3K27Ac ChIP Histone H3K27me3 Millipore 07-449 Sperm Histone H3K4me3 Millipore 17-614 Sperm Input control Input control None pro-B cell Histone H3K27ac H3K27ac mouse_E13.5_HL Histone H3K27ac H3K27ac mouse_E13.5_FL Histone H3K27ac H3K27ac mouse_E12.5_HL Histone H3K27ac H3K27ac mouse_E12.5_FL Unclassified Unclassified mouse_E13.5_HL Unclassified Unclassified mouse_E13.5_FL Unclassified Unclassified mouse_E12.5_HL Unclassified Unclassified mouse_E12.5_FL Histone H3 H3 Small intestine; duodenum Input control Input control Input Brown adipose tissue RNA polymerase RNA polymerase II Pol II ChIP DNA Histone H3K27ac H3K27ac ChIP DNA Input control Input control None Spleen Input control Input control None Mammary tissues Others Hif1a Hif1a Th17 in vitro Others Fosl2 Fosl2 Th17 in vitro Input control Input control Treg Input Histone H3K27ac anti-H3K27Ac (Abcam; Cat #: ab4729; Lot: GR117011-1) mTr_H3K27Ac Histone H3K27ac anti-H3K27Ac (Abcam; Cat #: ab4729; Lot: GR117011-1) aTr_H3K27Ac Histone H3K4me1 anti-H3K4me1 (Abcam; Cat #: ab8895; Lot:GR61306-1) mTr_H3K4me1 Histone H3K4me1 anti-H3K4me1 (Abcam; Cat #: ab8895; Lot:GR61306-1) aTr_H3K4me1 Histone H3K4me1 anti-H3K4me1 (Abcam; Cat #: ab8895; Lot:GR61306-1) rTr_H3K4me1 Input control Input control -- cerebellum Histone H2A.Zac H2A.z-ac cerebellum Input control Input control none Pre-H/S Input_ChIPSeq Histone H3K27ac H3K27Ac open chromatin Mouse Histone H3K27me2 abcam, ab24684-25 activated B cell Input control Input control None progenitor B Input control Input control input KP22_input Input control Input control input KP1_input Input control Input control input 16T_input Input control Input control none Cortex-Input Input control Input control none Wnt3KO EpiSCs Histone H3K4me3 Rabbit anti-H3K4me3 (07-473) F3_Testis_Atrazine_H3K4me3_ChIPseq Histone H3K4me3 Rabbit anti-H3K4me3 (07-473) F3_Testis_Control_H3K4me3_ChIPseq Histone H3K4me3 Rabbit anti-H3K4me3 (07-473) F1_Testis_Atrazine_H3K4me3_ChIPseq Histone H3K4me3 Rabbit anti-H3K4me3 (07-473) F1_Testis_Control_H3K4me3_ChIPseq Others Six2 six2 fresh Six2-expressing cells Histone H3K4me3 H3K4me3 : Millipore (04-745) liver Histone H3K27me3 antibody: millipore (07-449) mESCs Histone H3K4me3 H3K4me3 thymus Others Cxxc1 Cxxc1 thymus Histone H3K27ac H3k27Ac P19Cl6 Others Epitope tags FLAG (F1804; Sigma) RN2 Input control Input control none Oligodendrocyte progenitor cells Histone H3K9ac 07-352, Millipore Sperm Histone H3K27me3 07-449, Millipore Sperm Histone H3K36me3 05-801, Millipore Sperm Others Epitope tags HA MEF Unclassified Unclassified ESCs Unclassified Unclassified RA-treated ESCs Input control Input control none Forelimb Others Tcf3 Tcf3 PB Others Tcf3 Tcf3 Pre-PB Histone H3K27me3 H3K27Me3 MII oocyte Input control Input control Input EB Input control Input control Input mESC Input control Input control none RAW264.7 Histone H3K36me3 H3K36me6 spermatocytes Input control Input control bone marrow_day21_input Input control Input control bone marrow_day14_input Input control Input control bone marrow_day7_input Input control Input control bone marrow_day0_input Others Runx2 bone marrow_day21_runx2 Others Runx2 bone marrow_day14_runx2 Others Runx2 bone marrow_day7_runx2 Others Runx2 bone marrow_day0_runx2 Histone H3K9me3 bone marrow_day21_h3k9me3 Histone H3K9me3 bone marrow_day14_h3k9me3 Histone H3K9me3 bone marrow_day7_h3k9me3 Histone H3K9me3 bone marrow_day0_h3k9me3 Histone H3K9ac bone marrow_day21_h3k9ac Histone H3K9ac bone marrow_day14_h3k9ac Histone H3K9ac bone marrow_day7_h3k9ac Histone H3K9ac bone marrow_day0_h3k9ac Histone H3K4me1 bone marrow_day21_h3k4me Histone H3K4me1 bone marrow_day14_h3k4me Histone H3K4me1 bone marrow_day7_h3k4me Histone H3K4me1 bone marrow_day0_h3k4me Histone H3K4me3 bone marrow_day21_h3k4me3 Histone H3K4me3 bone marrow_day14_h3k4me3 Histone H3K4me3 bone marrow_day7_h3k4me3 Histone H3K4me3 bone marrow_day0_h3k4me3 Histone H3K36me3 bone marrow_day21_h3k36me3 Histone H3K36me3 bone marrow_day14_h3k36me3 Histone H3K36me3 bone marrow_day7_h3k36me3 Histone H3K36me3 bone marrow_day0_h3k36me3 Histone H3K27me3 bone marrow_day21_h3k27me3 Histone H3K27me3 bone marrow_day14_h3k27me3 Histone H3K27me3 bone marrow_day7_h3k27me3 Histone H3K27me3 bone marrow_day0_h3k27me3 Histone H3K27ac bone marrow_day21_h3k27ac Histone H3K27ac bone marrow_day14_h3k27ac Histone H3K27ac bone marrow_day7_h3k27ac Others Ctcf bone marrow_day21_CTCF Others Ctcf bone marrow_day14_CTCF Others Ctcf bone marrow_day0_CTCF Histone H3K27ac bone marrow_day0_h3k27ac Histone H3K4me3 H3K4me3 Macrophages Input control Input control Input-DNA KDM5c_Spikein_Input_Pooled_CN Input control Input control none Mouse V19-OSKM Fibroblast Others Zfp335 NIF1 lateral telencephalon Others Kdm1a Lsd1 neural stem cell RNA polymerase RNA polymerase II Pol2 Mll3/ MEF Others Kmt2c Mll3 Mll3/ MEF Histone H3K4me3 H3K4Me3 Mll3/ MEF Input control Input control none liver cell Others Nr0b2 SHP (sc-30169) liver cell Input control Input control none (INPUT) retina_input_P14 Histone H3K4me3 H3K4me3-AB2 retina_H3K4me3_P21 Histone H3K4me3 H3K4me3-AB2 retina_H3K4me3_P14 Histone H3K4me3 H3K4me3-AB2 retina_H3K4me3_P12 Histone H3K4me3 H3K4me3-AB2 retina_H3K4me3_P0 Histone H3K27me3 H3K27me3-AB1 retina_H3K27me3_P21 Histone H3K27me3 H3K27me3-AB1 retina_H3K27me3_P14 Histone H3K27me3 H3K27me3-AB1 retina_H3K27me3_P0 Histone H3K27ac H3K27Ac-AB2 retina_H3K27Ac_P21 Histone H3K27ac H3K27Ac-AB2 retina_H3K27Ac_P14 Histone H3K27ac H3K27Ac-AB2 retina_H3K27Ac_P0 Unclassified Unclassified MEF, click-ChIP-seq Others Parp1 MEF, PARP-1 Input control Input control none B cell enriched splenocytes Others Ctnnb1 B-catenin Resistant line Others Mbd1 MBD1 3T3-L1 preadipocytes Histone H3K4me2 H3K4me2 APC H3K4me2 ChIPseq Histone H3K4me3 H3K4me3 APC H3K4me3 ChIPseq Histone H3K9ac H3K9Ac CD8 T cells Others Tfap2a AP-2alpha (3B5):sc12726 melan-a cells Others Atf4 Atf4 ab28830-100 sc-200 bone marrow Others Cux2 Cux2 liver tissue Input control Input control none 8-cell embryos Input control Input control none 2-cell embryos Input control Input control none oocytes Others Rad21 Rad21 whole brain Others Ctcf CTCF whole brain Input control Input control none Mouse skin SCC Others Stat5a anti-STAT5 MEF_STAT5-OE-GH-IP Others Stat5a anti-STAT5 MEF_STAT5-OE-IP Histone H3K9ac H3K9ac T-ALL H3K9ac Histone H3K4me3 H3K4me3 DP H3K4me3 Histone H3K27me3 H3K27me3 DP H3K27me3 Histone H3K4me3 H3K4me3 Pre B cells Histone H3K4me1 H3K4me1 Pre B cells Histone H3K9ac H3K9Ac/H3K19Ac Lin-Sca1-cKit+ cells Unclassified Unclassified rabbit IgG IMCD3_IgG_ChIP-seq Others Hnf1a HNF-1 IMCD3_Hnf1b_ChIP-seq Input control Input control Input_WT Input control Input control none mouse ESCs (E14) Unclassified Unclassified mK4 Histone H3K27me3 H3K27me3 (Millipore, 07-449) ESC Histone H3K27me3 H3K27me3 (Millipore, 07-449) EpiSC Histone H3K27me3 H3K27me3 (Millipore, 07-449) EpiLC Histone H3K4me2 07-030 (Millipore) liver Histone H3K4me3 011013_H3K4me3 Input control Input control none C2C12 Others Rnf2 Ring1B (MBL D139-3) E14Tg2a mESCs Input control Input control none E14Tg2a mESCs Histone H3K27me3 H3K27me3 MEF Input control Input control IgG MEF Others Hells HELLS MEF Others E2f3 E2F3 MEF Input control Input control none input DNA_noTam Histone H4K8bhb H4K8bhb (PTM Biolabs) liver Histone H3K9bhb H3K9bhb (PTM Biolabs) liver Histone H3K4bhb H3K4bhb (PTM Biolabs) liver Histone H3K4me3 H3K4me3 ab8580 Mouse liver cells Histone H3K9ac H3K9ac Abcam ab4441 & Millipore ABE18 Hemogenic Endothelium Histone H3K4me1 anti-H3K4me1 (39635, Active Motif) Tet2-/-: AML1-ETO_anti-H3K4me1 Histone H3K27ac anti-H3K27ac (ab4729, Abcam) Tet2fl/fl; AML1-ETO_anti-H3K27ac Histone H3K4me3 anti-H3K4me3 (9751S, Cell signalling) Tet2fl/fl; AML1-ETO_anti-H3K4me3 RNA polymerase RNA polymerase II Pol II Liver Others Nr1d1 Rev-erba Liver Others Ncor1 NCoR Liver Input control Input control none primary myotubes Others Sox6 Sox6 primary myotubes Others Tnni2 sc-30486 osteoblast Histone H3K4me3 H3K4me3 H3K4me3_ChIPSeq Histone H3K9ac H3K9ac H3K9ac_ChIPSeq Histone H3K27me3 H3K27me3 H3K27me3_ChIPSeq Others Gata3 GATA3 GATA3_ChIPSeq Input control Input control control_Ab control_Ab_ChIPSeq Histone H3K27me3 H3K27me3 (Millipore 07-449) ThyDP Histone H3K27me3 H3K27me3 (Millipore 07-449) ThyDN3 Histone H3K27me3 H3K27me3 (Millipore 07-449) FLDN2b Histone H3K27me3 H3K27me3 (Millipore 07-449) FLDN1 Input control Input control none Frontal cortex Input control Input control ES_Input_ChIPseq Others Gata1 GATA1 sc-265 Ter119+ cells Histone H3K27me3 H3K27me3 07-449 G1E cells Others Foxa2 FoxA2 Control liver Histone H3K36me3 H3K36me3 Doxycycline-induced MEFs Histone H3K4me3 H3K4me3 Doxycycline-induced MEFs Histone H3K4me1 H3K4me1 Doxycycline-induced MEFs Others Nfya anti-NFYA Terminally differentiated Neurons (TN) Histone H3K27me3 H3K27Me3 liver Histone H3K4me2 H3K4me2 liver Histone H2BK5ac H2BK5ac mouse B cells Others Sin3b Sin3B C2C12 myoblasts Others Sin3a Sin3A C2C12 myotubes Others Sin3a Sin3A C2C12 myoblasts Input control Input control none C2C12 myotubes Others Ctcf CTCF Upstate 07-729 Mouse embryonic fibroblasts Others Smc3 Smc3 Abcam AB9263 Embyonic stem cells Histone H3K4me2 H3K4me2 mouse B cells RNA polymerase RNA polymerase II RNA Pol II (8WG16) Covance MMS-126R Mouse embryonic fibroblasts Input control Input control none WCE Histone H3K4me3 anti-H3K4me3 Double positive cells Histone H3K4me1 anti-H3K4me1 Double positive cells Histone H3K36me3 anti-H3K36me3 Neural progenitor cells Others Tal1 anti-Scl Histone H2Aub anti-uH2A(E6C5) Others Tcf3 Tcf3 Others Suz12 Suz12 Others Nanog Nanog Histone H3K36me3 H3K36me3 Histone H3K122ac H3k122 Histone H3K27ac H3K27ac Histone H3K27ac source 34 LGR5-K27ac-34 Histone H3K27ac source 31 LGR5-K27ac-31 Unclassified Unclassified ERS364247 Unclassified Unclassified ERS233566 RNA polymerase RNA polymerase III polIII Unclassified Unclassified source tc152039_spleen Input control Input control INPUT Histone H3K27me3 H3K27ME3 Histone H3K4me3 H3K4ME3 Unclassified Unclassified source Untreated-Female Histone H3K27ac H3K27ac (Abcam, ab4729) Mouse female cerebellum tissue Others Rora RORalpha liver Input control Input control none brain(ventral tegmental area) Others Nr1d1 Rev-erbalpha brain(ventral tegmental area) Input control Input control none eWAT Unclassified Unclassified spleen Others Prdm9 Prdm9 spermatocytes Histone H3K9me3 H3K9me3 spermatocytes Input control Input control - Mesoderm precursors Others Rybp RYBP (Millipore, catalog: Ab3637, lot: 2066315) Mesoderm precursors Others Rnf2 Ring1b (Home-made) Mesoderm precursors Others Cbx2 Cbx2 (Bethyl, catalog:A302-524A, lot: A302-524A-1) Mesoderm precursors Others Pcgf2 Mel18 (Santa Cruz, catalog: H-115-X, lot: D0903) Mesoderm precursors Others Pcgf2 Mel18 (Santa Cruz, catalog: H-115-X, lot: D0903) Undifferentiated ES cells Input control Input control None liver Histone H2AK119Ub Rabbit anti-ubH2A (Cell Signaling, #8240 ) Cultured germline stem cells Input control Input control none (input) Isolated pachytene spermatocytes Others Scml2 Rabbit anti-Scml2 (produced in-house; Hasegawa et al.) Isolated pachytene spermatocytes Others GFP anti-GFP (ab290, Abcam) caudate putamen Histone H3K4me3 anti-H3K4me3 (ab8580, Abcam) caudate putamen Others Rarb anti-RARbeta (sc-552, Santa Cruz) caudate putamen Histone H3R26cit H3R26Cit antibody (ab19847) Embryonic stem cells Input control Input control Control IgG (Santa Cruz, sc-2028, sc-3883, sc-3888) Skeletal muscle myoblast Others Gata4 Anti-GATA4 (Santa Cruz, C-20; Santa Cruz, H-112; eBioscience, eBioevan) Skeletal muscle myoblast Others Kdm3a Jmjd1a iBAT_D8_ISO_plus_JMJD1A Others Kdm3a Jmjd1a iBAT_D8_ISO_minus_JMJD1A Others Pparg Ppar-g iBAT_D8_ISO_plus_PPARg Others Pparg Ppar-g iBAT_D8_ISO_minus_PPARg Others Arid1a Arid1a iBAT_D8_ISO_plus_ARID1A Others Arid1a Arid1a iBAT_D8_ISO_minus_ARID1A Others Smarca4 Brg1 iBAT_D8_ISO_plus_BRG1 Others Smarca4 Brg1 iBAT_D8_ISO_minus_BRG1 Unclassified Unclassified FAIRE iBAT_D8_ISO_minus_FAIRE Histone H3K27ac H3K27Ac iBAT_D8_ISO_plus_H3K27Ac Histone H3K27ac H3K27Ac iBAT_D8_ISO_minus_H3K27Ac Histone H3K4me3 H3K4me3 iBAT_D8_ISO_plus_H3K4me3 Others GFP GFP antibody, vendor:Pierce, cat#:4B10B2m lot#: MA5-15349 mouse embryonic cortex Others GFP GFP antibody, vendor:Santa Cruz, cat#:sc-8334, lot#:H0612 mouse embryonic cortex Others Neurod2 NeuroD2 antibody, Abcam, cat#:ab109406, lot#:YK010204CS mouse embryonic cortex Others Neurod2 NeuroD2 antibody, vendor:Abcam, cat#:ab104430, lot#:GR94291-1 mouse embryonic cortex Others Neurod2 NeuroD2 antibody, vendor:Abcam, cat#:ab168932, lot#:GR161014-2 mouse embryonic cortex RNA polymerase RNA polymerase II anti-RNAP II(8WG16), Covance(MMS-126R) the corresponding 2nd iPS cell line RNA polymerase RNA polymerase II anti-RNAP II(8WG16), Covance(MMS-126R) reprogrammed cells after 15days induction and 3days dox-withdrawl treatment RNA polymerase RNA polymerase II anti-RNAP II(8WG16), Covance(MMS-126R) reprogramming intermediate after 15days of induction RNA polymerase RNA polymerase II anti-RNAP II(8WG16), Covance(MMS-126R) reprogramming intermediate after 11days of induction RNA polymerase RNA polymerase II anti-RNAP II(8WG16), Covance(MMS-126R) reprogramming intermediate after 7days of induction RNA polymerase RNA polymerase II anti-RNAP II(8WG16), Covance(MMS-126R) reprogramming intermediate after 5days of induction RNA polymerase RNA polymerase II anti-RNAP II(8WG16), Covance(MMS-126R) reprogramming intermediate after 3days of induction RNA polymerase RNA polymerase II anti-RNAP II(8WG16), Covance(MMS-126R) reprogramming intermediate after 24hour of induction RNA polymerase RNA polymerase II anti-RNAP II(8WG16), Covance(MMS-126R) 2nd mouse embryonic fibroblasts prior to induction Histone H3K27me3 anti-H3K27me3, Millipore(07-449) the corresponding 2nd iPS cell line Histone H3K27me3 anti-H3K27me3, Millipore(07-449) reprogrammed cells after 15days induction and 3days dox-withdrawl treatment Histone H3K27me3 anti-H3K27me3, Millipore(07-449) reprogramming intermediate after 15days of induction Histone H3K27me3 anti-H3K27me3, Millipore(07-449) reprogramming intermediate after 11days of induction Histone H3K27me3 anti-H3K27me3, Millipore(07-449) reprogramming intermediate after 7days of induction Histone H3K27me3 anti-H3K27me3, Millipore(07-449) reprogramming intermediate after 5days of induction Histone H3K27me3 anti-H3K27me3, Millipore(07-449) reprogramming intermediate after 3days of induction Histone H3K27me3 anti-H3K27me3, Millipore(07-449) reprogramming intermediate after 24hour of induction Histone H3K27me3 anti-H3K27me3, Millipore(07-449) 2nd mouse embryonic fibroblasts prior to induction Histone H3K4me3 anti-H3K4me3, Abcam(Ab8580) the corresponding 2nd iPS cell line Histone H3K4me3 anti-H3K4me3, Abcam(Ab8580) reprogrammed cells after 15days induction and 3days dox-withdrawl treatment Histone H3K4me3 anti-H3K4me3, Abcam(Ab8580) reprogramming intermediate after 15days of induction Histone H3K4me3 anti-H3K4me3, Abcam(Ab8580) reprogramming intermediate after 11days of induction Histone H3K4me3 anti-H3K4me3, Abcam(Ab8580) reprogramming intermediate after 7days of induction Histone H3K4me3 anti-H3K4me3, Abcam(Ab8580) reprogramming intermediate after 5days of induction Histone H3K4me3 anti-H3K4me3, Abcam(Ab8580) reprogramming intermediate after 3days of induction Histone H3K4me3 anti-H3K4me3, Abcam(Ab8580) reprogramming intermediate after 24hour of induction Histone H3K4me3 anti-H3K4me3, Abcam(Ab8580) 2nd mouse embryonic fibroblasts prior to induction Histone H3K27ac anti-H3K27ac, Abcam(Ab4729) the corresponding 2nd iPS cell line Histone H3K27ac anti-H3K27ac, Abcam(Ab4729) reprogrammed cells after 15days induction and 3days dox-withdrawl treatment Histone H3K27ac anti-H3K27ac, Abcam(Ab4729) reprogramming intermediate after 15days of induction Histone H3K27ac anti-H3K27ac, Abcam(Ab4729) reprogramming intermediate after 11days of induction Histone H3K27ac anti-H3K27ac, Abcam(Ab4729) reprogramming intermediate after 7days of induction Histone H3K27ac anti-H3K27ac, Abcam(Ab4729) reprogramming intermediate after 5days of induction Histone H3K27ac anti-H3K27ac, Abcam(Ab4729) reprogramming intermediate after 3days of induction Histone H3K27ac anti-H3K27ac, Abcam(Ab4729) reprogramming intermediate after 24hour of induction Histone H3K27ac anti-H3K27ac, Abcam(Ab4729) 2nd mouse embryonic fibroblasts prior to induction Histone H3K4me1 anti-H3K4me1, Abcam(Ab8895) the corresponding 2nd iPS cell line Histone H3K4me1 anti-H3K4me1, Abcam(Ab8895) reprogrammed cells after 15days induction and 3days dox-withdrawl treatment Histone H3K4me1 anti-H3K4me1, Abcam(Ab8895) reprogramming intermediate after 15days of induction Histone H3K4me1 anti-H3K4me1, Abcam(Ab8895) reprogramming intermediate after 11days of induction Histone H3K4me1 anti-H3K4me1, Abcam(Ab8895) reprogramming intermediate after 7days of induction Histone H3K4me1 anti-H3K4me1, Abcam(Ab8895) reprogramming intermediate after 5days of induction Histone H3K4me1 anti-H3K4me1, Abcam(Ab8895) reprogramming intermediate after 3days of induction Histone H3K4me1 anti-H3K4me1, Abcam(Ab8895) reprogramming intermediate after 24hour of induction Histone H3K4me1 anti-H3K4me1, Abcam(Ab8895) 2nd mouse embryonic fibroblasts prior to induction Input control Input control none the corresponding 2nd iPS cell line Input control Input control none reprogrammed cells after 15days induction and 3days dox-withdrawl treatment Input control Input control none reprogramming intermediate after 15days of induction Input control Input control none reprogramming intermediate after 11days of induction Input control Input control none reprogramming intermediate after 7days of induction Input control Input control none reprogramming intermediate after 5days of induction Input control Input control none reprogramming intermediate after 3days of induction Input control Input control none reprogramming intermediate after 24hour of induction Input control Input control none 2nd mouse embryonic fibroblasts prior to induction Others Pou5f1 anti-Oct4, Santa Cruz(Sc-8628X) the corresponding 2nd iPS cell line Others Pou5f1 anti-Oct4, Santa Cruz(Sc-8628X) reprogrammed cells after 15days induction and 3days dox-withdrawl treatment Others Pou5f1 anti-Oct4, Santa Cruz(Sc-8628X) reprogramming intermediate after 15days of induction Others Pou5f1 anti-Oct4, Santa Cruz(Sc-8628X) reprogramming intermediate after 11days of induction Others Pou5f1 anti-Oct4, Santa Cruz(Sc-8628X) reprogramming intermediate after 7days of induction Others Pou5f1 anti-Oct4, Santa Cruz(Sc-8628X) reprogramming intermediate after 5days of induction Others Pou5f1 anti-Oct4, Santa Cruz(Sc-8628X) reprogramming intermediate after 3days of induction Others Pou5f1 anti-Oct4, Santa Cruz(Sc-8628X) reprogramming intermediate after 24hour of induction Others Pou5f1 anti-Oct4, Santa Cruz(Sc-8628X) 2nd mouse embryonic fibroblasts prior to induction Others Epitope tags anti-Flag-M2, Sigma(F1804) reprogrammed cells after 15days induction and 3days dox-withdrawl treatment Others Epitope tags anti-Flag-M2, Sigma(F1804) reprogramming intermediate after 15days of induction Others Epitope tags anti-Flag-M2, Sigma(F1804) reprogramming intermediate after 11days of induction Others Epitope tags anti-Flag-M2, Sigma(F1804) reprogramming intermediate after 7days of induction Others Epitope tags anti-Flag-M2, Sigma(F1804) reprogramming intermediate after 5days of induction Others Epitope tags anti-Flag-M2, Sigma(F1804) reprogramming intermediate after 3days of induction Others Epitope tags anti-Flag-M2, Sigma(F1804) reprogramming intermediate after 24hour of induction Others Epitope tags anti-Flag-M2, Sigma(F1804) 2nd mouse embryonic fibroblasts prior to induction Input control Input control Input. Lin- HSC Others Runx1 Runx1 Nave splenic CD4+ T-cells Others Ets1 Ets1 Blast-cultured splenic CD4+ T-cells Others Ets1 Ets1 Nave splenic CD4+ T-cells Histone H3K4me2 H3K4me2 Blast-cultured splenic CD4+ T-cells Histone H3K4me2 H3K4me2 Nave splenic CD4+ T-cells Histone H3K36me3 Anti-H3K36me3 (AB9050, Abcam, Cambridge, MA and UK) B-lymphoid clonal cell line Abl1 / S1Cs-A5 Histone H3K27me3 Anti-H3K27me3 (ABE44 Millipore, Billerica, MA) B-lymphoid clonal cell line Abl1 / S1Cs-A5 Input control Input control none B-lymphoid clonal cell line Abl1 / S1Cs-A5 Input control Input control none Cortex Others Mecp2 Total MeCP2 antibody (Chen et al. 2003) Cortex Input control Input control none (input) chondrocytes Histone H3K27me3 H3K27Me3 (Cell signaling technologies # 9733) chondrocytes Input control Input control none (input) Cultured ProB Others Smarca4 Brg1 (Millipore, catalog# 07-478, lot# DAM1776465) Cultured ProB Others Ikzf1 Ikaros (Ik-C, rabbit antibody (kind gift of S.Smale)) Cultured PreProB Others Ikzf1 Ikaros (Ik-C, rabbit antibody (kind gift of S.Smale)) Cultured ProB Histone H3K27me3 H3K27me3 (Millipore, #07-449, lot# 1959680) newborn lens, H3K27me3 ChIP Histone H3K27me3 H3K27me3 (Millipore, #07-449, lot# 1959680) e12.5 embryonic forebrain, H3K27me3 ChIP RNA polymerase RNA polymerase II RNA polymerase II (Abcam, ab817, lot# GR153063-402) newborn lens, Pol2 ChIP RNA polymerase RNA polymerase II RNA polymerase II (Abcam, ab817, lot# GR153063-402) e12.5 embryonic forebrain, Pol2 ChIP Histone H3K27ac H3K27ac (Millipore, #07-360, lot# 961080) newborn lens, H3K27ac ChIP Histone H3K27ac H3K27ac (Millipore, #07-360, lot# 961080) e12.5 embryonic forebrain, H3K27ac ChIP Histone H3K4me3 H3K4me3 (Abcam, ab8580, lot# GR152121-1) newborn lens, H3K4me3 ChIP Histone H3K4me3 H3K4me3 (Abcam, ab8580, lot# GR152121-1) e12.5 embryonic forebrain, H3K4me3 ChIP Histone H3K4me1 H3K4me1 (Abcam, ab8895, lot# GR61280-1) newborn lens, H3K4me1 ChIP Histone H3K4me1 H3K4me1 (Abcam, ab8895, lot# GR61280-1) e12.5 embryonic forebrain, H3K4me1 ChIP Others Pax6 Pax6 (Millipore, ab2237, lot# NG1731333) newborn lens, Pax6 ChIP Histone H3K36me3 ab9050 (Abcam) embryonic testes FACS-sorted cells Input control Input control N/A embryonic testes FACS-sorted cells Histone H3K27me3 anti-H3K27me3 (Upstate 07-449, lot# 2455635) EED-null ES cells, H3K27me3 ChIP, Upstate antibody Histone H3K27me3 anti-H3K27me3 (Abcam 6002, lot# GR130002-1) EED-null ES cells, H3K27me3 ChIP, Abcam antibody Input control Input control none EED-null ES cells, input Histone H3K27me3 anti-H3K27me3 (Upstate 07-449, lot# 2455635) WT ES cells, H3K27me3 ChIP, Upstate antibody Histone H3K27me3 anti-H3K27me3 (Abcam 6002, lot# GR130002-1) WT ES cells, H3K27me3 ChIP, Abcam antibody Input control Input control none WT ES cells, input Input control Input control normal rabbit IgG C2C12 cells Input control Input control none Flt3L cultured dendritic cells Input control Input control total input RAW264.7 cell line (macrophages) Others Gps2 GPS2 C-terminal (home raised) RAW264.7 cell line (macrophages) Input control Input control total input Bone marrow derived macrophages Input control Input control Normal Mouse IgG (Millipore 12-371) Embryonic stem cells Others Epitope tags Flag (Sigma F1804) Embryonic stem cells Histone H3K27ac H3K27ac (ab4729, Abcam) MBD3-/- ES Others Pou5f1 Oct4 (sc5279(C-10), Santa Cruz) MBD3flox/- iPSC Histone H3K27ac H3K27ac (ab4729, Abcam) MBD3flox/- iPSC Others Pou5f1 Oct4 (sc5279(C-10), Santa Cruz) MBD3flox/- 8 days after dox induction Histone H3K27ac H3K27ac (ab4729, Abcam) MBD3flox/- 8 days after dox induction Others Pou5f1 Oct4 (sc5279(C-10), Santa Cruz) MBD3flox/- 4 days after dox induction Histone H3K27ac H3K27ac (ab4729, Abcam) MBD3flox/- 4 days after dox induction Others Pou5f1 Oct4 (sc5279(C-10), Santa Cruz) WT iPSC Histone H3K27ac H3K27ac (ab4729, Abcam) WT iPSC Histone H3K27ac H3K27ac (ab4729, Abcam) WT 8 days after dox induction Others Pou5f1 Oct4 (sc5279(C-10), Santa Cruz) WT 4 days after dox induction Histone H3K27ac H3K27ac (ab4729, Abcam) WT 4 days after dox induction Others Pou5f1 Oct4 (sc5279(C-10), Santa Cruz) MBD3flox/- MEF Histone H3K27ac H3K27ac (ab4729, Abcam) MBD3flox/- MEF Others Pou5f1 Oct4 (sc5279(C-10), Santa Cruz) WT MEF Histone H3K27ac H3K27ac (ab4729, Abcam) WT MEF Others Myo1c NM1 Mouse Embryonic Fibroblasts Others Ncor2 NCOR2 (PA1-843) (Thermo Scientific) Bone-marrow derived macrophages Others Hdac3 HDAC3 (sc-11417) (Santa Cruz Biotechnology) Bone-marrow derived macrophages RNA polymerase RNA polymerase II anti-Pol II (sc899-x, Santa Cruz Biotechnology) embryonic fibroblasts, HSV-1 infection, Pol II ChIP RNA polymerase RNA polymerase II anti-Pol II (sc899-x, Santa Cruz Biotechnology) embryonic fibroblasts, mock infection, Pol II ChIP RNA polymerase RNA polymerase II anti-RNA polymerase II (Millipore, 04-1572) splenic B cells Others Pml anti-PML (Millipore, catalog# 05-718, lot# 2684855) Mouse embryonic fibroblasts, wild-type Histone H3K9me3 anti-H3K9me3 (Diagenode, catalog# 068-050, lot# A1675-001P) Mouse embryonic fibroblasts, wild-type Histone H3K27me3 anti-H3K27me3 (Diagenode, catalog# 056-050, lot# A299-00242) Mouse embryonic fibroblasts, wild-type Others Epitope tags anti-Flag (Sigma, catalog# F-1804, lot# 124K6106) Mouse embryonic fibroblasts, wild-type Histone H3 anti-H3 (Abcam, catalog# ab1791) Mouse embryonic fibroblasts, wild-type Histone H3K9me3 anti-H3K9me3 (Diagenode, catalog# 068-050, lot# A1675-001P) Mouse embryonic fibroblasts, PML knock-out Histone H3K27me3 anti-H3K27me3 (Diagenode, catalog# 056-050, lot# A299-00242) Mouse embryonic fibroblasts, PML knock-out Others Epitope tags anti-Flag (Sigma, catalog# F-1804, lot# 124K6106) Mouse embryonic fibroblasts, PML knock-out Histone H3 anti-H3 (Abcam, catalog# ab1791) Mouse embryonic fibroblasts, PML knock-out Input control Input control none NIH3T3 cells Input control Input control none TAL transgenic/HEB heterozygous with Notch truncations (provided by I.Aifantis, NYU) Input control Input control none pro B-Cell Others Spi1 Pu.1 (SC-352, Santa Cruz) Bcr-Abl transformed p19Arf null B-ALL Others Spi1 Pu.1 (#2266, Cell Signaling) Bcr-Abl transformed p19Arf null B-ALL Input control Input control wild type anti-GFP input Others GFP GFP Tag Antibody (3E6) wild type anti-GFP ChIP Histone H3K27ac H3K27ac (Abcam, ab4729) 8946: H3K27ac Chromatin IP Histone H3K27me3 H3K27me3 (Millipore #07-449) 8946: H3K27me3 Chromatin IP Histone H3K4me3 H3K4me3 (Millipore, 07-473) 8946: H3K4me3 Chromatin IP Histone H3K4me1 H3K4me1 (Abcam, ab8895) 8946: H3K4me1 Chromatin IP Others Rbpj Rbpj (Cell Signaling Technology, 5313) 8946: Rbpj Chromatin IP Others Zmiz1 HA (Abcam, ab9110) 8946: HA-Zmiz1 Chromatin IP Others Zmiz1 Flag (F1804, Sigma) 8946: Flag-Zmiz1 Chromatin IP Others Ep300 p300 (sc-584; Santa Cruz) MLL-AF9/NrasG12D murine cell line Input control Input control none CGR8 ESC Unclassified Unclassified M2 beads (Sigma: M8823) CGR8 ESC Others Smarca4 anti-BRG1 (SMARCA4) antibody 3134 cells Input control Input control anti-IgG (Jackson ImmunoResearch, catalog# 011-000-003, lot# 79330) placenta tissue embryonic day 17.5 (E17.5) Others Grhl2 anti-Grhl2 (Sigma Aldrich, catalog# HPA004820, lot# A35809) placenta tissue embryonic day 17.5 (E17.5) Histone H3K9me3 H3K9me3(ab8898, Abcam) CGR8 Histone H3K27ac H3K27ac (ab4729, Abcam) CGR8 Histone H3K4me3 H3K4me3 (ab8580, Abcam) CGR8 Others GFP anti GFP antibody (made by David Drechsel lab at MPI-CBG Dresden, Germany) ES cells Others Sirt6 Sirt6 (Cell Signaling Technology, 12486 in a ratio of 5ml/2e7 cells) Embryonic stem cells (ESCs) Others Myc Myc (Santa Cruz; sc-764 X, lot# D2314) Intestinal villus cells, wild type, Myc ChIP Others E2f3 E2f3 (Santa Cruz; sc-878 X, lot# E1712) Intestinal villus cells, wild type, E2f3 ChIP Others Myc Myc (Santa Cruz; sc-764 X, lot# D2314) Intestinal crypt cells, wild type, Myc ChIP Others E2f3 E2f3 (Santa Cruz; sc-878 X, lot# E1712) Intestinal crypt cells, wild type, E2f3 ChIP Others Myc Myc (Santa Cruz; sc-764 X, lot# D2314) Intestinal villus cells, Rb KO, Myc ChIP Others E2f3 E2f3 (Santa Cruz; sc-878 X, lot# E1712) Intestinal villus cells, Rb KO, E2f3 ChIP Others Myc Myc (Santa Cruz; sc-764 X, lot# D2314) Intestinal crypt cells, Rb KO, Myc ChIP Others E2f3 E2f3 (Santa Cruz; sc-878 X, lot# E1712) Intestinal crypt cells, Rb KO, E2f3 ChIP Others Tgif2 streptavidin-conjugated beads (life technology, 64601). J1 ES cells containing BirA_Tgif2_ChIPSeq Input control Input control none embryonic stem cells (RA, day1) 46C mES cells Input control Input control none embryonic stem cells Haunt P-exon2 KO mES cells Others Zfp217 Zfp217 CCE Unclassified Unclassified CCE Histone H3.3 Histone H3.3 (Abcam, ab62642) Embryonic Stem Cells Input control Input control None (input) Mouse Embryonic day 14.5 Fetal Liver Histone H3K9me3 H3K9me3 Diagenode (pAb-056-050) C2C12 Others Rnf2 anti-Ring1b (Home made) IntestineStemCells Input control Input control input IntestineStemCells Histone H2AK119Ub anti-H2AK119 (Cell signaling, catalog 8240S and lot2) IntestineStemCells Others Rnf2 anti-Ring1b (Home made) Crypt Input control Input control input Crypt Histone H2AK119Ub anti-H2AK119 (Cell signaling, catalog 8240S and lot2) Crypt Unclassified Unclassified Mammary tissues Others Jmjd1c Jmjd1c embryonic stem cells Others Supt16 Spt16 embryonic stem cells Others Epitope tags V5 (Abcam ab15828) perfused primary hepatocytes Others Notch1 Anti-Notch1 antibody - ChIP Grade mitochondrial DNA (mtDNA) Raw 264.7_mtDNA Unclassified Unclassified mitochondrial DNA (mtDNA) Raw 264.7_mtDNA Others Notch1 Anti-Notch1 antibody - ChIP Grade nuclear genomic DNA Raw 264.7_nuclear DNA Unclassified Unclassified nuclear genomic DNA Raw 264.7_nuclear DNA Others Jun c-Jun mouse embryonic fibroblasts (MEFs) Input control Input control input mouse embryonic stem cells(mESCs) Others Jun c-Jun mouse embryonic stem cells(mESCs) Others Pou5f1 4-Oct Abcam ab19857 mouse embryonic stem cells (E14) Input control Input control none Mouse ESCs, input Others Cbx1 HP1 (Euromedex 1MOD-1A9-AS, lot# 091809) Mouse ESCs, HP1 ChIP Others Myod1 MyoD antibody 6975 Negative control. ChIP-Seq with MyoD antibody 6975 in mouse P19 cells Others Neurod2 NeuroD2 antibody 1240 Negative control. ChIP-Seq with NeuroD2 antibody 1240 in mouse P19 cells Others Neurod2 NeuroD2 antibody 1240 ChIP-Seq with NeuroD2 antibody 1240 in mouse P19 cells transduced with NeuroD2 Others Neurod2 NeuroD2 antibody 1165 ChIP-Seq with NeuroD2 antibody 1165 in mouse P19 cells transduced with NeuroD2 Others Myod1 MyoD antibody 6975 ChIP-Seq with MyoD antibody 6975 in mouse P19 cells transduced with MD(ND2bHLH)WCS mutant Others Myod1 MyoD antibody 6196 ChIP-Seq with MyoD antibody 6196 in mouse P19 cells transduced with MD(ND2bHLH)WCS mutant Others Myod1 MyoD antibody 6975 ChIP-Seq with MyoD antibody 6975 in mouse P19 cells transduced with MD(ND2bHLH)WC mutant Others Myod1 MyoD antibody 6196 ChIP-Seq with MyoD antibody 6196 in mouse P19 cells transduced with MD(ND2bHLH)WC mutant Others Myod1 MyoD antibody 6975 ChIP-Seq with MyoD antibody 6975 in mouse P19 cells transduced with MD(ND2bHLH) chimera Others Myod1 MyoD antibody 6196 ChIP-Seq with MyoD antibody 6196 in mouse P19 cells transduced with MD(ND2bHLH) chimera Others Myod1 MyoD antibody 6975 ChIP-Seq with MyoD antibody 6975 in mouse P19 cells transduced with MyoD Others Myod1 MyoD antibody 6196 ChIP-Seq with MyoD antibody 6196 in mouse P19 cells transduced with MyoD Histone H3K27me3 H3K27me3 (Diagenode, pAb-069-050) Plasmacytoid dendritic cell (pDC) Histone H3K27me3 H3K27me3 (Diagenode, pAb-069-050) Classical dendritic cell (cDC) Histone H3K27me3 H3K27me3 (Diagenode, pAb-069-050) Common dendritic cell progenitor (CDP) Histone H3K27me3 H3K27me3 (Diagenode, pAb-069-050) Multipotent progenitor (MPP) Histone H3K9me3 H3K9me3 (Diagenode, pAb-056-050) Plasmacytoid dendritic cell (pDC) Histone H3K9me3 H3K9me3 (Diagenode, pAb-056-050) Classical dendritic cell (cDC) Histone H3K9me3 H3K9me3 (Diagenode, pAb-056-050) Common dendritic cell progenitor (CDP) Histone H3K9me3 H3K9me3 (Diagenode, pAb-056-050) Multipotent progenitor (MPP) Histone H3K4me3 H3K4me3 (Diagenode, pAb-003-050) Plasmacytoid dendritic cell (pDC) Histone H3K4me3 H3K4me3 (Diagenode, pAb-003-050) Classical dendritic cell (cDC) Histone H3K4me3 H3K4me3 (Diagenode, pAb-003-050) Common dendritic cell progenitor (CDP) Histone H3K4me3 H3K4me3 (Diagenode, pAb-003-050) Multipotent progenitor (MPP) RNA polymerase RNA polymerase II Pol II Antibody (N-20) primary Rag2 -/- thymocytes Others Runx1 RUNX1/ETO myeloid progenitors _expansion cells Others Runx1 RUNX1/ETO Floating progenitors cells Unclassified Unclassified D3.75 Bry+ cells 48h+Dox Unclassified Unclassified D3.75 Bry+ cells 48h-Dox Input control Input control IgG (normal rabbit) Mnase-dY-Tam-IgG Input control Input control IgG (normal rabbit) Mnase-dY-EtOH-IgG Input control Input control IgG (normal rabbit) Mnase-R-Tam-IgG Input control Input control IgG (normal rabbit) Mnase-R-EtOH-IgG Input control Input control IgG (normal rabbit) dY-Tam-IgG Input control Input control IgG (normal rabbit) dY-EtOH-IgG Input control Input control IgG (normal rabbit) R-Tam-IgG Input control Input control IgG (normal rabbit) R-EtOH-IgG Others Epitope tags M2 anti-Flag dY-E2-Flag Others Epitope tags M2 anti-Flag dY-FCKO-Flag Others Epitope tags M2 anti-Flag R-E2-Flag Others Epitope tags M2 anti-Flag R-FCKO-Flag Others Aff3 Aff3 (Homemade#13) ES cell culture Others Tbx19 anti-TBX19 (HPA005800, Sigma-Aldrich) AtT20 cells Histone H3K4me1 anti-H3K4me1 (07-436, Millipore) AtT20 cells Histone H3K27ac anti-H3K27ac (b4729, Abcam) AtT20 cells Others Ep300 anti-P300 (sc585) AtT20 cells Others Zic3 Zic3 (Abcam, ab80966) ES cell culture Others Nr3c1 anti-GR antibody 129_eWAT_chow_GR Others Nr3c1 anti-GR antibody B6_eWAT_chow_GR Others Nr3c1 anti-GR antibody 129_iWAT_chow_GR Others Nr3c1 anti-GR antibody B6_iWAT_chow_GR Input control Input control anti-PPAR? antibody input_F1_iWAT_gsnap Input control Input control anti-PPAR? antibody input_129_iWAT_gsnap Input control Input control anti-PPAR? antibody input_B6_iWAT_gsnap Others Pparg anti-PPAR? antibody 3T3L1 Others Pparg anti-PPAR? antibody F1_iWAT_chow Others Pparg anti-PPAR? antibody 129_iWAT_chow Others Pparg anti-PPAR? antibody B6_iWAT_chow Others Mycn B8.4.B (sc-53993, Lot#D0214) SHH-medulloblastoma Unclassified Unclassified 10E2 SHH-medulloblastoma Input control Input control none (input) SHH-medulloblastoma Others Mycn B8.4.B (sc-53993, Lot#D0214) G3-medulloblastoma Others Myc N262 (sc-764) G3-medulloblastoma Others Gata1 MigR1-HA-Gata1 G1ME cells Others Gata1 MigR1-HA-Gata1s anti-HA G1ME cells Others Gata1 MigR1-HA-Gata1 anti-HA G1ME cells Others Kdm2b V5-Fbxl10 D2_V5_Fbxl10-1_peaks Others Rnf2 RING1B D2_RING1B_Fbxl10_Exp.2 Others Rnf2 RING1B D2_RING1B_Fbxl10_Exp.1 Others Rnf2 RING1B D2_RING1B_dFbox_Exp.2 Others Rnf2 RING1B D2_RING1B_dFbox_Exp.1 Others Rnf2 RING1B D2_RING1B_Empty_Exp.2 Others Rnf2 RING1B D2_RING1B_Empty_Exp.1 Input control Input control none sciatic nerve Histone H3K27me3 H3K27me3 Millipore 07-449, Lot#2064519 sciatic nerve Histone H3K4me3 anti-H3K4me3 p30-GMP-blast cells Others Cebpa anti-CEBPA p30-GMP-blast cells Histone H3K79me2 H3K79me2 (Abcam, 3594, lot GR173874-1) Embryonic stem cells Histone H3K36me3 H3K36me3 (Abcam, 9050, lot GR165936-1 Embryonic stem cells Histone H3K27me3 H3K27me3 (Millipore, 07-449, lot 2275589) Embryonic stem cells Histone H3K9me3 H3K9me3 (Hattori T. et al. 309M3A, lot 3) Embryonic stem cells Histone H3K4me3 H3K4me3 (Active Motif, 39159, lot 12613005) Embryonic stem cells Input control Input control none embryonic flank Histone H3K27ac H3K27ac (Millipore, catalog# 05-1334, lot# NG1948294) embryonic flank Input control Input control none embryonic genital tubercle Input control Input control none embryonic forelimb Others Rad23b RAD23B murine embryonic stem cells Input control Input control IgG murine embryonic stem cells Input control Input control none mouse embryonic stem cells E14 Others Cbx7 ab21873, Abcam mouse embryonic stem cells E14 Others Rnf2 39663, Active Motif Neural progenitor cells Input control Input control None Spleen red pulp macrophages Input control Input control None Neutrophils Input control Input control None Monocytes Input control Input control None Peritoneal cavity macrophages Input control Input control None Lung macrophages Input control Input control None Small intestine macrophages Input control Input control None Large intestine macrophages Input control Input control None Kupffer cells Input control Input control None Brain microglia Unclassified Unclassified Wildtype BAT Histone H3K27ac H3K27ac (Abcam ab4729) Prdm16 Knockout BAT Histone H3K27ac H3K27ac (Abcam ab4729) Wildtype BAT Others Med1 Med1(Bethyl A300-793A) Prdm16 Knockout BAT Others Med1 Med1(Bethyl A300-793A) Wildtype BAT RNA polymerase RNA polymerase II PolII (Santa Cruz sc-899 or sc-9001) Prdm16 Knockout BAT RNA polymerase RNA polymerase II PolII (Santa Cruz sc-899 or sc-9001) Wildtype BAT RNA polymerase RNA polymerase II PolII (Santa Cruz sc-899, sc-9001) Epididymal white adipose tissue RNA polymerase RNA polymerase II PolII (Santa Cruz sc-899, sc-9001) Brown adipose tissue Histone H3K27ac H3K27ac (Abcam ab4729) Epididymal white adipose tissue Input control Input control none Non-neuronal nuclei from 10 month old APP/PS1-21 SAHA-treated animals Input control Input control none Non-neuronal nuclei from 10 month old APP/PS1-21 vehicle-treated animals Input control Input control none Non-neuronal nuclei from 10 month old vehicle-treated WT littermates of APP/PS1-21 animals Input control Input control none Neuronal nuclei from 10 month old APP/PS1-21 SAHA-treated animals Input control Input control none Neuronal nuclei from 10 month old APP/PS1-21 vehicle-treated animals Input control Input control none Neuronal nuclei from 10 month old vehicle-treated WT littermates of APP/PS1-21 animals Histone H4K12ac Anti-Histone H4 (acetyl K12) antibody (Abcam, catalog# ab61238, lot# GR38757-5) Non-neuronal nuclei from 10 month old APP/PS1-21 SAHA-treated animals Histone H4K12ac Anti-Histone H4 (acetyl K12) antibody (Abcam, catalog# ab61238, lot# GR38757-5) Non-neuronal nuclei from 10 month old APP/PS1-21 vehicle-treated animals Histone H4K12ac Anti-Histone H4 (acetyl K12) antibody (Abcam, catalog# ab61238, lot# GR38757-5) Non-neuronal nuclei from 10 month old vehicle-treated WT littermates of APP/PS1-21 animals Histone H4K12ac Anti-Histone H4 (acetyl K12) antibody (Abcam, catalog# ab61238, lot# GR38757-5) Neuronal nuclei from 10 month old APP/PS1-21 SAHA-treated animals Histone H4K12ac Anti-Histone H4 (acetyl K12) antibody (Abcam, catalog# ab61238, lot# GR38757-5) Neuronal nuclei from 10 month old APP/PS1-21 vehicle-treated animals Histone H4K12ac Anti-Histone H4 (acetyl K12) antibody (Abcam, catalog# ab61238, lot# GR38757-5) Neuronal nuclei from 10 month old vehicle-treated WT littermates of APP/PS1-21 animals Input control Input control none Non-neuronal nuclei from 20 month old SAHA-treated animals Input control Input control none Non-neuronal nuclei from 20 month old vehicle-treated animals Input control Input control none Non-neuronal nuclei from 3 month old vehicle-treated animals Input control Input control none Neuronal nuclei from 20 month old SAHA-treated animals Input control Input control none Neuronal nuclei from 20 month old vehicle-treated animals Input control Input control none Neuronal nuclei from 3 month old vehicle-treated animals Histone H4K12ac Anti-Histone H4 (acetyl K12) antibody (Abcam, catalog# ab61238, lot# GR38757-5) Non-neuronal nuclei from 20 month old SAHA-treated animals Histone H4K12ac Anti-Histone H4 (acetyl K12) antibody (Abcam, catalog# ab61238, lot# GR38757-5) Non-neuronal nuclei from 20 month old vehicle-treated animals Histone H4K12ac Anti-Histone H4 (acetyl K12) antibody (Abcam, catalog# ab61238, lot# GR38757-5) Non-neuronal nuclei from 3 month old vehicle-treated animals Histone H4K12ac Anti-Histone H4 (acetyl K12) antibody (Abcam, catalog# ab61238, lot# GR38757-5) Neuronal nuclei from 20 month old SAHA-treated animals Histone H4K12ac Anti-Histone H4 (acetyl K12) antibody (Abcam, catalog# ab61238, lot# GR38757-5) Neuronal nuclei from 20 month old vehicle-treated animals Histone H4K12ac Anti-Histone H4 (acetyl K12) antibody (Abcam, catalog# ab61238, lot# GR38757-5) Neuronal nuclei from 3 month old vehicle-treated animals Input control Input control input_LPS(120') Input control Input control input_unstimulated Histone H3K18cr H3K18Cr_LPS(120') Histone H3K18cr H3K18Cr_unstimulated Histone H3K18ac H3K18Ac_LPS(120') Histone H3K18ac H3K18Ac_unstimulated Input control Input control input Bone marrow derived macrophage- stimulated 240' Input control Input control input Bone marrow derived macrophage- stimulated 120' Input control Input control input Bone marrow derived macrophage- stimulated 60' Input control Input control input Bone marrow derived macrophage- stimulated 30' Input control Input control input Bone marrow derived macrophage- unstimulated Input control Input control input Bone marrow derived macrophage- unstimulated/DMSO treated Histone H3S28ph H3S28ph Bone marrow derived macrophage- stimulated 240' Histone H3S28ph H3S28ph Bone marrow derived macrophage- stimulated 180' Histone H3S28ph H3S28ph Bone marrow derived macrophage- stimulated 120' Histone H3S28ph H3S28ph Bone marrow derived macrophage- stimulated 60' Histone H3S28ph H3S28ph Bone marrow derived macrophage- stimulated 30' Histone H3S28ph H3S28ph Bone marrow derived macrophage- unstimulated Histone H3S28ph H3S28ph Bone marrow derived macrophage- unstimulated/DMSO treated Histone H3K27ac H3K27ac Bone marrow derived macrophage- stimulated 240' Histone H3K27ac H3K27ac Bone marrow derived macrophage- stimulated 120' Histone H3K27ac H3K27ac Bone marrow derived macrophage- stimulated 60' Histone H3K27ac H3K27ac Bone marrow derived macrophage- stimulated 30' Histone H3K27ac H3K27ac Bone marrow derived macrophage- unstimulated Input control Input control input mouse saline NAc ChIP input Input control Input control input mouse cocaine NAc ChIP input Histone H3K27ac H3K27ac Double Positive thymocytes Histone H3K9me3 H3K9me3 Double Positive thymocytes Input control Input control none (input) Differentiated C2C12 cells Others Myod1 MyoD (Santa Cruz, sc-760) Differentiated C2C12 cells Histone H3K4me3 H3K4me3 (Abcam ab8580) Differentiated C2C12 cells Histone H3K4me2 H3K4me2 (Abcam ab7766) Differentiated C2C12 cells Input control Input control none (input) Undifferentiated C2C12 cells Others Myod1 MyoD (Santa Cruz, sc-760) Undifferentiated C2C12 cells Histone H3K4me3 H3K4me3 (Abcam ab8580) Undifferentiated C2C12 cells Histone H3K4me2 H3K4me2 (Abcam ab7766) Undifferentiated C2C12 cells Others Srebf1 SREBP-1 sc-13551, sc-8984, sc-367 Primary thioglycollate-elicited peritoneal macrophages Others Pparg PPARg sc-7196, sc-1984 Primary thioglycollate-elicited peritoneal macrophages Others Rxra RXR sc-553, sc-774 Primary thioglycollate-elicited peritoneal macrophages Input control Input control none mouse hippocampus Others Neurog2 anti-Neurog2, non-commercial: a gift of Prof. Yongchao Ma, Chicago E14.5 cerebral cortices Others Eomes anti-Tbr2, Chemicon cat.no AB9618 E14.5 cerebral cortices Input control Input control none (input) E14.5 cerebral cortices Histone H3ac Anti-acetyl-Histone H3 TAC TSA H3Ac Histone H3ac Anti-acetyl-Histone H3 TAC Veh H3Ac Histone H3ac Anti-acetyl-Histone H3 Sham TSA H3Ac Histone H3ac Anti-acetyl-Histone H3 Sham Veh H3Ac Others Epitope tags Flag-M2 (Sigma Aldrich) E14 Histone H3K4me3 H3K4me3 P5424 H3K4me3 (KM) Histone H3K4me3 H3K4me3 P5424 H3K4me3 (DMSO) Histone H3K4me2 H3K4me2 P5424 H3K4me2 (KM) Histone H3K4me2 H3K4me2 P5424 H3K4me2 (DMSO) Histone H3K4me1 H3K4me1 P5424 H3K4me1 (KM) Histone H3K4me1 H3K4me1 P5424 H3K4me1 (DMSO) RNA polymerase RNA polymerase II RNA Pol II P5424 RNA Pol II (KM) RNA polymerase RNA polymerase II RNA Pol II P5424 RNA Pol II (DMSO) Input control Input control none (whole cell extract) Lung macrophages with CD45.1 mark Input control Input control none (whole cell extract) Kupffer cells with CD45.1 mark Input control Input control none (whole cell extract) Spleen red pulp macrophages with CD45.1 mark Input control Input control none (whole cell extract) Peritoneal cavity macrophages with CD45.1 mark Histone H3K27ac anti-H3K27ac Spleen red pulp macrophages Histone H3K4me2 anti-H3K4me2 Neutrophils Histone H3K4me2 anti-H3K4me2 Monocytes Histone H3K4me2 anti-H3K4me2 Lung macrophages Histone H3K4me2 anti-H3K4me2 Small intestine macrophages Histone H3K4me2 anti-H3K4me2 Large intestine macrophages Histone H3K4me2 anti-H3K4me2 Brain microglia Input control Input control Rabbit IgG (Sigma I5006) X18.1.1 AML cell line, empty vector, IgG ChIP Input control Input control Rabbit IgG (Sigma I5006) X18.1.1 AML cell line, PuER, IgG ChIP Histone H3K27ac H3K27Ac (Abcam ab4729) X18.1.1 AML cell line, empty vector, H3K27Ac ChIP Histone H3K27ac H3K27Ac (Abcam ab4729) X18.1.1 AML cell line, PuER, H3K27Ac ChIP Others Cebpa CEBPA (Santa Cruz sc61x) X18.1.1 AML cell line, empty vector, CEBPA ChIP Others Cebpa CEBPA (Santa Cruz sc61x) X18.1.1 AML cell line, PuER, CEBPA ChIP Others Spi1 Pu.1 (Santa Cruz sc352x) X18.1.1 AML cell line, empty vector, Pu.1 ChIP Others Spi1 Pu.1 (Santa Cruz sc352x) X18.1.1 AML cell line, PuER, Pu.1 ChIP Others Hand1 Hand1 ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells Others Pknox1 PREP-1 N-15 (Santa Cruz Biotechnology, sc-6245) ES cells Input control Input control NOT APPLICABLE Hematopoietic stem cells (HSC) Histone H3K4me1 Abcam ab8895 Hematopoietic stem cells (HSC) Histone H3K27ac Abcam ab4729 Hematopoietic stem cells (HSC) Histone H3K36me3 Millipore 07-549 Hematopoietic stem cells (HSC) Histone H3K9me1 H3K9me1, Ab8896 (Abcam) RA-treated WT ESC Histone H3K9me1 H3K9me1, Ab8896 (Abcam) WT ESC Histone H3K9me1 H3K9me1, Ab8896 (Abcam) RA-treated Mutant ESC Histone H3K9me1 H3K9me1, Ab8896 (Abcam) Mutant ESC Histone H3K9me2 H3K9me2, mAbcam 1220 WT ESC Histone H3K9me2 H3K9me, mAbcam 1220 WT ESC Unclassified Unclassified ES cells Histone H3K27me3 H3K27me3 pancreatic islet tumor Histone H3K4me3 H3K4me3 pancreatic islet tumor Input control Input control none (input) pancreatic islet tumor Others Sox2 anti-Sox2 (R&D Systems, Cat. # AF2018, Lot # KOY0112011) ES cells treated with TSA, Sox2 ChIP Others Hnrnpl ESC, hnRNP L, Adriamycin Others Hnrnpl ESC, hnRNP L, untreated RNA polymerase RNA polymerase II ESC, RNA Pol II, Adriamycin RNA polymerase RNA polymerase II ESC, RNA Pol II, untreated Histone H3K79me2 ESC, H3K79me2, Adriamycin Histone H3K79me2 ESC, H3K79me2, untreated Histone H3K27me3 ESC, H3K27me3, Adriamycin Histone H3K27me3 ESC, H3K27me3, untreated Histone H3K4me3 ESC, H3K4me3, Adriamycin Histone H3K4me3 ESC, H3K4me3, untreated Input control Input control IgG ckit and sca1 positive cells Others Usp16 anti-Usp16 ckit and sca1 positive cells Input control Input control none (input) burst-forming unit erythroid (BFU-E) Others Meis1 Meis1/2 (K830, K844) mouse optic cups_WT_ChIP Others Brd3 BRD3 sera G1E_BRD3 +GATA1 Others Brd3 BRD3 sera G1E_BRD3 G1E Histone H3K4me1 H3K4me1 MC_A12_pDC_sh-Irf8_K4me1 Histone H3K4me1 H3K4me1 MC_A10_cDC_sh-Cebpb_K4me1 Histone H3K4me1 H3K4me1 MC_A11_pDC_sh-control_K4me1 Histone H3K4me1 H3K4me1 MC_A09_cDC_sh-control_K4me1 Others Cebpb Cebpb pdc_cebpb Others Cebpb Cebpb cdc_cebpb Others Irf8 Irf8 pdc_irf8 Others Irf8 Irf8 cdc_irf8 Others Spi1 Pu.1 Sample_MC_12_pDC_pu1 Others Spi1 Pu.1 Sample_MC_05_cDC_pu1 Histone H3K27ac H3K27Ac 05_MC_in_vivo_pDC_K27Ac_1 Histone H3K27ac H3K27Ac 03_MC_moDC_K27Ac_1 Histone H3K27ac H3K27Ac 01_MC_moDC_K27Ac_1 Histone H3K4me3 H3K4me3 pdc_k4me3 Histone H3K4me3 H3K4me3 cdc_k4me3 Histone H3K4me1 H3K4me1 Sample_MC_16_InVivo_pDC_K4me1 Histone H3K4me1 H3K4me1 pdc_k4me1 Histone H3K4me1 H3K4me1 cdc_k4me1 Input control Input control none (input) ESC_Setdb1_KO_+Tam Histone H3K27me3 H3K27me3 (Millipore: 07-449) ESC_Setdb1_KO_+Tam Input control Input control none (input) ESC_Setdb1_KO_noTam Histone H3K27me3 H3K27me3 (Millipore: 07-449) ESC_Setdb1_KO_noTam Histone H3K9me3 H3K9me3 (Active Motif: 39161) ESC_Setdb1_KO_noTam Others Ar AR IP (Epitomics clone ER179(2)) Mouse Prostate, enzalutamide (30 mg/kg) oral gavage x 3 days Others Ar AR IP (Epitomics clone ER179(2)) Mouse Prostate, bicalutamide (30 mg/kg) oral gavage x 3 days Others Ar AR IP (Epitomics clone ER179(2)) Mouse Prostate, Castration 3 days prior Others Ar AR IP (Epitomics clone ER179(2)) Mouse Prostate, Vehicle x 3 days Input control Input control Input DNA Mouse Prostate, Vehicle x 3 days Input control Input control primary keratinocytes_input Others Epitope tags Flag primary keratinocytes_Flag_ChIP-seq Others Gata6 Gata6 (D61E4) primary keratinocytes_Gata6_ChIP-seq Others Gata6 Gata6 primary keratinocytes_Gata6_ChIP-seq Others Esr1 anti-ESR1 C-terminal antibody (Santa Cruz sc543) cells from preantral follicles maintained for 9 days in vitro and treated for 45 minutes with 10-7M estradiol Others Foxl2 anti-FOXL2 C-terminal antibody (from lab) cells from preantral follicles maintained for 9 days in vitro and treated for 45 minutes with 10-7M estradiol Input control Input control none cells from preantral follicles maintained for 9 days in vitro and treated for 45 minutes with 10-7M estradiol Input control Input control none iMOP cells Input control Input control NA EL4-T-bet cell line, unstimulated Input control Input control NA EL4-GFP cell line, unstimulated Others Ccnt1 Pool of Santa-Cruz CyclinT1 T-18 (sc-8127), C-20 (sc-8128), CDK9 H-169 (sc-8338) and CDK9 C-20 (sc-484) EL4-T-bet cell line, unstimulated Others Ccnt1 Pool of Santa-Cruz CyclinT1 T-18 (sc-8127), C-20 (sc-8128), CDK9 H-169 (sc-8338) and CDK9 C-20 (sc-484) EL4-GFP cell line, unstimulated Others Ccnt1 Pool of Santa-Cruz CyclinT1 T-18 (sc-8127), C-20 (sc-8128), CDK9 H-169 (sc-8338) and CDK9 C-20 (sc-484) In vitro differentiated Th2 cells, wild-type Others Ccnt1 Pool of Santa-Cruz CyclinT1 T-18 (sc-8127), C-20 (sc-8128), CDK9 H-169 (sc-8338) and CDK9 C-20 (sc-484) In vitro differentiated Th1 cells, T-bet-/- Others Ccnt1 Pool of Santa-Cruz CyclinT1 T-18 (sc-8127), C-20 (sc-8128), CDK9 H-169 (sc-8338) and CDK9 C-20 (sc-484) In vitro differentiated Th1 cells, wild-type Input control Input control NA In vitro differentiated Th2 cells, wild-type Input control Input control NA In vitro differentiated Th1 cells, T-bet-/- Input control Input control NA In vitro differentiated Th1 cells, wild-type Input control Input control NA EL4-GFP cell line, stimulated Others Ccnt1 Pool of Santa-Cruz CyclinT1 T-18 (sc-8127), C-20 (sc-8128), CDK9 H-169 (sc-8338) and CDK9 C-20 (sc-484) EL4-T-bet cell line, stimulated Input control Input control NA EL4-T-bet cell line, stimulated Others Ccnt1 Pool of Santa-Cruz CyclinT1 T-18 (sc-8127), C-20 (sc-8128), CDK9 H-169 (sc-8338) and CDK9 C-20 (sc-484) EL4-GFP cell line, stimulated Histone H3K9me3 H3K9me3 ab8898 Embryonic stem cells Histone H3K27me3 H3K27me3 ab6002 Embryonic stem cells Histone H3K36me3 H3K36me3 ab9050 Embryonic stem cells Histone H3K79me2 H3K79me2 ab3594 Embryonic stem cells Histone H3K4me3 H3K4me3 ab8580 Embryonic stem cells Histone H3K27ac H3K27Ac ab4729 Embryonic stem cells Input control Input control IgG 12-370 Embryonic stem cells Input control Input control input GC B cells Input control Input control input CSR activated B cells Histone H3K27ac H3K27Ac (abcam, ab4729) GC B cells Histone H3K27ac H3K27Ac (abcam, ab4729) CSR activated B cells RNA polymerase RNA polymerase II PolII MC3T3 mouse cell line Histone H3K9me1 H3K9Me1 MC3T3 mouse cell line Histone H3K4me3 H3K4Me3 MC3T3 mouse cell line Input control Input control NA activated B cell Others Eed EED (Millipore, 17-663) Spermatocytes Histone H3K4me3 H3K4me3 (Abcam, ab8580) Spermatocytes Input control Input control ChIP-Seq ETOPOSIDE INPUT_TOP2B Others Top2b Topo IIb Abcam-ab58442 ChIP-Seq ETOPOSIDE TOP2B Input control Input control ChIP-Seq ETOPOSIDE INPUT_?H2AX Histone H2A.XS139ph ?H2AX Abcam-ab2893 ChIP-Seq ETOPOSIDE ?H2AX Input control Input control ChIP-Seq NMDA INPUT_TOP2B Others Top2b Topo IIb Abcam-ab58442 ChIP-Seq NMDA TOP2B Input control Input control ChIP-Seq NMDA INPUT_?H2AX Histone H2A.XS139ph ?H2AX Abcam-ab2893 ChIP-Seq NMDA ?H2AX Input control Input control ChIP-Seq CTRL INPUT_TOP2B Others Top2b Topo IIb Abcam-ab58442 ChIP-Seq CTRL TOP2B Input control Input control ChIP-Seq CTRL INPUT_?H2AX Histone H2A.XS139ph ?H2AX Abcam-ab2893 ChIP-Seq CTRL ?H2AX Input control Input control none Liver, Bmal1 KO, ZT 26, input Input control Input control none Liver, Bmal1 KO, ZT 22, input Input control Input control none Liver, Bmal1 KO, ZT 18, input Input control Input control none Liver, Bmal1 KO, ZT 14, input Input control Input control none Liver, Bmal1 KO, ZT 10, input Input control Input control none Liver, Bmal1 KO, ZT 6, input Input control Input control none Liver, Bmal1 KO, ZT 2, input Others Clock anti-CLOCK Liver, CLOCK ChIP Others Clock anti-CLOCK NIH3T3 cells, 38h, CLOCK ChIP Others Clock anti-CLOCK NIH3T3 cells, 34h, CLOCK ChIP Others Clock anti-CLOCK NIH3T3 cells, 30h, CLOCK ChIP Others Clock anti-CLOCK NIH3T3 cells, 26h, CLOCK ChIP Others Clock anti-CLOCK NIH3T3 cells, 22h, CLOCK ChIP Others Clock anti-CLOCK NIH3T3 cells, 18h, CLOCK ChIP Others Arntl anti-BMAL1 NIH3T3 cells, 38h, BMAL1 ChIP Others Arntl anti-BMAL1 NIH3T3 cells, 30h, BMAL1 ChIP Others Arntl anti-BMAL1 NIH3T3 cells, 26h, BMAL1 ChIP Others Arntl anti-BMAL1 NIH3T3 cells, 22h, BMAL1 ChIP Others Arntl anti-BMAL1 NIH3T3 cells, 18h, BMAL1 ChIP Others Arntl anti-BMAL1 NIH3T3 cells, 20h, BMAL1 ChIP Others Arntl anti-BMAL1 NIH3T3 cells, 12h, BMAL1 ChIP RNA polymerase RNA polymerase II anti-RNA PolII NIH3T3 cells, 20h, RNA PolII ChIP RNA polymerase RNA polymerase II anti-RNA PolII NIH3T3 cells, 12h, RNA PolII ChIP Others Epitope tags anti-FLAG M2 clone Neural progenitor cells Others Olig2 Anti-Olig-2 Antibody Neural progenitor cells Others Nkx6-1 anti-NKX6.1 Cocktail of DSHB (F55A10, F55A12, F64A6B4, and F65A2), RD Systems (AF5857) and custom (from T. Jessell) Neural progenitor cells Others Nkx2-2 Anti-NKX2-2 Cocktail of DSHB (74.5A5), Sigma (HPA003468), and custom (from T. Jessell) Neural progenitor cells Input control Input control none Neuro2a cells transfected with a FLAG-tag expressing vector Others Epitope tags anti-FLAG antibody (Sigma, F2426) Neuro2a cells transfected with a FLAG-tag expressing vector Input control Input control none Neuro2a cells expressing doxycycline-dependent Lhx5 Others Epitope tags anti-FLAG antibody (Sigma, F2426) Neuro2a cells expressing doxycycline-dependent Lhx5 RNA polymerase RNA polymerase II serine 5-phosphorylated RNA Polymerase II (Abcam) primary MEFs Histone H3K27me3 H3K27me3 T cell acute lymphocytic leukemia Histone H3K4me3 H3K4me3 T cell acute lymphocytic leukemia Histone H3K4me1 H3K4me1 T cell acute lymphocytic leukemia Others Mnx1 anti-HB9PO4 IP MIN6-4N cells Input control Input control none input MIN6-4N cells Input control Input control none Mouse hair follicle TACs Others Smad1 Cell Signal pSmad1/5/8 no 9511 Mouse hair follicle TACs Input control Input control none Mouse hair follicle stem cells Others Smad1 Cell Signal pSmad1/5/8 no 9511 Mouse hair follicle stem cells Input control Input control Splenic B cells, Input Others Spi1 Splenic B cells, miR-155 KO, PU.1 IP Others Spi1 Splenic B cells, PU.1 KI, PU.1 IP Others Spi1 Splenic B cells, Wild type, PU.1 IP RNA polymerase RNA polymerase II RNAPol_II Millipore 05-623-Z Neu-positive mouse mammary tumor Others Tfap2c TFAP2C Millipore 05-909 Neu-positive mouse mammary tumor Histone H3K27me3 H3K27me3 (#17-622, Millipore) Junction E10.5 Histone H3K27me3 H3K27me3 (#17-622, Millipore) Maxillary arch E10.5 Histone H3K27ac H3K27ac (abcam, catalog# ab4729, lot# GR132150-1) primary HFSCs Input control Input control none primary HFSCs Input control Input control none embryonic heart Others Ctcf anti-CTCF antibody CTCF ChIP-Seq 0 min Cort Input control Input control Input Pol II RNA polymerase RNA polymerase II RNA polymerase II phosphoS5 antibody Pol II ChIP-Seq 60 min Cort Constant RNA polymerase RNA polymerase II RNA polymerase II phosphoS5 antibody Pol II ChIP-Seq 60 min Cort Pulsed RNA polymerase RNA polymerase II RNA polymerase II phosphoS5 antibody Pol II ChIP-Seq 20 min Cort RNA polymerase RNA polymerase II RNA polymerase II phosphoS5 antibody Pol II ChIP-Seq 0 min Cort Input control Input control GR ChIP-Seq input 60 min Cort Constant Input control Input control GR ChIP-Seq input 60 min Cort Pulsed Input control Input control GR ChIP-Seq input 20 min Cort Input control Input control GR ChIP-Seq input 0 min Cort Others Nr3c1 GR Antibody GR ChIP-Seq 60 min Cort Constant Others Nr3c1 GR Antibody GR ChIP-Seq 60 min Cort Pulsed Others Nr3c1 GR Antibody GR ChIP-Seq 20 min Cort Others Nr3c1 GR Antibody GR ChIP-Seq 0 min Cort Input control Input control Normal Rabbit IgG Myoblast Others Mef2a MEF2A Myoblast Others Snai1 Anti-SNAIL + SLUG antibody PyMT_high Snail expression Others Snai2 Slug (C19G7) Rabbit mAb PyMT_high Slug expression Unclassified Unclassified PyMT_high Snail expression Unclassified Unclassified PyMT_high Slug expression Others Epitope tags anti-HA 416B expressing HA-T-VP64-PU.1-14 Others Epitope tags anti-HA 416B WT control Input control Input control none lung tumors Others Suz12 anti-Suz12 IkL/L_DN3_Suz12 Others Suz12 anti-Suz12 WT_DN3_Suz12 Histone H3K27me3 anti-H3K27me3 ILC87-Ik1-ER_4OHT_3d_H3K27me3 Histone H3K27me3 anti-H3K27me3 ILC87-Ik1-ER_EtOH_3d_H3K27me3 Input control Input control none ILC87-Ik1-ER_4OHT_1d_input Input control Input control none ILC87-Ik1-ER_EtOH_1d_input Others Ikzf1 Ikaros ILC87-Ik1-ER_4OHT_1d_Ikaros Others Ikzf1 Ikaros ILC87-Ik1-ER_EtOH_1d_Ikaros Others Ikzf1 Ikaros WT_DP_Ikaros Others Ikzf1 Ikaros WT_DN4_Ikaros Others Ikzf1 Ikaros WT_DN3_Ikaros Histone H3K27me3 anti-H3K27me3 IkL/L_DP_H3K27me3 Histone H3K27me3 anti-H3K27me3 IkL/L_DN4_H3K27me3 Histone H3K27me3 anti-H3K27me3 IkL/L_DN3_H3K27me3 Histone H3K27me3 anti-H3K27me3 IkL/L_DN2_H3K27me3 Histone H3K27me3 anti-H3K27me3 IkL/L_DN1_H3K27me3 Histone H3K27me3 anti-H3K27me3 WT_DN2_H3K27me3 Histone H3K27me3 anti-H3K27me3 WT_DN1_H3K27me3 Others Ikzf1 Ikaros WT_DPe_Ikaros Histone H3K4me3 anti-H3K4me3 IkL/L_DPe_H3K4me3 Histone H3K4me3 anti-H3K4me3 WT_DPe_H3K4me3 Others Epitope tags Flag (SIGMA M2 F1804) dCas9-noED + control gRNA Others Epitope tags Flag (SIGMA M2 F1804) dCas9-KRAB + S2 gRNA Others Epitope tags Flag (SIGMA M2 F1804) dCas9-KRAB + S1 gRNA Input control Input control none VEC_Input Histone H3K9ac H3K9ac (Epitomics, 1328-1) VEC_H3K9ac Input control Input control none CRE_Input Histone H3K9ac H3K9ac (Epitomics, 1328-1) CRE_H3K9ac Unclassified Unclassified testis Others Prdm9 PRDM9 testis Others Foxl2 anti-FOXL2 C-terminal antibody (from lab) cells from preantral follicles maintained for 9 days in vitro Input control Input control none cells from preantral follicles maintained for 9 days in vitro Histone H3K4me3 H3K4me3 (Abcam ab8580) mouse embryonic stem cell Input control Input control Whole cell extract Dgcr8 knockout mouse embryonic stem cells RNA polymerase RNA polymerase II RNAP2 antibody: Covance MMS-128P Dgcr8 knockout mouse embryonic stem cells Histone H3K36me3 H3K36me3 antibody: Abcam ab9050 Dgcr8 knockout mouse embryonic stem cells Histone H3K27ac H3K27ac antibody: Abcam ab4729 Dgcr8 knockout mouse embryonic stem cells Histone H3K9me3 H3K9me3 antibody: Abcam ab8898 Dgcr8 knockout mouse embryonic stem cells Histone H3K27me3 H3K27me3 antibody: Upstate 07-449 Dgcr8 knockout mouse embryonic stem cells Histone H3K4me3 H3K4me3 antibody: Millipore 07-473 Dgcr8 knockout mouse embryonic stem cells Histone H3K27me3S28ph H3K27me3S28p (Hansen lab) 6-OHDA lesioned striatum, L-DOPA injected Histone H3K27me3S28ph H3K27me3S28p (Hansen lab) unlesioned striatum, L-DOPA injected Histone H3K4me3 H3K4me3 (9751, Cell Signaling) 6-OHDA lesioned striatum, L-DOPA injected Histone H3K4me3 H3K4me3 (9751, Cell Signaling) unlesioned striatum, L-DOPA injected Histone H3K27me3 H3K27me3 (9756, Cell Signaling) 6-OHDA lesioned striatum, L-DOPA injected Histone H3K27me3 H3K27me3 (9756, Cell Signaling) unlesioned striatum, L-DOPA injected Input control Input control none 6-OHDA lesioned striatum, L-DOPA injected Input control Input control none unlesioned striatum, L-DOPA injected Input control Input control total rabbit IgG, Millipore, Cat. #12-370 cerebral cortex Histone H3 pan-H3 (Sigma #I8140) primordial germ cells Histone H3K9me3 H3K9me3 (Active Motif #39161) somatic gonadal cells RNA polymerase RNA polymerase II RNAPol2Ser5 clone4H8 genomic DNA bisulfite converted RNAPol2Ser5_ChIPbisSeq RNA polymerase RNA polymerase II RNAPol2Ser5 clone4H8 genomic DNA RNAPol2Ser5_ChIPSeq Histone H3K9me3 anti-Histone H3K9me3 antibody (ab8898, ChIP grade) induced pluripotent stem cells Histone H3K9me3 anti-Histone H3K9me3 antibody (ab8898, ChIP grade) intermediate stage of somatic cell reprogramming Histone H3K9me3 anti-Histone H3K9me3 antibody (ab8898, ChIP grade) mouse embryo fibroblasts Others Ctcf chip antibody: anti-CTCF primary CD4+ T cells from spleen and lymph nodes Others Ep300 chip antibody: anti-p300, antibody vendor/catalog#: sc-585, Santa Cruz Biotechnology primary CD4+ T cells from spleen and lymph nodes Unclassified Unclassified CD4+ cells, Foxo1tagBirA mice Unclassified Unclassified CD4+ cells Others Biotin Strepdavidin CD4+ cells, Foxo1tagBirA mice Others Foxo1 Foxo1 antibody (Abcam, Ab39670) CD4+ cells Others Dmrtb1 Rabbit polyclonal antibodies to DMRT6 Dmrt6 ChIP Histone H3K27ac anti-H3K27ac Liver, Bmal1 KO, ZT 26, H3K27ac ChIP Histone H3K27ac anti-H3K27ac Liver, Bmal1 KO, ZT 22, H3K27ac ChIP Histone H3K27ac anti-H3K27ac Liver, Bmal1 KO, ZT 18, H3K27ac ChIP Histone H3K27ac anti-H3K27ac Liver, Bmal1 KO, ZT 14, H3K27ac ChIP Histone H3K27ac anti-H3K27ac Liver, Bmal1 KO, ZT 10, H3K27ac ChIP Histone H3K27ac anti-H3K27ac Liver, Bmal1 KO, ZT 6, H3K27ac ChIP Histone H3K27ac anti-H3K27ac Liver, Bmal1 KO, ZT 2, H3K27ac ChIP Histone H3K27ac anti-H3K27ac Liver, WT, ZT 26, H3K27ac ChIP Histone H3K27ac anti-H3K27ac Liver, WT, ZT 22, H3K27ac ChIP Histone H3K27ac anti-H3K27ac Liver, WT, ZT 18, H3K27ac ChIP Histone H3K27ac anti-H3K27ac Liver, WT, ZT 14, H3K27ac ChIP Histone H3K27ac anti-H3K27ac Liver, WT, ZT 10, H3K27ac ChIP Histone H3K27ac anti-H3K27ac Liver, WT, ZT 6, H3K27ac ChIP Histone H3K27ac anti-H3K27ac Liver, WT, ZT 2, H3K27ac ChIP RNA polymerase RNA polymerase II anti-PolII Liver, Bmal1 KO, ZT 26, PolII ChIP RNA polymerase RNA polymerase II anti-PolII Liver, Bmal1 KO, ZT 22, PolII ChIP RNA polymerase RNA polymerase II anti-PolII Liver, Bmal1 KO, ZT 18, PolII ChIP RNA polymerase RNA polymerase II anti-PolII Liver, Bmal1 KO, ZT 14, PolII ChIP RNA polymerase RNA polymerase II anti-PolII Liver, Bmal1 KO, ZT 10, PolII ChIP RNA polymerase RNA polymerase II anti-PolII Liver, Bmal1 KO, ZT 6, PolII ChIP RNA polymerase RNA polymerase II anti-PolII Liver, Bmal1 KO, ZT 2, PolII ChIP RNA polymerase RNA polymerase II anti-PolII Liver, WT, ZT 26, PolII ChIP RNA polymerase RNA polymerase II anti-PolII Liver, WT, ZT 22, PolII ChIP RNA polymerase RNA polymerase II anti-PolII Liver, WT, ZT 18, PolII ChIP RNA polymerase RNA polymerase II anti-PolII Liver, WT, ZT 14, PolII ChIP RNA polymerase RNA polymerase II anti-PolII Liver, WT, ZT 10, PolII ChIP RNA polymerase RNA polymerase II anti-PolII Liver, WT, ZT 6, PolII ChIP RNA polymerase RNA polymerase II anti-PolII Liver, WT, ZT 2, PolII ChIP Others Ep300 P300 (Santa Cruz, sc585, lot# B0413) brain Others Bmi1 BMI1 (Bethyl, A301-694A, lot# A301-694A-3) brain Histone H2AK119Ub H2AK119ub1 (Cell Signaling, 8240, lot# 1) brain Histone H3K27me3 H3K27me3 (Millipore, 07-449, lot# JBC1873477) brain Histone H3K36me3 H3K36me3 (abcam, ab9050, lot#, GR75636-1) brain Histone H3K4me3 H3K4me3 (abcam, ab8580, lot# GR86940-1) brain Histone H3K27ac H3K27ac (abcam, ab4729, lot# GR103379-1) brain RNA polymerase RNA polymerase II PolII (Santa Cruz, sc899, lot#, G2414) brain Others Rnf2 RING1B (form Luciano Di Croce) brain Others Auts2 AUTS2 (house made) brain Input control Input control none brain Unclassified Unclassified primary CD4+ T cells from spleen Others Rara anti-RARa (Diagenode C15310155) primary CD4+ T cells from spleen Input control Input control none pancreatic tissue Others Atf3 Anti-ATF3 (cat#sc-188 Santa Cruz) pancreatic tissue Histone H2AK119Ub H2AK119Ub1 Cell Signaling #8240 Differentiated motor neuron Input control Input control input DNA none embryonic stem cells, TC11, empty vector, input Unclassified Unclassified In-vivo leukemia cells from spleen Input control Input control none In-vivo leukemia cells from spleen Input control Input control None Dicer KO_ES Others Ezh2 anti-Ezh2 antibody Dicer KO_ES Input control Input control None WT_ES Others Ezh2 anti-Ezh2 antibody WT_ES Input control Input control none Forebrain Others Mecp2 Total MeCP2 antibody (Chen et al. 2003) Forebrain Input control Input control none mature B cells Histone H3K9me2 H3K9me2 (abcam #1220) mature B cells Histone H3K4me3 H3K4me3 (Millipore 07-473) mature B cells Input control Input control none Pro B Histone H3K9me2 H3K9me2 (abcam #1220) Pro B Histone H3K4me3 H3K4me3 (Millipore 07-473) Pro B Input control Input control none HSC Histone H3K9me2 H3K9me2 HSC Histone H3K9me2 H3K9me2 (abcam #1220) HSC Histone H3K4me3 H3K4me3 (Millipore 07-473) HSC Others Cdk7 Cdk7 Bethyl A300-405A Embryonic stem cells RNA polymerase RNA polymerase II RNA Pol II (Ser7 phospho CTD) Millipore 04-1570 Embryonic stem cells Input control Input control dendritic cells, D1 curdlan + Fk506 Input Histone H3K4me3 dendritic cells, D1 curdlan+Fk506 2h H3K4me3 Input control Input control dendritic cells, D1 curdlan Input Histone H3K4me3 dendritic cells, D1 curdlan 2h H3K4me3 Input control Input control dendritic cells, D1 NT Input Histone H3K4me3 dendritic cells, D1 NT H3K4me3 Input control Input control dendritic cells, NFAT1 curdlan Input Others Nfatc2 dendritic cells, NFAT1 curdlan V5 Input control Input control normal rabbit IgG MEL_LSD1 IgG Control Others Kdm1a Anti-KDM1 / LSD1 antibody MEL_LSD1 ChIP Input control Input control normal rat IgG MEL_IRF2BP2 IgG Control Others Irf2bp2 Irf2bp2 Absea antibody 10G3 custom-made MEL_IRF2BP2 ChIP Input control Input control normal goat IgG MEL_GFI1B IgG Control Others Gfi1b Gfi-1B Antibody (D-19) MEL_GFI1B ChIP RNA polymerase RNA polymerase II Pol II (N20) Santa Cruze, SC-899 mouse embryonic pluripotent stem cells RNA polymerase RNA polymerase II Pol II (N20) Santa Cruze, SC-899 mouse reprogramming intermediates at Day8 RNA polymerase RNA polymerase II Pol II (N20) Santa Cruze, SC-899 mouse reprogramming intermediates at Day5 RNA polymerase RNA polymerase II Pol II (N20) Santa Cruze, SC-899 mouse embryonic fibroblasts Others Ctcf CTCF, MillIpore 07-730 Patski cells Others Ctcf CTCF, MillIpore 07-729 Mouse adult hybrid brain Histone H3K4me3 H3K4me3 1 million mEpiSCs Histone H3K4me3 H3K4me3 1 million mESCs Histone H3K4me3 H3K4me3 Common Lymphoid Progenitor (CLP) Histone H3K4me3 H3K4me3 NK Cells Histone H3K4me3 H3K4me3 T CD8+ cells Histone H3K4me3 H3K4me3 T CD4+ cells Histone H3K4me3 H3K4me3 B cells Histone H3K4me3 H3K4me3 Bone Marrow Macrophages Histone H3K4me3 H3K4me3 Monocytes Histone H3K4me3 H3K4me3 Granulocytes Histone H3K4me3 H3K4me3 Erythrocytes B (Ery B) Histone H3K4me3 H3K4me3 Erythrocytes A (Ery A) Histone H3K4me3 H3K4me3 Megakaryocitic erythroyd progenitor (MEP) Histone H3K4me3 H3K4me3 Granulocyte Monocyte Progenitor (GMP) Histone H3K4me3 H3K4me3 Common Myeloid Progenitor (CMP) Histone H3K4me3 H3K4me3 Multipotent Progenitor (MPP) Histone H3K4me3 H3K4me3 Short Term Hematopoietic Stem Cell (ST-HSC) Histone H3K4me3 H3K4me3 Long Term Hematopoietic Stem Cell (LT-HSC) Histone H3K4me2 H3K4me2 T CD8+ cells Histone H3K4me2 H3K4me2 T CD4+ cells Histone H3K4me2 H3K4me2 Common Lymphoid Progenitor (CLP) Histone H3K4me2 H3K4me2 NK Cells Histone H3K4me2 H3K4me2 B cells Histone H3K4me2 H3K4me2 Bone Marrow Macrophages Histone H3K4me2 H3K4me2 Monocytes Histone H3K4me2 H3K4me2 Granulocytes Histone H3K4me2 H3K4me2 Erythrocytes B (Ery B) Histone H3K4me2 H3K4me2 Erythrocytes A (Ery A) Histone H3K4me2 H3K4me2 Megakaryocitic erythroyd progenitor (MEP) Histone H3K4me2 H3K4me2 Granulocyte Monocyte Progenitor (GMP) Histone H3K4me2 H3K4me2 Common Myeloid Progenitor (CMP) Histone H3K4me2 H3K4me2 Multipotent Progenitor (MPP) Histone H3K4me2 H3K4me2 Short Term Hematopoietic Stem Cell (ST-HSC) Histone H3K4me2 H3K4me2 Long Term Hematopoietic Stem Cell (LT-HSC) Histone H3K4me1 H3K4me1 Common Lymphoid Progenitor (CLP) Histone H3K4me1 H3K4me1 NK Cells Histone H3K4me1 H3K4me1 T CD8+ cells Histone H3K4me1 H3K4me1 T CD4+ cells Histone H3K4me1 H3K4me1 B cells Histone H3K4me1 H3K4me1 Bone Marrow Macrophages Histone H3K4me1 H3K4me1 Monocytes Histone H3K4me1 H3K4me1 Granulocytes Histone H3K4me1 H3K4me1 Erythrocytes B (Ery B) Histone H3K4me1 H3K4me1 Erythrocytes A (Ery A) Histone H3K4me1 H3K4me1 Megakaryocitic erythroyd progenitor (MEP) Histone H3K4me1 H3K4me1 Granulocyte Monocyte Progenitor (GMP) Histone H3K4me1 H3K4me1 Common Myeloid Progenitor (CMP) Histone H3K4me1 H3K4me1 Multipotent Progenitor (MPP) Histone H3K4me1 H3K4me1 Short Term Hematopoietic Stem Cell (ST-HSC) Histone H3K4me1 H3K4me1 Long Term Hematopoietic Stem Cell (LT-HSC) Histone H3K27ac H3K27Ac Common Lymphoid Progenitor (CLP) Histone H3K27ac H3K27Ac NK Cells Histone H3K27ac H3K27Ac T CD8+ cells Histone H3K27ac H3K27Ac T CD4+ cells Histone H3K27ac H3K27Ac B cells Histone H3K27ac H3K27Ac Bone Marrow Macrophages Histone H3K27ac H3K27Ac Monocytes Histone H3K27ac H3K27Ac Granulocytes Histone H3K27ac H3K27Ac Erythrocytes B (Ery B) Histone H3K27ac H3K27Ac Erythrocytes A (Ery A) Histone H3K27ac H3K27Ac Megakaryocitic erythroyd progenitor (MEP) Histone H3K27ac H3K27Ac Granulocyte Monocyte Progenitor (GMP) Histone H3K27ac H3K27Ac Common Myeloid Progenitor (CMP) Histone H3K27ac H3K27Ac Multipotent Progenitor (MPP) Histone H3K27ac H3K27Ac Short Term Hematopoietic Stem Cell (ST-HSC) Histone H3K27ac H3K27Ac Long Term Hematopoietic Stem Cell (LT-HSC) Input control Input control R6_striatum_Input Input control Input control WT_striatum_Input Input control Input control None None Embryonic stem cells Others Med1 Med1/TRAP220 Santa Cruz SC-5334 Embryonic stem cells Others Med1 Med1/TRAP220 Bethyl A300-793A Embryonic stem cells Input control Input control None None Mouse embryonic fibroblasts Unclassified Unclassified MEFs cells knockout MED23 Unclassified Unclassified MEFs cells wildtype Histone H2Bub H2Bub MEFs cells knockout MED23 Histone H2Bub H2Bub MEFs cells wildtype RNA polymerase RNA polymerase II Pol II MEFs cells knockout MED23 RNA polymerase RNA polymerase II Pol II MEFs cells wildtype Others Rora ROR alpha RORalpha (Santa Cruz, sc-6062) liver Others Nfil3 E4BP4 E4BP4 (Santa Cruz, sc-9550 and sc-9549, mixed in 1:1 ratio.) liver Others Etv2 V5-4 Doxycycline treated iER71, ES cell Others Etv2 V5-1 Doxycycline treated iER71, ES cell Input control Input control IgG Doxycycline treated iER71, ES cell Unclassified Unclassified pAb-2 Doxycycline treated iER71, ES cell Unclassified Unclassified pAb-1 Doxycycline treated iER71, ES cell Unclassified Unclassified pAb-0 No doxycycline treated iER71, ES cell Histone H3K27me3 H3K27me3 ChIP (clone 7b11) C2 iMEFs Ezh2 pre-rescue condition Histone H3K27me3 H3K27me3 ChIP (clone 7b11) C2 iMEFs Ezh1 pre-rescue condition Input control Input control none C2 iMEFs Ezh2 WT/WT Input control Input control none (input) mouse embryonic stem cells Others Pwp1 anti-Pwp1 sc-107983 mouse embryonic stem cells Others Med12 anti-Med12 (Bethyl #A300-774A) mouse embryonic stem cells Others Med1 anti-Med1 (CRSP1/TRAP220) (Bethyl #A300-793A) mouse embryonic stem cells Others Sox2 anti-Sox2 (Santa Cruz #sc-17320) mouse embryonic stem cells Others Nanog anti-Nanog (D2A3) XP (Cell Signaling #8822) mouse embryonic stem cells Others Pou5f1 anti-Oct3/4 (N-19) (Santa Cruz #sc-8628) mouse embryonic stem cells Others Rad21 Rad21 Apc Min small intestinal adenoma Unclassified Unclassified Apc Min small intestinal adenoma Others Rad21 Rad21 WT small intestinal crypts Unclassified Unclassified WT small intestinal crypts Unclassified Unclassified mES Cells ATRX Knockout Unclassified Unclassified mES Cells Histone H3.3 Millipore 09-838 mES Cells ATRX Knockout Histone H3.3 Millipore 09-838 mES Cells Others Nlrc5 Rabbit polyclonal anti-mouse NLRC5 (aa 1139) custom antibody generated by Adipogen Rfx5-/- T-cells Others Nlrc5 Rabbit polyclonal anti-mouse NLRC5 (aa 1139) custom antibody generated by Adipogen Nlrc5-/- T-cells Others Nlrc5 Rabbit polyclonal anti-mouse NLRC5 (aa 1139) custom antibody generated by Adipogen Nlrc5F/F T-cells Histone H3K4me3 H3K4me3 sFB Histone H3K27me3 H3K27me3 sFB Histone H3K4me3 H3K4me3 sFB-G Histone H3K27me3 H3K27me3 sFB-G Histone H3K4me3 H3K4me3 mESC Histone H3K27me3 H3K27me3 mESC Histone H3K4me3 H3K4me3 iPSCp Histone H3K27me3 H3K27me3 iPSCp Histone H3K4me3 H3K4me3 iPSC2 Histone H3K27me3 H3K27me3 iPSC2 Histone H3K4me3 H3K4me3 iPSC1 Histone H3K27me3 H3K27me3 iPSC1 Histone H3K4me3 H3K4me3 cFB Histone H3K27me3 H3K27me3 cFB Histone H3K4me1 H3K4me1_repeat_2 3T3L1 Histone H3K4me1 H3K4me1_repeat_1 3T3L1 Histone H3K36me3 H3K36me3_repeat_2 3T3L1 Histone H3K36me3 H3K36me3_repeat_1 3T3L1 Histone H3K27me3 H3K27me3_repeat_2 3T3L1 Histone H3K27me3 H3K27me3_repeat_1 3T3L1 RNA polymerase Polr2b anti-RPB2, Santa Cruz Biotechnology, sc-673-18 liver Histone H3 Histone H3, C-terminal antibody (pAb) miwi2KO_GermCellsTestis_MACS_H3 Histone H3 Histone H3, C-terminal antibody (pAb) miwi2HET_GermCellsTestis_MACS_H3 Histone H3K9me3 a-H3K9me3 miwi2KO_GermCellsTestis_FACS_H3K9me3 Input control Input control miwi2KO_GermCellsTestis_FACS_inputDNA Histone H3K9me3 a-H3K9me3 miwi2HET_GermCellsTestis_FACS_H3K9me3 Input control Input control miwi2HET_GermCellsTestis_FACS_inputDNA RNA polymerase RNA polymerase II Pan-RNA Pol2 G-RNA Pol2 ChIP Others Ep300 p300 G-p300 ChIP Histone H3K4me3 H3K4me3 G-H3K27me3 ChIP Histone H3K27ac H3K27ac G-H3K27ac ChIP Histone H3K4me3 H3K4me3 G-H3K4me3 ChIP Histone H3K4me1 H3K4me1 G-H3K4me1 ChIP Input control Input control IgG (normal rabbit) G-IgG ChIP RNA polymerase RNA polymerase II Pan-RNA Pol2 dY-RNA Pol2 ChIP Others Pou5f1 Oct3/4 dY-Oct4 ChIP Others Ep300 p300 dY-p300 ChIP Histone H3K4me3 H3K4me3 dY-H3K27me3 ChIP Histone H3K27ac H3K27ac dY-H3K27ac ChIP Histone H3K4me3 H3K4me3 dY-H3K4me3 ChIP Histone H3K4me1 H3K4me1 dY-H3K4me1 ChIP Input control Input control IgG (normal rabbit) dY-IgG ChIP RNA polymerase RNA polymerase II Pan-RNA Pol2 dR-RNA Pol2 ChIP Others Pou5f1 Oct3/4 dR-Oct4 ChIP Others Ep300 p300 dR-p300 ChIP Histone H3K4me3 H3K4me3 dR-H3K27me3 ChIP Histone H3K27ac H3K27ac dR-H3K27ac ChIP Histone H3K4me3 H3K4me3 dR-H3K4me3 ChIP Histone H3K4me1 H3K4me1 dR-H3K4me1 ChIP Input control Input control IgG (normal rabbit) dR-IgG ChIP RNA polymerase RNA polymerase II Pan-RNA Pol2 R-RNA Pol2 ChIP Others Pou5f1 Oct3/4 R-Oct4 ChIP Others Ep300 p300 R-p300 ChIP Histone H3K4me3 H3K4me3 R-H3K27me3 ChIP Histone H3K27ac H3K27ac R-H3K27ac ChIP Histone H3K4me3 H3K4me3 R-H3K4me3 ChIP Histone H3K4me1 H3K4me1 R-H3K4me1 ChIP Input control Input control IgG (normal rabbit) R-IgG ChIP Input control Input control Input WT_Retinoic acid treated ES cells Input control Input control Input WT_ES cells Input control Input control none Hoxa9/Meis1-transformed HSCs_input Histone H3K27me3 anti-H3K27me3 Hoxa9/Meis1-transformed HSCs_ChIP-seq Histone H3K4me1 anti-H3K4me1 Hoxa9/Meis1-transformed HSCs_ChIP-seq Others Cebpa anti-C/EBP Hoxa9/Meis1-transformed HSCs_ChIP-seq Others Epitope tags anti-HA Hoxa9/Meis1-transformed HSCs_ChIP-seq Input control Input control WCE none mouse adipocyte Others Ebf1 Ebf1 anti-Ebf1 antibody (Abnova H00001879-M01) mouse adipocyte Others Zfp335 Zfp335/NIF1 (A300-798A, Bethyl Laboratories, lot no. A300-798A-1) thymocytes, blt/blt, Zfp335/NIF1 ChIP Others Zfp335 Zfp335/NIF1 (A300-798A, Bethyl Laboratories, lot no. A300-798A-1) thymocytes, WT, Zfp335/NIF1 ChIP Others Zfp335 Zfp335/NIF1 (A300-797A, Bethyl Laboratories, lot no. A300-797A-1) thymocytes, blt/blt, Zfp335/NIF1 ChIP Others Zfp335 Zfp335/NIF1 (A300-797A, Bethyl Laboratories, lot no. A300-797A-1) thymocytes, WT, Zfp335/NIF1 ChIP Input control Input control none thymocytes, blt/blt, input Input control Input control none thymocytes, WT, input Input control Input control none (input) Embryonic stem cells (J1) Others Trim28 Custom rabbit anti-KAP1 antibody, 5ug per IP Embryonic stem cells (J1) Input control Input control none (input) Embryonic stem cells (ES3) Others Epitope tags Mouse anti-HA antibody (Covance, catalog# MMS-101P) Embryonic stem cells (ES3) Input control Input control v5 control ChIP-seq in CGR8 Embryonic Stem Cells Others Dppa2 v5-Dppa2 ChIP-seq in CGR8 Embryonic Stem Cells Input control Input control none mouse primary hepatocyte Others Nucks1 NUCKS (Rabbit polyclonal antibody is generated by i-DNA Biotechnology Pte Ltd by immunizing rabbits with bacterially expressed full-length NUCKS protein) mouse primary hepatocyte Histone H3 panH3 (Abcam ab1791, lot# 940378) Sperm, PanH3 ChIP Input control Input control none Sperm, input Input control Input control none (input) In vitro activated CD8 T cells RNA polymerase RNA polymerase II Anti-PolII-S5 Abcam ab5131 In vitro activated CD8 T cells RNA polymerase RNA polymerase II Anti-PolII-S2 Abcam ab5095 In vitro activated CD8 T cells Others Myc Anti-Myc Santa Cruz sc-764 In vitro activated CD8 T cells Others Tfap4 Anti-AP4 in house In vitro activated CD8 T cells Input control Input control MEFs-Input-siSUZ12-ChIPseq Input control Input control MEFs-Input-DRB-ChIPseq Input control Input control MEFs-Input-siRBFox2-ChIPseq Input control Input control MEFs-Input-NC-ChIPseq Others Rbfox2 anti-RBFox2 MEFs-RBFox2-siSUZ12-ChIPseq Others Suz12 anti-SUZ12 MEFs-SUZ12-DRB-ChIPseq Others Rbfox2 anti-RBFox2 MEFs-RBFox2-DRB-ChIPseq Histone H3K27me3 anti-H3k27me3 MEFs-H3K27Me3-siRBFox2-ChIPseq Others Suz12 anti-SUZ12 MEFs-SUZ12-siRBFox2-ChIPseq Histone H3K27me3 anti-H3k27me3 MEFs-H3K27Me3-NC-ChIPseq Others Suz12 anti-SUZ12 MEFs-SUZ12-NC-ChIPseq Others Rbfox2 anti-RBFox2 MEFs-RBFox2-siRBFox2-ChIPseq Others Rbfox2 anti-RBFox2 MEFs-RBFox2-NC-ChIPseq Others Suz12 anti-SUZ12 WT mouse hearts Unclassified Unclassified WT mouse hearts Others Rbfox2 anti-RBFox2 WT mouse hearts Histone H3K27me3 H3K27me3 Abcam AB6002 Embryonic stem cells Input control Input control none P12_Liver Others Hnf4a HNF4A (Santa Cruz sc-8987 X) E18_Liver Histone H3K4me3 H3K4me3 ((Millipore 04-745) P12_Liver Histone H3K4me3 H3K4me3 (Millipore 04-745) P12_Liver Input control Input control Input_KO_P22 Input control Input control Input_WT_P22 Histone H3K27ac H3K27Ac 70Z3 ChIP-Seq H3K27Ac Histone H3K9ac H3K9Ac 70Z3 ChIP-Seq H3K9Ac Histone H3K4me3 H3K4Me3 70Z3 ChIP-Seq H3K4Me3 Others Zbtb17 rabbit anti-Miz-1 70Z3 ChIP-Seq Miz1 Input control Input control 70Z3 ChIP-Seq Input Histone H3K27ac H3K27Ac P6D4 ChIP-Seq H3K27Ac Histone H3K9ac H3K9Ac P6D4 ChIP-Seq H3K9Ac Histone H3K4me3 H3K4Me3 P6D4 ChIP-Seq H3K4Me3 Others Zbtb17 rabbit anti-Miz-1 P6D4 ChIP-Seq Miz1 Input control Input control P6D4 ChIP-Seq Input Histone macroH2A2 MacroH2A2 antibody, Abcam ab4173 embryonic fibroblasts Histone macroH2A2 MacroH2A2 antibody, Abcam ab4173 Embryonic Stem Cells Input control Input control No antibody ChIPseq WT WCE Others Epitope tags FLAG antibody F1804, SIGMA ChIPseq WT IP Input control Input control No antibody dmCas9-ChIPseq sgRNA p53-3 WCE Others Epitope tags FLAG antibody F1804, SIGMA dmCas9-ChIPseq sgRNA p53-3 IP Input control Input control No antibody dmCas9-ChIPseq No sgRNA WCE Input control Input control No antibody dmCas9-ChIPseq sgRNA p53-1 WCE Others Epitope tags FLAG antibody F1804, SIGMA dmCas9-ChIPseq No trgRNA IP Others Epitope tags FLAG antibody F1804, SIGMA dmCas9-ChIPseq sgRNA p53-1 IP Others Spi1 PU.1 ( Santa Cruz, sc-352) Plasmacytoid dendritic cell (pDC) Others Spi1 PU.1 ( Santa Cruz, sc-352) Classical dendritic cell (cDC) Others Spi1 PU.1 ( Santa Cruz, sc-352) Common dendritic cell progenitor (CDP) Others Spi1 PU.1 ( Santa Cruz, sc-352) Multipotent progenitor (MPP) Histone H3K4me1 H3K4me1 (Abcam, ab8895) Plasmacytoid dendritic cell (pDC) Histone H3K4me1 H3K4me1 (Abcam, ab8895) Classical dendritic cell (cDC) Histone H3K4me1 H3K4me1 (Abcam, ab8895) Common dendritic cell progenitor (CDP) Histone H3K4me1 H3K4me1 (Abcam, ab8895) Multipotent progenitor (MPP) Histone H3K4me3 Abcam, ab8580 KO MEF Histone H3K4me3 Abcam, ab8580 WT MEF Unclassified Unclassified embryonic stem cells, 75 uM DRB, 10 h Input control Input control N/A Epiblast stem cells Histone H3K27me3 H3K27me3 (Abcam #6002) Epiblast stem cells Histone H3K27ac H3K27ac (Abcam #4729) Epiblast stem cells Histone H3K4me3 H3K4me3 (Active Motif #39159) Epiblast stem cells Histone H3K4me1 H3K4me1 (Abcam #8895) Epiblast stem cells Input control Input control none p53KORasV12 MEF, input Others E4f1 rabbit polyclonal anti-E4F1 p53KORasV12 MEF, E4F1 ChIP Input control Input control none MEF, input Others E4f1 rabbit polyclonal anti-E4F1 MEF, E4F1 ChIP Input control Input control none mESC, input Others E4f1 rabbit polyclonal anti-E4F1 mESC, E4F1 ChIP Unclassified Unclassified TS cell Histone H2A.X anti-H2A.X TS cell Input control Input control none Neural Progenitor Cells Input control Input control none lung Others Smad4 Smad4 R&D Systems, cat.# AF2097, Lot# KUH0311081 lung Others Gsk3b GSK3beta Mouse Embryonic Fibroblasts Histone H3K27ac H3K27ac Hematopoietic progenitors Input control Input control none (Input) Neural precursors cells Others GFP -EGFP (invitrogen, A11122) Embryonic Stem cells Input control Input control none (input) myoblasts Others Foxk1 Santa Cruz sc-13450, Lot D1911 myoblasts Others Sin3a Hassig, C. A. et al. Cell 89, 341347 (1997) myoblasts Histone H3K27me3 H3K27me3 Mouse embryonic day 11.5 (e11.5) forebrain Histone H3K4me3 H3K4me3 Mouse embryonic day 11.5 (e11.5) forebrain Histone H3K4me1 H3K4me1 Mouse embryonic day 11.5 (e11.5) forebrain Input control Input control input Mouse embryonic day 11.5 (e11.5) forebrain Histone H3K27ac H3K27ac Mouse embryonic day 11.5 (e11.5) limb Histone H3K27me3 H3K27me3 Mouse embryonic day 11.5 (e11.5) limb Histone H3K4me3 H3K4me3 Mouse embryonic day 11.5 (e11.5) limb Histone H3K4me1 H3K4me1 Mouse embryonic day 11.5 (e11.5) limb Others Rxra anti-panRXR (Santa Cruz, Sc-553) F9 cells, RA, 48h, RXR ChIP Others Rara anti-panRAR (Santa Cruz, Sc-773) F9 cells, RA, 48h, RAR ChIP Others Rxra anti-panRXR (Santa Cruz, Sc-553) F9 cells, RA, 24h, RXR ChIP Others Rara anti-panRAR (Santa Cruz, Sc-773) F9 cells, RA, 24h, RAR ChIP Others Rxra anti-panRXR (Santa Cruz, Sc-553) F9 cells, RA, 2h, RXR ChIP Others Rara anti-panRAR (Santa Cruz, Sc-773) F9 cells, RA, 2h, RAR ChIP Others Rxra anti-panRXR (Santa Cruz, Sc-553) F9 cells, RA, 0h, RXR ChIP Others Rara anti-panRAR (Santa Cruz, Sc-773) F9 cells, RA, 0h, RAR ChIP Input control Input control none F9 cells, RA, 0h, total chromatin Others Smarca4 BRG1 3T3-L1 pre-adipocytes (4h) Others Ep300 p300 (N-15) 3T3-L1 pre-adipocytes (4h) Others Rxra RXR (N-197) 3T3-L1 pre-adipocytes (4h) Others Vdr VDR (C-20) 3T3-L1 pre-adipocytes (4h) Others Stat1 STAT1 (E-23) 3T3-L1 pre-adipocytes (4h) Others Pbx1 PBX1 3T3-L1 pre-adipocytes (4h) Others Klf5 KLF5 3T3-L1 pre-adipocytes (4h) Others Klf4 KLF4 (H-180) 3T3-L1 pre-adipocytes (4h) Others Junb JunB (210) 3T3-L1 pre-adipocytes (4h) Others Fosl2 FOSL2 (L-15) 3T3-L1 pre-adipocytes (4h) Others Jun cJun (H79) 3T3-L1 pre-adipocytes (4h) Others Atf7 ATF7 (S-15) 3T3-L1 pre-adipocytes (4h) Others Atf2 ATF2 (N-96) 3T3-L1 pre-adipocytes (4h) Others Nfyc NFYC: Santa-cruz, NF-YC (N-19)X, sc-7715X, Rabbit polyclonal E14Tg2a ES Cells Others Nfyb NFYB: Santa-cruz, NF-YB (FL-207)X, sc-13045X, Rabbit polyclonal E14Tg2a ES Cells Others Nfya NFYA: Santa-cruz, NF-YA (G-2)X, sc-17753X, Mouse monoclonal IgG2a E14Tg2a ES Cells Input control Input control none E14Tg2a ES Cells Input control Input control IgG (Santa Cruz, SC-2027) Neural progenitor cells_IgG_ChIP Others Tet3 mTet3FL (in house) Neural progenitor cells_Tet3FL_ChIP Input control Input control None whole heart Input control Input control none Primary gd T cells Others Notch1 Rabbit Notch1 mAb (D1E11, Cell Signaling Technology) Primary gd T cells Others Fosl2 FOSL2 sc-13017x, Santa Cruz ChIP-seq, 3T3-L1 adipocyte FOSL2 untreated Others Jund JUND sc-74x, Santa Cruz ChIP-seq, 3T3-L1 adipocyte JUND untreated Others Atf2 ATF2 sc-6233x, Santa Cruz ChIP-seq, 3T3-L1 adipocyte ATF2 untreated Others Cebpb CEBPb sc-150x, Santa Cruz ChIP-seq, 3T3-L1 adipocyte CEBPb untreated Others Cebpa CEBPa sc-61x, Santa Cruz ChIP-seq, 3T3-L1 adipocyte CEBPa untreated Others Ncor1 NCOR rosi treated rabbit polyclonal, generated in-lab ChIP-seq, 3T3-L1 adipocyte NCOR rosi treated Others Ncor1 NCOR rabbit polyclonal, generated in-lab ChIP-seq, 3T3-L1 adipocyte NCOR untreated Others Ep300 p300 rosi treated sc-585x, Santa Cruz ChIP-seq, 3T3-L1 adipocyte p300 rosi treated Others Ep300 p300 sc-585x, Santa Cruz ChIP-seq, 3T3-L1 adipocyte p300 untreated Others Crebbp CBP rosi treated sc-369x, Santa Cruz ChIP-seq, 3T3-L1 adipocyte CBP rosi treated Others Crebbp CBP sc-369x, Santa Cruz ChIP-seq, 3T3-L1 adipocyte CBP untreated Others Med1 MED1 A300-793A, Bethyl ChIP-seq, 3T3-L1 adipocyte MED1 rosi treated, replicate 2 Others Med1 MED1 A300-793A, Bethyl ChIP-seq, 3T3-L1 adipocyte MED1 untreated, replicate 2 Input control Input control 3T3-L1 adipocyte input Others Med1 MED1 A300-793A, Bethyl ChIP-seq, 3T3-L1 adipocyte MED1 rosi treated, replicate 1 Others Med1 MED1 A300-793A, Bethyl ChIP-seq, 3T3-L1 adipocyte MED1 untreated, replicate 1 Input control Input control normal goat serum (negative control) mock ChIP from spermatocytes heat shocked at 43C Input control Input control normal goat serum (negative control) mock ChIP from spermatocytes heat shocked at 38C Input control Input control normal goat serum (negative control) mock ChIP from untreated spermatocytes Others Hsf2 anti-HSF2 (cat. no AF5227, R&D Systems) HSF2 ChIP DNA from spermatocytes heat shocked at 43C Others Hsf2 anti-HSF2 (cat. no AF5227, R&D Systems) HSF2 ChIP DNA from spermatocytes heat shocked at 38C Others Hsf2 anti-HSF2 (cat. no AF5227, R&D Systems) HSF2 ChIP DNA from untreated spermatocytes Others Hsf1 anti-HSF1 (cat. no SPA-901, Enzo) HSF1 ChIP DNA from spermatocytes heat shocked at 43C Others Hsf1 anti-HSF1 (cat. no SPA-901, Enzo) HSF1 ChIP DNA from spermatocytes heat shocked at 38C Others Hsf1 anti-HSF1 (cat. no SPA-901, Enzo) HSF1 ChIP DNA from untreated spermatocytes Input control Input control None Ventral Proliferating neural stem cells Histone H3K4me3 H3K4me3 Active Motif 39159 Ventral Proliferating neural stem cells Input control Input control None Proliferating Neural Stem Cells Histone H3K27me3 H3K27me3 Millipore 07-449 Proliferating Neural Stem Cells Input control Input control None 30 hr differentiation Neural Stem Cells Histone H3K27me3 H3K27me3 Millipore 07-449 30 hr differentiation Neural Stem Cells Input control Input control N/A primary Rag2 -/- thymocytes Unclassified Unclassified Cardiomyocytes Histone H3K27ac H3K27ac Cardiomyocytes Histone H3K4me1 H3K4me1 Cardiomyocytes Unclassified Unclassified endoderm Others Epitope tags anti-V5 (Abcam, ab15828) endoderm Histone H3K27me3 H3K27me3 WT 8 days after dox induction Input control Input control KO MEF_input Unclassified Unclassified KO MEF_IP Input control Input control WT MEF_input Unclassified Unclassified WT MEF_IP Others Esrrb Esrrb (H6705, Perseus Proteomics) ZHBTc4 ES cells, +Tet, Day 4 Others Esrrb Esrrb (H6705, Perseus Proteomics) ZHBTc4 ES cells, +Tet, Day 3 Others Esrrb Esrrb (H6705, Perseus Proteomics) ZHBTc4 ES cells, +Tet, Day 2 Others Esrrb Esrrb (H6705, Perseus Proteomics) ZHBTc4 ES cells, +Tet, Day 1 Others Esrrb Esrrb (H6705, Perseus Proteomics) ZHBTc4 ES cells, untreated Histone H3K27me3 H3K27me3 (Millipore, 07-449) DNMT triple knockout ESCs Others Foxp3 Rabbit Anti-Foxp3( Nature. 2007;445:936-40. iTreg cells Others Foxp3 Rabbit Anti-Foxp3( Nature. 2007;445:936-40. EL4 cells Input control Input control rat IgG2a, eBioscience, 14-6988, Th17 cells Input control Input control IgG EB-Motor neuron, WT, IgG control ChIP Others Taf9b TAF9B EB-Motor neuron, WT, TAF9B ChIP RNA polymerase RNA polymerase II RNA Pol2 EB-Motor neuron, WT, RNA Pol2 ChIP Histone H3K4me3 H3K4me3 p30-GMP-blast cells, Biological repl_III, H3K4me3 ChIP Histone H3K4me3 H3K4me3 p30-GMP-blast cells, Biological repl_II, H3K4me3 ChIP Histone H3K27me3 H3K27me3 p30-GMP-blast cells, Biological repl_II, H3K27me3 ChIP Histone H3K27me3 H3K27me3 p30-GMP-blast cells, Biological repl_I, H3K27me3 ChIP Others Cebpa CEBPA p30-GMP-blast cells, Biological repl_II, CEBPA ChIP Others Cebpa CEBPA p30-GMP-blast cells, Biological repl_I, CEBPA ChIP Others Rbpj Lab generated rabbit anti-Rbpj E12.5 Neural Tube Others Ascl1 BD Pharmigen mouse anti-Ascl1 (catalog# 556604) E12.5 Neural Tube RNA polymerase RNA polymerase II RNAPIIS2ph (Bethyl, cat number A300-654A) RNAPIIS2ph, Serum-starved (72h) Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 2 RNA polymerase RNA polymerase II RNAPIIS2ph (Bethyl, cat number A300-654A) RNAPIIS2ph, Serum-starved (72h) Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 1 RNA polymerase RNA polymerase II RNAPIIS2ph (Bethyl, cat number A300-654A) RNAPIIS2ph, Serum-starved (72h) Swiss 3T3 fibroblasts, replicate 2 RNA polymerase RNA polymerase II RNAPIIS2ph (Bethyl, cat number A300-654A) RNAPIIS2ph, Serum-starved (72h) Swiss 3T3 fibroblasts, replicate 1 RNA polymerase RNA polymerase II RNAPIIS5ph (Bethyl, cat number A300-655A) RNAPIIS5ph, Serum-starved (72h) Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 2 RNA polymerase RNA polymerase II RNAPIIS5ph (Bethyl, cat number A300-655A) RNAPIIS5ph, Serum-starved (72h) Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 1 RNA polymerase RNA polymerase II RNAPIIS5ph (Bethyl, cat number A300-655A) RNAPIIS5ph, Serum-starved (72h) Swiss 3T3 fibroblasts, replicate 2 RNA polymerase RNA polymerase II RNAPIIS5ph (Bethyl, cat number A300-655A) RNAPIIS5ph, Serum-starved (72h) Swiss 3T3 fibroblasts, replicate 1 Histone H3K4me3 H3K4me3 (Millipore, cat number 07-473) H3K4me3, Serum-starved (72h) Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 2 Histone H3K4me3 H3K4me3 (Millipore, cat number 07-473) H3K4me3, Serum-starved (72h) Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 1 Histone H3K4me3 H3K4me3 (Millipore, cat number 07-473) H3K4me3, Serum-starved (72h) Swiss 3T3 fibroblasts, replicate 2 Histone H3K4me3 H3K4me3 (Millipore, cat number 07-473) H3K4me3, Serum-starved (72h) Swiss 3T3 fibroblasts, replicate 1 Histone H3K9ac H3K9ac (Millipore, cat number 06-942) H3K9ac, Serum-starved (72h) Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 2 Histone H3K9ac H3K9ac (Millipore, cat number 06-942) H3K9ac, Serum-starved (72h) Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 1 Histone H3K9ac H3K9ac (Millipore, cat number 06-942) H3K9ac, Serum-starved (72h) Swiss 3T3 fibroblasts, replicate 2 Histone H3K9ac H3K9ac (Millipore, cat number 06-942) H3K9ac, Serum-starved (72h) Swiss 3T3 fibroblasts, replicate 1 Histone H3S28ph H3S28ph (Sigma, cat number H9908) H3S28ph, Serum-starved (72h) Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 2 Histone H3S28ph H3S28ph (Sigma, cat number H9908) H3S28ph, Serum-starved (72h) Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 1 Histone H3S28ph H3S28ph (Sigma, cat number H9908) H3S28ph, Serum-starved (72h) Swiss 3T3 fibroblasts, replicate 2 Histone H3S28ph H3S28ph (Sigma, cat number H9908) H3S28ph, Serum-starved (72h) Swiss 3T3 fibroblasts, replicate 1 Input control Input control none Input, Serum-starved (72h) Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM) Input control Input control none Input, Serum-starved (72h) Swiss 3T3 fibroblasts Input control Input control None Activated Treg Others Trp53 p53 Mouse embryonic fibroblasts Input control Input control input Mouse embryonic fibroblasts Others Tdg Bio-Tdg cells ESC E14 Unclassified Unclassified BirA cells (mock) ESC E14 Others Jarid2 Jarid2 K116me2 IP (this study, Sanulli et al.) embryonic stem cells Others Jarid2 Jarid2 IP (Li et al. Gene & development 2010) embryonic stem cells Histone H3K4me2 anti-H3K4me2 (Millipore 07-030) Sperm, non-transgenic, H3K4me2 ChIP Histone H3K4me2 anti-H3K4me2 (Millipore 07-030) Sperm, KDM1A transgenic, H3K4me2 ChIP Input control Input control none mature brown adipocytes, input Histone H3K27me3 H3K27me3 (Millipore, Cat# 07-449, Lot# 2194165) mature brown adipocytes, H3K27me3 ChIP Input control Input control none brown preadipocytes, input Histone H3K27me3 H3K27me3 (Millipore, Cat# 07-449, Lot# 2194165) brown preadipocytes, H3K27me3 ChIP Others Smad3 Smad3 (Abcam, ab28379) embryonic stem cells Others Tgif1 Tgif1 (Santa Cruz, SC9084X) embryonic stem cells Histone H3K36me3 antiH3K36me3 Abcam (Cat #: ab9050,Lot #: GR66372-1) Dcr Knockout mouse embryonic stem cells Histone H3K4me3 antiH3K4me3 Abcam (Cat #: ab8580, Lot #: GR87168-1) Dcr Knockout mouse embryonic stem cells Histone H3K36me3 antiH3K36me3 Abcam (Cat #: ab9050,Lot #: GR66372-1) Dcr Wild type mouse embryonic stem cells Histone H3K4me3 antiH3K4me3 Abcam (Cat #: ab8580, Lot #: GR87168-1) Dcr Wild type mouse embryonic stem cells Others Atf3 rabbit polyclonal anti-Atf3 antibody Atf3_HDL_CpG_KO Others Atf3 rabbit polyclonal anti-Atf3 antibody Atf3_HDL_CpG_wildtype Others Atf3 rabbit polyclonal anti-Atf3 antibody Atf3_HDL_KO Others Atf3 rabbit polyclonal anti-Atf3 antibody Atf3_HDL_wildtype Others Atf3 rabbit polyclonal anti-Atf3 antibody Atf3_Unstim_KO Others Atf3 rabbit polyclonal anti-Atf3 antibody Atf3_Unstim_wildtype Input control Input control IgG (Sigma, catalog# I8140, lot# 115k7551) c-kit+ bone marrow cells Input control Input control none A2lox FMsgn1 embryonic stem cells Others Epitope tags anti-Flag M2 (Sigma, Cat#F3165) A2lox FMsgn1 embryonic stem cells Histone H3K27me3 H3K27me3 (#17-622, Millipore) Pre-somitic mesoderm E8.5 Histone H3K4me3 H3K4me3 (#17-614, Millipore) Pre-somitic mesoderm E8.5 Histone H3K27me3 H3K27me3 (#17-622, Millipore) ES cells Histone H3K4me3 H3K4me3 (#17-614, Millipore) ES cells Input control Input control none Nucleus accumbens tissue Unclassified Unclassified mast Unclassified Unclassified HPC7 Input control Input control none Maxillary arch Cells Histone H3K27ac H3K27Ac antibody (Active Motif, cat# AM 39133) Maxillary arch Cells Input control Input control none (input) Cultured germline stem cells Others Bmi1 Mouse anti-Bmi1 (Millipore, catalog#05-637, lot#2019726) Cultured germline stem cells Others Rnf2 Mouse anti-Rnf2 (MBL, catalog#D139-3, lot#014) Cultured germline stem cells Others Scml2 Rabbit anti-Scml2 (produced in-house; Hasegawa et al.) Cultured germline stem cells Others T Anti-Brachyury antibody Rabbit #2, Custom-made, rabbits were immunized with Brachyury residues 249-436 GST fusion protein ES cell derived Mesoendoderm Cells Others T Anti-Brachyury antibody Rabbit #1, Custom-made, rabbits were immunized with Brachyury residues 249-436 GST fusion protein ES cell derived Mesoendoderm Cells Input control Input control pre-immune IgG ES cell derived Mesoendoderm Cells Others T Anti-Brachyury antibody, Custom-made, rabbits were immunized with Brachyury residues 249-436 GST fusion proteins ES cell derived Mesoendoderm Cells Input control Input control none Rif1 knockdown ESCs Histone H3K9me3 Abcam ab8898 Rif1 knockdown ESCs Input control Input control none Control ESCs Histone H3K9me3 Abcam ab8898 Control ESCs Histone H3ac Anti-acetyl-Histone H3 TSA H3Ac_ChIP-seq Histone H3ac Anti-acetyl-Histone H3 DMSO H3Ac_ChIP-seq Histone H3K27me3 H3K27me3 07-449 Trimethylated histone H3 (Lys27). Broad species cross-reactivity expected. rabbit polyclonal. Antibody Target: H3K27me3 MEL Input control Input control Input Cytokine independent 106A cell line Histone H3K4me3 H3K4me3 Cytokine independent 106A cell line Histone H3K27me3 H3K27me3 Cytokine independent 106A cell line Input control Input control Input Cytokine independent 961C cell line Unclassified Unclassified NP23 Cytokine independent 961C cell line Histone H3K4me3 H3K4me3 Cytokine independent 961C cell line Histone H3K27me3 H3K27me3 Cytokine independent 961C cell line Input control Input control Input Cytokine independent 748T cell line Histone H3K4me3 H3K4me3 Cytokine independent 748T cell line Histone H3K27me3 H3K27me3 Cytokine independent 748T cell line Input control Input control Input Cytokine independent 7298/2 cell line Histone H3K4me3 H3K4me3 Cytokine independent 7298/2 cell line Histone H3K27me3 H3K27me3 Cytokine independent 7298/2 cell line Input control Input control None Input_IDGSW3_d35 Input control Input control None Input_IDGSW3_d3 Histone H3K9me3 H3K9me3 H3K9me3_IDGSW3_d35 Histone H3K36me3 H3K36me3 H3K36me3_IDGSW3_d35 Histone H4K20me1 H4K20me1 H4K20me1_IDGSW3_d35 Histone H3K9ac H3K9Ac H3K9Ac_IDGSW3_d35 Histone H4K5ac H4K5Ac H4K5Ac_IDGSW3_d35 Histone H3K27ac H3K27Ac H3K27Ac_IDGSW3_d35 Histone H3K4me3 H3K4me3 H3K4me3_IDGSW3_d35 Histone H3K4me2 H3K4me2 H3K4me2_IDGSW3_d35 Histone H3K4me1 H3K4me1 H3K4me1_IDGSW3_d35 Histone H3K9me3 H3K9me3 H3K9me3_IDGSW3_d3 Histone H3K36me3 H3K36me3 H3K36me3_IDGSW3_d3 Histone H4K20me1 H4K20me1 H4K20me1_IDGSW3_d3 Histone H3K9ac H3K9Ac H3K9Ac_IDGSW3_d3 Histone H4K5ac H4K5Ac H4K5Ac_IDGSW3_d3 Histone H3K27ac H3K27Ac H3K27Ac_IDGSW3_d3 Histone H3K4me3 H3K4me3 H3K4me3_IDGSW3_d3 Histone H3K4me2 H3K4me2 H3K4me2_IDGSW3_d3 Histone H3K4me1 H3K4me1 H3K4me1_IDGSW3_d3 Input control Input control None SRC-2OE/+ prostate Others Ncoa2 SRC-2 (A300-346A, Bethyl Lab., Inc.) SRC-2OE/+ prostate Others Klf6 V5-KLF6 HCC cell line Input control Input control none HCC cell line Others Epitope tags anti-HA No-sgRNA-IP Others Epitope tags anti-HA Nanog-sg3-IP Others Epitope tags anti-HA Nanog-sg2-IP Others Epitope tags anti-HA Phc1-sg2-IP Others Epitope tags anti-HA Phc1-sg1-IP Others Hnf4a HNF4a SantaCruz H191 sc-8987 lot #J1003 Dlk1+ hepatoblasts Others Kmt2c MLL3 Growing C1C12 myoblasts Others Kdm1a LSD1 C1C12 myotubes differentiated for 96h Others Kdm1a LSD1 Growing C1C12 myoblasts Others Sox9 Sox9 Ab IFE_Sox9_ChIPSeq Input control Input control none IFE_input DNA_ChIP-Seq Others Sox9 Sox9 Ab HFSC_Sox9_ChIPSeq Others Sox9 Sox9 Ab HFSC_Sox9_ChIP-Seq Others Rela p65 BMM_NoStim_0000_P65 Others Rela p65 BMM_LPS_0120_P65 Others Rela p65 BMM_LPS_0060_P65 Histone H3K27me3 Methylated Histone H3K27me3 BMM_LPS_0060_7hdelay_meH3K27 Histone H3K27me3 Methylated Histone H3K27me3 BMM_LPS_0480_meH3K27 Histone H3K27me3 Methylated Histone H3K27me3 BMM_NoStim_0000_meH3K27 RNA polymerase RNA polymerase II Anti-RNA polymerase II, clone CTD4H8 BMM_LPS_0360_PolII RNA polymerase RNA polymerase II Anti-RNA polymerase II, clone CTD4H8 BMM_LPS_0120_PolII RNA polymerase RNA polymerase II Anti-RNA polymerase II, clone CTD4H8 BMM_NoStim_0000_PolII Histone H3K27me3 Methylated Histone H3K27me3 BMM_LPS_0240_meH3K27 Histone H3K27me3 Methylated Histone H3K27me3 BMM_LPS_0120_meH3K27 Input control Input control IgG pancreatic beta cells Others Foxa2 Foxa2 (sc-6554, Santa Cruz Biotechnology) pancreatic beta cells Others Neurod1 Neurod1 (#4373, Cell Signaling Technology, Danvers, MA) pancreatic beta cells Others Insm1 Insm1 (Welcker et al , 2013) pancreatic beta cells Input control Input control none cornea Input control Input control Normal Rabbit IgG (Life Technologies, 10500C, Lot 939223A) In vitro effector CD8+ T cells Others Jund JunD (329) (Santa Cruz, sc-74, Lot I1510) In vitro effector CD8+ T cells Others Junb JunB (210) (Santa Cruz, sc-73, Lot D2610) In vitro effector CD8+ T cells Others Jun cJun (N) (Santa Cruz, sc-45, Lot K3010) In vitro effector CD8+ T cells Input control Input control None NIPS Others Meis1 Anti-Meis Millipore 05-779 SCGM Others Sox2 Anti-Sox2 (R&D Systems, Cat. # AF2018, Lot # KOY0112011) Embryonic Stem Cells Others Lmnb1 Laminin B (Santa-Cruz, California) Neural Retina Others Otx2 OTX2 (R&D systems, Minneapolis, MN, USA) Neural Retina Others GFP GFP (Abcam, Cambridge, UK) RPE Others Lmnb1 Laminin B (Santa-Cruz, California) RPE Others Otx2 OTX2 (R&D systems, Minneapolis, MN, USA) RPE Input control Input control IgG ES E14 mouse cells Others Runx2 Runx2 antibody (M70, Santa Cruz Biotechnologies, Inc.) mineralizing MC3T3-E1 subclone 4 cells at day 28 Others Runx2 Runx2 antibody (M70, Santa Cruz Biotechnologies, Inc.) matrix-depositing MC3T3-E1 subclone 4 cells at day 9 Others Runx2 Runx2 antibody (M70, Santa Cruz Biotechnologies, Inc.) proliferating preosteoblast MC3T3-E1 subclone 4 cells at day 0 Input control Input control none matrix-depositing MC3T3-E1 subclone 4 cells Input control Input control control IgG HC11 Others Ovol2 antibody against Ovol2 HC11 Input control Input control IgG mouse embryonic fibroblasts Input control Input control IgG Conditional Jmjd2c knockout ESCs Others Men1 Menin KJ1+ transferred CD4 T cells Others Men1 Menin KJ1+ naive CD4 T cells Others Cry1 CRY1 Liver Others Nsl1 Nsl1 mESCs Others Msl1 Msl1 mESCs Input control Input control none EGFP-TS3.5 TS cells Input control Input control none ZHBTc4-TS cells Others Sox2 Sox2 raised by ourselves EGFP-TS3.5 TS cells Others Cdx2 Cdx2 (CDX2-88, BioGenex) ZHBTc4-TS cells Others Tfap2c Tfap2c (sc-8977, Santa Cruz) ZHBTc4-TS cells Others Sox2 Sox2 raised by ourselves ZHBTc4-TS cells Input control Input control none KH2 mouse embryonic stem cells Input control Input control none MECs, p13, no treatment, input Histone H3K4me3 H3K4me3 MECs, control, p13, no treatment, H3K4me3 ChIP Histone H3K4me3 H3K4me3 MECs, E2KO, p13, no treatment, H3K4me3 ChIP Others Stat5a Stat5 mammary tissues, control, p13, no treatment, Stat5 ChIP Others Stat5a Stat5 mammary tissues, E2KO, p13, no treatment, Stat5 ChIP Histone H3K27me3 H3K27me3 mammary tissues, control, p13, no treatment, H3K27me3 ChIP Histone H3K27me3 H3K27me3 mammary tissues, E2KO, p13, no treatment, H3K27me3 ChIP Input control Input control none Liver tissue, pooled, 3 months, input Histone H3K27me3 H3K27me3 (in-house antibody by Active Motif, Carlsbad, CA) Liver tissue, DKO, 3 months, H3K27me3 ChIP Histone H3K27me3 H3K27me3 (in-house antibody by Active Motif, Carlsbad, CA) Liver tissue, E2KO, 3 months, H3K27me3 ChIP Histone H3K27me3 H3K27me3 (in-house antibody by Active Motif, Carlsbad, CA) Liver tissue, E1KO, 3 months, H3K27me3 ChIP Histone H3K27me3 H3K27me3 (in-house antibody by Active Motif, Carlsbad, CA) Liver tissue, WT, 3 months, H3K27me3 ChIP Histone H3K4me3 H3K4me3 (in-house antibody by Active Motif, Carlsbad, CA) Liver tissue, DKO, 3 months, H3K4me3 ChIP Histone H3K4me3 H3K4me3 (in-house antibody by Active Motif, Carlsbad, CA) Liver tissue, E2KO, 3 months, H3K4me3 ChIP Histone H3K4me3 H3K4me3 (in-house antibody by Active Motif, Carlsbad, CA) Liver tissue, E1KO, 3 months, H3K4me3 ChIP Histone H3K4me3 H3K4me3 (in-house antibody by Active Motif, Carlsbad, CA) Liver tissue, WT, 3 months, H3K4me3 ChIP Unclassified Unclassified n.a. Pre-pro-B cell Unclassified Unclassified n.a. DP-T cell Unclassified Unclassified n.a. DN3 cell Others Irf4 anti IRF4 (M-17), Santa Cruz sc-6059x, lot:E0608 Pro-B cell Others Epitope tags anti V5 (clone V5-10)-agarose, Sigma A7345 Pro-B cell Others Dnajc2 Zrf1 Ab generated in Di Croces lab Neural Progenitor cell (NPC) Input control Input control Rabbit IgG Abcam, ab37415 Neural Progenitor cell (NPC) Others Rnf2 Ring1B Ab generated in Di Croces lab Neural Progenitor cell (NPC) Input control Input control none MECs (mammary epithelial cells), p13, input Histone H3K4me3 H3K4me3 (Millipore, 17-614, lot# 2055519) MECs (mammary epithelial cells), p13, H3K4me3 ChIP Others Stat5a STAT5A (Santa Cruz, sc-1081, lot# J3007) Mammary gland tissues, p13, STAT5A ChIP Input control Input control none Mammary gland tissues, p13, input Others Stat5a STAT5A (Santa Cruz, sc-1081, lot# J3007) Mammary gland tissues, L1, STAT5A ChIP Input control Input control none Mammary gland tissues, L1, input Histone H3K4me3 H3K4me3 (Millipore, 17-614, lot# 2055519) Mammary gland tissues, L1, H3K4me3 ChIP Others Yy1 anti-YY1 (Santa Cruz, catalog# SC-1703, lot# E0511) jejunal crypt intestinal epithelial cells Others Junb anti-JunB (Santa Cruz Biotechnology, sc-73x (210x), Lot# D1210) BMDCs, LPS, 6 hrs, JunB ChIP Others Batf anti-BATF (in-house) BMDCs, LPS, 6 hrs, BATF ChIP Others Spi1 anti-PU.1 (Santa Cruz Biotechnology, sc-352x (T-21x), Lot# J2411) BMDCs, LPS, 6 hrs, PU.1 ChIP Others Smad2 SMAD2/3 (R&D Systems, AF3797, lot XHY01) ESC-derived endoderm Others Smad2 SMAD2/3 (R&D Systems, AF3797, lot XHY01) Embryonic stem cells Histone H3K4me3 H3K4me3 07-473 thymus Unclassified Unclassified thymus Histone H3K27ac Anti-H3K27ac antibody (Abcam; ab4729) shKdm5b ES cells Histone H3K27ac Anti-H3K27ac antibody (Abcam; ab4729) shLuc ES cells Input control Input control NULL shKdm5b noLIF day4 ES cells Input control Input control NULL shLuc noLIF day4 ES cells Histone H3K4me1 Anti-H3K4me1 antibody (Abcam; ab8895) shKdm5b noLIF day4 ES cells Histone H3K4me2 Anti-H3K4me2 antibody (Abcam; ab32356) shKdm5b noLIF day4 ES cells Histone H3K4me3 Anti-H3K4me3 antibody (Millipore; CS200580) shKdm5b noLIF day4 ES cells Histone H3K4me1 Anti-H3K4me1 antibody (Abcam; ab8895) shLuc noLIF day4 ES cells Histone H3K4me2 Anti-H3K4me2 antibody (Abcam; ab32356) shLuc noLIF day4 ES cells Histone H3K4me3 Anti-H3K4me3 antibody (Millipore; CS200580) shLuc noLIF day4 ES cells Input control Input control NULL shKdm5b noLIF day3 ES cells Input control Input control NULL shLuc noLIF day3 ES cells Histone H3K4me1 Anti-H3K4me1 antibody (Abcam; ab8895) shKdm5b noLIF day3 ES cells Histone H3K4me2 Anti-H3K4me2 antibody (Abcam; ab32356) shKdm5b noLIF day3 ES cells Histone H3K4me3 Anti-H3K4me3 antibody (Millipore; CS200580) shKdm5b noLIF day3 ES cells Histone H3K4me1 Anti-H3K4me1 antibody (Abcam; ab8895) shLuc noLIF day3 ES cells Histone H3K4me2 Anti-H3K4me2 antibody (Abcam; ab32356) shLuc noLIF day3 ES cells Histone H3K4me3 Anti-H3K4me3 antibody (Millipore; CS200580) shLuc noLIF day3 ES cells Input control Input control NULL shKdm5b noLIF day2 ES cells Input control Input control NULL shLuc noLIF day2 ES cells Histone H3K4me1 Anti-H3K4me1 antibody (Abcam; ab8895) shKdm5b noLIF day2 ES cells Histone H3K4me2 Anti-H3K4me2 antibody (Abcam; ab32356) shKdm5b noLIF day2 ES cells Histone H3K4me3 Anti-H3K4me3 antibody (Millipore; CS200580) shKdm5b noLIF day2 ES cells Histone H3K4me1 Anti-H3K4me1 antibody (Abcam; ab8895) shLuc noLIF day2 ES cells Histone H3K4me2 Anti-H3K4me2 antibody (Abcam; ab32356) shLuc noLIF day2 ES cells Histone H3K4me3 Anti-H3K4me3 antibody (Millipore; CS200580) shLuc noLIF day2 ES cells Input control Input control NULL shKdm5b ES cells Others Kdm5b Anti-KDM5B antibody (Abcam; ab50958) ES cells Input control Input control none facial mesenchyme Histone H3K4me1 anti-H3K4me1 antibody (Abcam, catalog# ab8895, lot# GR61294-1) facial mesenchyme Histone H3K27ac anti-H3K27ac antibody (Abcam, catalog# ab4729, lot# GR7675-1) facial mesenchyme Histone H3K27me3 H3K27me3 lincRNA-p21+/+ murine MEF H3K27me3 ChIP-seq with Doxorubicin Histone H3K27me3 H3K27me3 lincRNA-p21+/+ murine MEF H3K27me3 ChIP-seq without Doxorubicin. Histone H3K27me3 H3K27me3 lincRNA-p21-/- murine MEF H3K27me3 ChIP-seq with Doxorubicin Histone H3K27me3 H3K27me3 lincRNA-p21-/- murine MEF H3K27me3 ChIP-seq without Doxorubicin. Histone H3K4me3 H3K4me3 lincRNA-p21+/+ murine MEF H3K4me3 ChIP-seq with Doxorubicin Histone H3K4me3 H3K4me3 lincRNA-p21+/+ murine MEF H3K4me3 ChIP-seq without Doxorubicin. Histone H3K4me3 H3K4me3 lincRNA-p21-/- murine MEF H3K4me3 ChIP-seq with Doxorubicin Histone H3K4me3 H3K4me3 lincRNA-p21-/- murine MEF H3K4me3 ChIP-seq without Doxorubicin. Input control Input control none (input) lincRNA-p21+/+ murine MEF WCE input with Doxorubicin Input control Input control none (input) lincRNA-p21+/+ murine MEF WCE input without Doxorubicin. Input control Input control none (input) lincRNA-p21-/- murine MEF WCE input with Doxorubicin Input control Input control none (input) lincRNA-p21-/- murine MEF WCE input without Doxorubicin. Others Epitope tags FLAG-M2 monoclonal (Sigma, F3165) E11.5 limb bud, mock ChIP Others Epitope tags FLAG-M2 monoclonal (Sigma, F3165) E11.5 limb bud, FLAG-Gli3 ChIP Input control Input control Millipore, AP132 mouse embryoid bodies Input control Input control Millipore, AP132 mouse embryonic stem cell Others Ar AR (Sahu et al. 2011) Pro-AR_SPARKI1 Others Ar AR (Sahu et al. 2011) Pro-AR_wt1 Input control Input control rIgG (sc-2027, SantaCruz) Pro-rIgG RNA polymerase RNA polymerase II Antibody RNA Pol II Embryonic Stem Cells (ESCs) Input control Input control none adult mouse epidermis Input control Input control none whole embryonic mouse skin Input control Input control none Embryonic stem cells, untreated control, sonicated control RNA polymerase RNA polymerase II Ser2 (Abcam anti-RNA polymerase II CTD (phospho Serine-2) catalog #ab5095) wildtype-Chd1 MEFs Ser2 ChIP_seq RNA polymerase RNA polymerase II N20 (Santa Cruz catalog #sc-899) wildtype-Chd1 MEFs N20 ChIP_seq Others Epitope tags FLAG (Sigma anti-FLAG M2 agarose beads catalog #A2220) wildtype-Chd1 MEFs FLAG ChIP_seq RNA polymerase RNA polymerase II Ser2 (Abcam anti-RNA polymerase II CTD (phospho Serine-2) catalog #ab5095) K510R-Chd1 MEFs Ser2 ChIP_seq RNA polymerase RNA polymerase II N20 (Santa Cruz catalog #sc-899) K510R-Chd1 MEFs N20 ChIP_seq Others Epitope tags FLAG (Sigma anti-FLAG M2 agarose beads catalog #A2220) K510R-Chd1 MEFs FLAG ChIP_seq Others Sp1 anti-Sp1 antibody (Santa Cruz sc-17824X) Sp1 from cKitPlus progenitors Others Sp1 anti-Sp1 antibody (Santa Cruz sc-17824X) Sp1 from E14 Flk1Plus Input control Input control none distal forelimb Others Med12 Med12 (Bethyl, A300-774A, lotA300-774A-)1 distal forelimb RNA polymerase RNA polymerase II PolII (Abcam, ab5131, lot GR37362-1) distal forelimb Others Cebpa anti-Cebpa (Santa Cruz, catalog: sc-61, lot: k1009) primary Bcell after 18h treatment of estradiol Others Cebpa anti-Cebpa (Santa Cruz, catalog: sc-61, lot: k1009) primary Bcells untreated Input control Input control none male_WT_LF.input Input control Input control none male_WT_HF.input Others Nfatc1 NFATc1 (Abcam, ab2796) Mouse back skins Histone H3K27ac H3K27ac 11 dpc embryonic forebrain_H3K27ac ChIP-seq Histone H3K4me1 H3K4me1 11 dpc embryonic forebrain_H3K4me1 ChIP-seq Histone H3K27ac anti-H3K27ac (Abcam, ab4729, GR104852-1) MLL-AF9/NrasG12D murine cell line Histone H3K4me3 anti-H3K4me3 (Abcam, ab8580) MLL-AF9/NrasG12D murine cell line Others Smarca4 anti-Brg1 (Abcam, ab4081) MLL-AF9/NrasG12D murine cell line Others Brd4 anti-Brd4 (Bethyl, A301-985A, A301-985A-1) MLL-AF9/NrasG12D murine cell line Histone H3K27ac H3K27ac (ab4729, Abcam) H3K27ac_Epi Histone H3K4me1 H3K4me1 (ab8895, Abcam) H3K4me1_Epi Histone H3K27ac H3K27ac (ab4729, Abcam) H3K27ac_Kid Histone H3K4me1 H3K4me1 (ab8895, Abcam) H3K4me1_Kid Histone H3K27ac H3K27ac (ab4729, Abcam) H3K27ac_Pro Histone H3K4me1 H3K4me1 (ab8895, Abcam) H3K4me1_Pro Input control Input control rabbit IgG (pre-immune rabbit serum) mouse splenic CD8 T cells Others Tcf7 custom made antiserum for Tcf1 mouse splenic CD8 T cells Input control Input control none Mouse Liver Others Mcrs1 MCRS1 (Proteintech, 11362-1-AP) Embryonic stem cells Others Mcrs1 MCRS1 ( Proteintech, 11362-1-AP) Embryonic stem cells Others Ctcf CTCF (Pugacheva et. al. 2005 Hum Mol Genet 14, 953-965; PMID: 15731119) F1 BC.1 trophoblast stem cells Others Stat1 STAT1(sc-592, SantaCruz) primary CD4+ T cells from spleen and lymph nodes Histone H3K36me3 H3K36me3 NIH/3T3 Tet-On 3G cells Histone H2A.Z H2AZ NIH/3T3 Tet-On 3G cells Histone H3K27me3 H3K27me3 NIH/3T3 Tet-On 3G cells Histone H3K27ac H3K27ac NIH/3T3 Tet-On 3G cells Histone H3K9me2 H3K9me2 NIH/3T3 Tet-On 3G cells Histone H3K9ac H3K9ac NIH/3T3 Tet-On 3G cells Histone H3K4me3 H3K4me3 NIH/3T3 Tet-On 3G cells Histone H3K4me1 H3K4me1 NIH/3T3 Tet-On 3G cells Others Thap11 Ronin Lab Generated (Zwaka) ANTI-RONIN G4275 Embryonic stem cells Others Mbd3 MBD3 Embryonic stem cells Others Crebbp CBP Embryonic stem cells Unclassified Unclassified Intestinal villus cells Unclassified Unclassified Intestinal crypt cells Unclassified Unclassified Lgr5+ intestinal stem cells Others Epitope tags FLAG (Sigma F3165) Intestinal crypt secretory progenitors Histone H3K27ac H3K27ac (Abcam ab4729) Intestinal crypt enterocyte progenitors Histone H3K27ac H3K27ac (Abcam ab4729) Intestinal crypt secretory progenitors Histone H3K4me2 H3K4me2 (Millipore 07-030) Intestinal villus enterocytes Histone H3K4me2 H3K4me2 (Millipore 07-030) Intestinal villus goblet cells Histone H3K4me2 H3K4me2 (Millipore 07-030) Lgr5+ intestinal stem cells Input control Input control IgG (Millipore, Cat # 12-370) Astrocyte cell line Others Stat3 STAT3 antibody (Cell Signaling Technology, Cat# 9132) Astrocyte cell line Others Kmt2d (rb) -MLL4 (#403; Ali Shilatifard) ES cell culture Unclassified Unclassified Nave CD4 T cells from spleen cultured for 5 days in Th2 polarizing conditions Unclassified Unclassified Nave CD4 T cells from spleen cultured for 5 days in Th1 polarizing conditions Others Ezh2 anti-Ezh2 polyclonal Nave CD4 T cells from spleen cultured for 5 days in Th2 polarizing conditions Others Ezh2 anti-Ezh2 polyclonal Nave CD4 T cells from spleen cultured for 5 days in Th1 polarizing conditions Input control Input control Rabbit IgG polyclonal Nave CD4 T cells from spleen cultured for 5 days in Th2 polarizing conditions Input control Input control Rabbit IgG polyclonal Nave CD4 T cells from spleen cultured for 5 days in Th1 polarizing conditions Others Stat5b STAT5B (R&D Systems, Sta5B) Th9 cells, 16h, STAT5B ChIP Others Stat5b STAT5B (R&D Systems, Sta5B) Th9 cells, 0h, STAT5B ChIP Unclassified Unclassified Blrp-Ctrl RAW264.7 cells Others Nrf1 Nrf1 (ab55744, Abcam) Nrf1_ChIPseq 3T3-L1_LSD1 cells day 7 Input control Input control None Input_Nrf1 3T3-L1_LSD1 cells day 7 Others Nrf1 Nrf1 (ab55744, Abcam) Nrf1_ChIPseq 3T3-L1 cells day 0 Input control Input control None Input_Nrf1 3T3-L1 cells day 0 Others Kdm1a LSD1 (20752, homemade, Schle lab) LSD1_ChIPseq 3T3-L1_LSD1 cells day 7 Input control Input control None Input_LSD1 3T3-L1_LSD1 cells day 7 Others Kdm1a LSD1 (20752, homemade, Schle lab) LSD1_ChIPseq 3T3-L1_LSD1 cells day 0 Input control Input control None Input_LSD1 3T3-L1_LSD1 cells day 0 Others Kdm1a LSD1 (20752, homemade, Schle lab) LSD1_ChIPseq 3T3-L1 cells day 7 Input control Input control None Input_LSD1 3T3-L1 cells day 7 Others Kdm1a LSD1 (20752, homemade, Schle lab) LSD1_ChIPseq 3T3-L1 cells day 0 Input control Input control None Input_LSD1 3T3-L1 cells day 0 Unclassified Unclassified mouse primary epidermal keratinocytes Others Smarca4 anti-Brg1 (H-88) mouse primary epidermal keratinocytes Input control Input control none Germinal Center Histone H3K27me3 H3K27me3 (C36B11; Cell Signaling) Germinal Center Histone H3K4me3 H3K4me3 (MC315, Millipore) Germinal Center RNA polymerase RNA polymerase II Pol II ChIP in testis Others Taf7l TAF7L ChIP in testis Input control Input control IgG IP testis samples as control Input control Input control none Innate type-2 lymphocytes Others Gfi1 anti-Gfi1 (a custom rabbit polyclonal antibody raised against N- and C-terminal peptides) Innate type-2 lymphocytes Unclassified Unclassified TT2 G9a-/-andGLP-/- Others Ehmt2 anti-G9a : Cell Signalling Technologies ref : 3306S TT2 KO for G9a and GLP rescued with G9a-wt Others Ehmt2 anti-G9a : Cell Signalling Technologies ref : 3306S TT2 Input control Input control None Whole heart RNA polymerase RNA polymerase II anti-pol II CTD (abcam ab5095) whole heart Others Cebpa C/EBPalpha CEBPa from macrophages cells Input control Input control none MyoD-induced mouse brown preadipocytes, MLL4 KO, input Input control Input control none MyoD-induced mouse brown preadipocytes, WT, input Histone H3K27ac H3K27ac MyoD-induced mouse brown preadipocytes, MLL4 KO, H3K27ac ChIP Histone H3K27ac H3K27ac MyoD-induced mouse brown preadipocytes, WT, H3K27ac ChIP Histone H3K4me3 H3K4me3 MyoD-induced mouse brown preadipocytes, MLL4 KO, H3K4me3 ChIP Histone H3K4me3 H3K4me3 MyoD-induced mouse brown preadipocytes, WT, H3K4me3 ChIP Histone H3K4me1 H3K4me1 MyoD-induced mouse brown preadipocytes, MLL4 KO, H3K4me1 ChIP Histone H3K4me1 H3K4me1 MyoD-induced mouse brown preadipocytes, WT, H3K4me1 ChIP Others Kmt2d MLL4 MyoD-induced mouse brown preadipocytes, MLL4 KO, MLL4 ChIP Others Kmt2d MLL4 MyoD-induced mouse brown preadipocytes, WT, MLL4 ChIP Others Myod1 MyoD MyoD-induced mouse brown preadipocytes, MLL4 KO, MyoD ChIP Others Myod1 MyoD mouse brown preadipocytes, MLL4 KO, MyoD ChIP Others Myod1 MyoD MyoD-induced mouse brown preadipocytes, WT, MyoD ChIP Others Myod1 MyoD mouse brown preadipocytes, WT, MyoD ChIP Input control Input control none mouse brown preadipocytes, MLL4 KO, C/EBPbeta Cre, input Input control Input control none mouse brown preadipocytes, WT, C/EBPbeta GFP, input Histone H3K27ac H3K27ac mouse brown preadipocytes, MLL4 KO, C/EBPbeta Cre, H3K27ac ChIP Histone H3K27ac H3K27ac mouse brown preadipocytes, WT, C/EBPbeta GFP, H3K27ac ChIP Histone H3K4me1 H3K4me1 mouse brown preadipocytes, MLL4 KO, C/EBPbeta Cre, H3K4me1 ChIP Histone H3K4me1 H3K4me1 mouse brown preadipocytes, WT, C/EBPbeta GFP, H3K4me1 ChIP Others Kmt2d MLL4 mouse brown preadipocytes, MLL4 KO, C/EBPbeta Cre, MLL4 ChIP Others Kmt2d MLL4 mouse brown preadipocytes, WT, C/EBPbeta GFP, MLL4 ChIP Others Cebpb C/EBPbeta mouse brown preadipocytes, MLL4 KO, C/EBPbeta Cre, C/EBPbeta ChIP Others Cebpb C/EBPbeta mouse brown preadipocytes, MLL4 KO, Vec Cre, C/EBPbeta ChIP Others Cebpb C/EBPbeta mouse brown preadipocytes, WT, C/EBPbeta GFP, C/EBPbeta ChIP Others Cebpb C/EBPbeta mouse brown preadipocytes, WT, Vec GFP, C/EBPbeta ChIP RNA polymerase RNA polymerase II anti-POL-II-S5P Transformed mouse embryonic fibroblast line, POL-II-S5P ChIP RNA polymerase RNA polymerase II anti-POL-II-S2P Transformed mouse embryonic fibroblast line, POL-II-S2P ChIP Input control Input control IgG rabbit serum Transformed mouse embryonic fibroblast line, input Input control Input control IgG FDCPmix Others Twist1 Twist1 (Sigma, T6451, 5 g) Peripheral nerve sheath tumor cell line Others Twist1 Twist1 (Sigma, T6451, 5 g) E10.5 forelimb buds Others Twist1 Twist1 (Sigma, T6451, 5 g) E12.5 atrioventricular canal endocardial cushion Input control Input control input p190 Bcr-Abl immortalized progenitor B cells Others Sox4 SOX4 p190 Bcr-Abl immortalized progenitor B cells Others Rara RAR antibody Liver Input control Input control none Undifferentiated mouse ES cells Others Ctcf CTCF (Millipore, 07-729, lot 2054523) Undifferentiated mouse ES cells Input control Input control input Mouse uterus Input control Input control input Mouse liver Others Esr1 ESR1 Mouse uterus Others Esr1 ESR1 Mouse liver Input control Input control Input DNA Others Irf4 anti-IRF4 IRF4 ChIPSeq Histone H3K9me3 H3K9me3 (Abcam, cat# ab8898) Histone H3K4me3 H3K4me3 (Millipore, cat# 17-614, part# CS200580) Histone H3K9ac H3K9Ac (Active Motif, cat# 39137) Histone H3K27ac H3K27Ac (Active Motif, cat# 39133) RNA polymerase RNA polymerase II Polymerase II (Covance, cat# MMS-126R) Histone H3K36me3 H3K36me3 (Abcam, cat# ab9050) Input control Input control none E15.5 WT kidney Others Trp53 anti-p53 antibody (Santa Cruz Biotech; catalog# sc-6243; lot# C1609) E15.5 WT kidney Others Epitope tags anti-Flag (M2) Embryonic stem cells Input control Input control None mouse ESCs Input control Input control none MBD3-/- ES Others Chd4 Mi2B (ab70469, Abcam) MBD3-/- ES Histone H3K27me3 H3K27me3 (07-449, Millipore) MBD3-/- ES Histone H3K4me3 H3K4me3 (ab8580, Abcam) MBD3-/- ES Input control Input control none MBD3flox/- iPSC Others Chd4 Mi2B (ab70469, Abcam) MBD3flox/- iPSC Histone H3K27me3 H3K27me3 (07-449, Millipore) MBD3flox/- iPSC Histone H3K4me3 H3K4me3 (ab8580, Abcam) MBD3flox/- iPSC Input control Input control none MBD3flox/- 8 days after dox induction Others Chd4 Mi2B (ab70469, Abcam) MBD3flox/- 8 days after dox induction Histone H3K4me3 H3K4me3 (ab8580, Abcam) MBD3flox/- 8 days after dox induction Input control Input control none MBD3flox/- 4 days after dox induction Others Chd4 Mi2B (ab70469, Abcam) MBD3flox/- 4 days after dox induction Histone H3K27me3 H3K27me3 (07-449, Millipore) MBD3flox/- 4 days after dox induction Histone H3K4me3 H3K4me3 (ab8580, Abcam) MBD3flox/- 4 days after dox induction Input control Input control none MBD3flox/- MEF Histone H3K27me3 H3K27me3 (07-449, Millipore) MBD3flox/- MEF Histone H3K4me3 H3K4me3 (ab8580, Abcam) MBD3flox/- MEF Input control Input control none WT iPSC Others Chd4 Mi2B (ab70469, Abcam) WT iPSC Others Mbd3 Mbd3 (ab16057, Abcam & Bethyl laboratories A302-528\9A) WT iPSC Histone H3K27me3 H3K27me3 (07-449, Millipore) WT iPSC Histone H3K4me3 H3K4me3 (ab8580, Abcam) WT iPSC Input control Input control none WT 8 days after dox induction Others Chd4 Mi2B (ab70469, Abcam) WT 8 days after dox induction Histone H3K4me3 H3K4me3 (ab8580, Abcam) WT 8 days after dox induction Input control Input control none WT 4 days after dox induction Others Chd4 Mi2B (ab70469, Abcam) WT 4 days after dox induction Others Mbd3 Mbd3 (ab16057, Abcam & Bethyl laboratories A302-528\9A) WT 4 days after dox induction Histone H3K27me3 H3K27me3 (07-449, Millipore) WT 4 days after dox induction Histone H3K4me3 H3K4me3 (ab8580, Abcam) WT 4 days after dox induction Others Mbd3 Mbd3 (ab16057, Abcam & Bethyl laboratories A302-528\9A) WT MEF Histone H3K27me3 H3K27me3 (07-449, Millipore) WT MEF Histone H3K4me3 H3K4me3 (ab8580, Abcam) WT MEF Histone H3ac AcH3 (Millipore, 06-600, Lot: 2068182) Nave T cells Histone H3K9K14ac AcH3 (Millipore, 06-599, Lot: 2068182) Nave T cells Histone H3K27ac H3K27ac(Active Motif 39134) midbrain Histone H3K4me1 H3K4me1 (Abcam ab8895) midbrain Input control Input control Input_ChIPSeq_ST Input control Input control Input_ChIPSeq_SC Input control Input control Input_ChIPSeq_AGSC Histone H2A.Z Anti-Histone H2A.Z antibody H2AZ_ChIPSeq_ST Histone H3K9ac Anti-acetyl-Histone H3 (Lys9) Antibody H3K9ac_ChIPSeq_ST RNA polymerase RNA polymerase II RNA Pol2 antibody Pol2_ChIPSeq_ST Others 5-hmC 5-Hydroxymethylcytosine (5-hmC) antibody 5hMC_M Others 5-hmC 5-Hydroxymethylcytosine (5-hmC) antibody 5hMC_ST Others 5-hmC 5-Hydroxymethylcytosine (5-hmC) antibody 5hMC_SC Histone H3K27ac Histone H3K27ac antibody H3K27ac_ChIPSeq_ST Histone H3K27ac Histone H3K27ac antibody H3K27ac_ChIPSeq_SC Histone H3K27ac Histone H3K27ac antibody H3K27ac_ChIPSeq_AGSC Histone H3K4me1 Anti-Histone H3 (mono methyl K4) antibody H3K4me1_ChIPSeq_ST Histone H3K4me1 Anti-Histone H3 (mono methyl K4) antibody H3K4me1_ChIPSeq_SC Histone H3K27me3 Anti-trimethyl-Histone H3 (Lys27) Antibody H27me3_ChIPSeq_ST Histone H3K27me3 Anti-trimethyl-Histone H3 (Lys27) Antibody H27me3_ChIPSeq_SC Histone H3K27me3 Anti-trimethyl-Histone H3 (Lys27) Antibody H27me3_ChIPSeq_AGSC Histone H3K4me3 Histone H3K4me3 antibody H3K4me3_ChIPSeq_ST Histone H3K4me3 Histone H3K4me3 antibody H3K4me3_ChIPSeq_SC Histone H3K4me3 Histone H3K4me3 antibody H3K4me3_ChIPSeq_AGSC Histone H3K4me3 Millipore, 05-745R clone 15-10C-E4 H3K4me3_Ter119_Positive Histone H3K4me1 Millipore, 07-436 H3K4me1_Ter119_Positive RNA polymerase RNA polymerase II polII mouse dendritic cells Histone H3K4me3 H3K4me3 mouse dendritic cells Input control Input control input NA E14 Histone H3K27me3 H3K27me3 Millipore #07-449 E14::N3-EZH2 Others Ep300 p300 (SC-585) craniofacial tissue Input control Input control Rabbit IgG (R&D systems.) T cells Histone H3K9ac H3K9ac Millipore 06-942 lot#1973414 H3K9ac ChIPSeq HEBI_cohort2 Histone H3K9ac H3K9ac Millipore 06-942 lot#1973414 H3K9ac ChIPSeq YF_cohort2 Histone H3K9ac H3K9ac Millipore 06-942 lot#1973414 H3K9ac ChIPSeq WT_cohort2 Histone H3K9ac H3K9ac Millipore 06-942 lot#1973414 H3K9ac ChIPSeq Cre_cohort2 Histone H3K9ac H3K9ac Millipore 06-942 lot#1973414 H3K9ac ChIPSeq KA_cohort1 Histone H3K9ac H3K9ac Millipore 06-942 lot#1973414 H3K9ac ChIPSeq HAHA_cohort1 Histone H3K9ac H3K9ac Millipore 06-942 lot#1973414 H3K9ac ChIPSeq WT_cohort1 Histone H3K9ac H3K9ac Millipore 06-942 lot#1973414 H3K9ac ChIPSeq Cre_cohort1 Others Myog MyoG (M-225, Santa Cruz) C2C12 RNA polymerase RNA polymerase II anti-POL-II-S5P Transformed mouse embryonic fibroblast line Others Ezh2 Ezh2 Transformed mouse embryonic fibroblast line Input control Input control none Transformed mouse embryonic fibroblast line RNA polymerase RNA polymerase II anti-POL-II-S5P Differentiating mouse embryonic stem cell line Histone H3K36me3 anti-H3K36me3 Differentiating mouse embryonic stem cell line Histone H3K4me3 anti-H3K4me3 Differentiating mouse embryonic stem cell line Histone H3K27me3 H3K27me3 Differentiating mouse embryonic stem cell line Others Ezh2 Ezh2 Differentiating mouse embryonic stem cell line Input control Input control none Differentiating mouse embryonic stem cell line RNA polymerase RNA polymerase II anti-POL-II-S5P Undifferentiated mouse embryonic stem cell line Histone H3K36me3 anti-H3K36me3 Undifferentiated mouse embryonic stem cell line Histone H3K4me3 anti-H3K4me3 Undifferentiated mouse embryonic stem cell line Histone H3K27me3 H3K27me3 Undifferentiated mouse embryonic stem cell line Others Ezh2 Ezh2 Undifferentiated mouse embryonic stem cell line Others Biotin Dynabeads MyOne Streptavidin T1 (Invitrogen, #65601) E14-BioDnmt3L embryonic stem cells, shSuz12, Dnmt3L ChIP Others Biotin Dynabeads MyOne Streptavidin T1 (Invitrogen, #65601) E14-BioDnmt3L embryonic stem cells, shGFP, Dnmt3L ChIP Others Ezh2 Ezh2 (D2C9) (Cell Signaling, #5246) E14 embryonic stem cells, shDnmt3L, Ezh2 ChIP Others Ezh2 Ezh2 (D2C9) (Cell Signaling, #5246) E14 embryonic stem cells, shGFP, Ezh2 ChIP Input control Input control J1_Ino80_input Others Ino80 J1_Ino80 Others Gata4 GATA4 C-20 (Santa Cruz sc-1237) Liver Unclassified Unclassified Bethyl Laboratories (#A302-175A) ES cell culture Histone H3K27me3 Active Motif (#39155) ES cell culture RNA polymerase RNA polymerase II mouse anti-Pol2 (Millipore, 17-672) Forelimb Histone H3K27me3 rabbit anti-H3K27me3 (Millipore, 07-449) Forelimb Histone H3K4me3 rabbit anti-H3K4me3 (Abcam, ab1342) Forelimb Others Rad21 Rad21 astrocyte Input control Input control none astrocyte Others Rad21 Rad21 neural stem cell Histone H3K4me3 H3K4me3 (Millipore, cat 17-614) R6/2, striatum, 12 weeks Histone H3K4me3 H3K4me3 (Millipore, cat 17-614) R6/2 wildtype littermate, striatum, 12 weeks Histone H3K4me3 H3K4me3 (Millipore, cat 17-614, lot JBC1793805) R6/2, striatum, 8 weeks Histone H3K4me3 H3K4me3 (Millipore, cat 17-614, lot JBC1793805) R6/2 wildtype littermate, striatum, 8 weeks Histone H3K4me3 H3K4me3 (Millipore, cat 17-614) R6/2, cortex, 12 weeks Histone H3K4me3 H3K4me3 (Millipore, cat 17-614) R6/2 wildtype littermate, cortex, 12 weeks Histone H3K4me3 H3K4me3 (Millipore, cat 17-614, lot JBC1793805) R6/2, cortex, 8 weeks Histone H3K4me3 H3K4me3 (Millipore, cat 17-614, lot JBC1793805) R6/2 wildtype littermate, cortex, 8 weeks Others Tle1 TLE Antibody (C-19) Mouse back skins Others Tcf4 TCF-4 Antibody (N-20) Mouse back skins Others Tcf3 TCF3 Mouse back skins Histone H3 Histone mark H3 (ab1791-100) embryonic fibroblasts Histone H3K27ac Histone mark H3K27acetyl (ab4729) embryonic fibroblasts Others Myt1l Myt1l (ab15828) embryonic fibroblasts treated with BAM factors Input control Input control none (input) neural progenitor Others Pou3f2 Santa Cruz Biotechnology SC-6029 neural progenitor Others Pou3f2 Brn2 (ab15828) embryonic fibroblasts treated with BAM factors Others Pou3f2 Brn2 (ab15828) embryonic fibroblasts Others Ascl1 Ascl1 (ab74065) neural progenitor treated with Ascl1 Input control Input control none (input) neural progenitor treated with Ascl1 Others Ascl1 Ascl1 (ab74065) embryonic fibroblasts Others Cebpa Cebpa: Santa Cruz 14-AA LSK_CebpaWT Input control Input control input control Rag1 -/- DN thymocytes Histone H3K4me3 H3K4me3 from Active Motif (Carlsbad, CA) Rag1 -/- DN thymocytes Histone H3ac H3ac from EMD Millipore (Billerica, MA) Rag1 -/- DN thymocytes Others Rad21 Rad21 (Abcam, ab992, Multiple Lots) CD4+ CD8+ Double Positive Thymocytes Others Nipbl NIPBL (Bethyl Laboratories, A301-779A, lot A301-779A-2) CD4+ CD8+ Double Positive Thymocytes Others Med1 Med1 (Bethyl Laboratories, A300-793A, lot A300-793A-1) CD4+ CD8+ Double Positive Thymocytes Histone H3K27me3 H3K27me3 (Millipore 07-449) Primary thioglycollate-elicited peritoneal macrophages Others Stat5a STAT5A (Santa Cruz, sc-1081) Mammary gland tissues, p6, STAT5A ChIP Input control Input control none Mammary gland tissues, p6, input Histone H3K4me3 H3K4me3 (Millipore, Temecula, 17-614) Mammary gland tissues, p6, H3K4me3 ChIP Input control Input control none Hoxa9/Meis1 AML Others Pbx1 Pbx1/2/3 (Santa Cruz, sc-888, lot J157) Hoxa9 only AML Others Pbx1 Pbx1/2/3 (Santa Cruz, sc-888, lot J157) Hoxa9/Meis1 AML Others Epitope tags FLAG (Sigma, F7425, lot 011M4789) Hoxa9 only AML Others Epitope tags FLAG (Sigma, F7425, lot 011M4789) Hoxa9/Meis1 AML Others Meis1 Meis1 (Abcam, ab19867, lot 676286) Hoxa9/Meis1 AML Unclassified Unclassified control_BirA ChIP DNA from ES cells Others Nanog bioNanog ChIP DNA from ES cells Others Max bioMax ChIP DNA from ES cells Others Kat5 bioTip60 ChIP DNA from ES cells Others E2f4 bioE2F4 ChIP DNA from ES cells Others Dmap1 bioDmap1 ChIP DNA from ES cells Input control Input control none neuronal progenitor cells, input Others Myc H190 (Santa Cruz, sc764) neuronal progenitor cells, H190 ChIP RNA polymerase Polr2b RPB2 sc-67318 RPB2_ZT22, liver cells RNA polymerase Polr2b RPB2 sc-67318 RPB2_ZT18, liver cells RNA polymerase Polr2b RPB2 sc-67318 RPB2_ZT14, liver cells RNA polymerase Polr2b RPB2 sc-67318 RPB2_ZT10, liver cells RNA polymerase Polr2b RPB2 sc-67318 RPB2_ZT06, liver cells RNA polymerase Polr2b RPB2 sc-67318 RPB2_ZT02, liver cells Input control Input control non-immuned rabbit serum MSC clone - control Histone H4K20me1 H4K20ME1 (Abcam, ab9051, lot 602259) MSC clone - H4K20ME1 antibody Input control Input control non-immuned rabbit serum MSC population - control Histone H4K20me1 H4K20ME1 (Abcam, ab9051, lot 602259) MSC population - H4K20ME1 antibody Histone H3K27ac H3K27ac (Active, Motif, lot AM) ES cells Histone H3K36me3 H3K36Me3 (Abcam, ab9050-100, lot 707946) ES cells Histone H3K9me3 H3K9Me3 (Abcam, ab8898, lot GR88132-1) ES cells Histone H3K4me3 H3K4Me3 (Active, Motif, lot 39159) ES cells Histone H3K4me1 H3K4Me (Abcam, ab8895-50, lot 720417) ES cells Histone H4K91ac H4K91Ac mouse, in vitro activated B cells Histone H2BK120ac H2BK120Ac mouse, in vitro activated B cells Histone H3K9ac H3K9Ac mouse plasmacytoma PCT6937 RNA polymerase RNA polymerase II PolII mouse plasmacytoma PCT4961 Histone H2BK5ac H2BK5Ac mouse, in vitro activated B cells Others Rnf2 anti-RING1B antibody PMID: 11289226 forelimb Others Rnf2 anti-RING1B antibody PMID: 11289226 midbrain Others Rnf2 anti-RING1B antibody PMID: 11289226 forebrain Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008018 Liver Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008017 Liver Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008016 Liver Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008015 Liver Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008014 Liver Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008013 Liver Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008012 Liver Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008011 Liver Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008010 Liver Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008009 Liver Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008008 Liver Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008007 Liver Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008006 Liver Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008005 Liver Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008004 Liver Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008003 Liver Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008002 Liver Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008001 Liver Input control Input control none Input DNA Others Srebf1 SREBP1 sc-8984x SREBP1_ZT22, liver cells Others Srebf1 SREBP1 sc-8984x SREBP1_ZT18, liver cells Others Srebf1 SREBP1 sc-8984x SREBP1_ZT14, liver cells Others Srebf1 SREBP1 sc-8984x SREBP1_ZT10, liver cells Others Srebf1 SREBP1 sc-8984x SREBP1_ZT06, liver cells Others Srebf1 SREBP1 sc-8984x SREBP1_ZT02, liver cells Others Spi1 anti-PU.1 (Santa Cruz; sc-352) purified primary B cells from Bi-8i mice; stimulated for 3 Days; anti-PU.1 ChIP Input control Input control none mouse CD8+ T cells Others Spi1 PU.1 T-21 (Santa Cruz, sc-352x) 3T3-L1 adipocyte, day 10, adeno-PU1 72hrs, PU.1 ChIP Others Pparg PPARg H-100 (Santa Cruz, sc-7196x) 3T3-L1 adipocyte, day 10, adeno-PU1 72hrs, PPARg ChIP Others Pparg PPARg H-100 (Santa Cruz, sc-7196x) 3T3-L1 adipocyte, day 10, adeno-LACZ 72hrs, PPARg ChIP Input control Input control none 3T3-L1 adipocyte, day 10, adeno-PU1 72hrs, input Input control Input control none 3T3-L1 adipocyte, day 10, adeno-LACZ 72hrs, input Histone H3K4me3 H3K4me3: Active Motif 39159, lot# 0169004 Neural progenitor cells Histone H3K4me1 H3K4me1: Abcam ab8895, lot# 961813 Neural progenitor cells Histone H3K27me3 H3K27me3: Millipore 07-449 lot# DAM1588246 Neural progenitor cells Others Foxo3 Foxo3-NFL: Brunet Lab (Greer et al., 2007 PMID 17900900) Neural progenitor cells Others Ascl1 Ascl1: Abcam ab74065, lot# 830280 Neural progenitor cells Input control Input control N/A Embryonic stem cell culture Others Rest anti-REST (Rabbit polyclonal antibody raised against a peptide corresponding to the C-terminal portion of REST and described in Nurit Ballas et al. Cell. (2005).) Embryonic stem cell culture RNA polymerase RNA polymerase II POL2 day of pseudopregnancy 2.5 and 3.5 female mouse uterus RNA polymerase RNA polymerase II POL2 postnatal day 12 female mouse uterus Others Foxa2 FOXA2 day of pseudopregnancy 2.5 and 3.5 female mouse uterus Others Foxa2 FOXA2 postnatal day 12 female mouse uterus Others Kdm6a KDM6A ES-E14TG2a Others Suz12 Suz12 ES-E14TG2a Input control Input control anti-IgG ESC E14 Others Max anti-Max ESC E14 Others Fos ChIPseq_cFos_mast Others Mitf ChIPseq_Mitf_mast Others Tal1 ChIPseq_Scl_mast Others Runx1 ChIPseq_Runx1_mast Others Spi1 ChIPseq_PU1_mast Others Meis1 ChIPseq_Meis1_mast Others Lmo2 ChIPseq_Lmo2_mast Others Gata2 ChIPseq_Gata2_mast Others Fli1 ChIPseq_Fli1_mast Others Erg ChIPseq_Erg_mast Others Tcf3 ChIPseq_E2A_mast Others Ctcf ChIPseq_Ctcf_mast Others Tcf3 ChIPseq_E2A_HPC7 Others Ctcf ChIPseq_Ctcf_HPC7 RNA polymerase RNA polymerase II Ser5ph RNA Pol II CD43 negative mouse resting B cells RNA polymerase RNA polymerase II 8WG16 CD43 negative mouse resting B cells Histone H3K4me1 H3K4me1 (Abcam, #ab8895) hipocampal tissue from adult mice Input control Input control none DPdouble positive thymocytes derived from in vitro expanded bone marrow cells transduced with Nup98-HoxB4, grown with IL7 and DLL4 (Notch signaling) and injected into Rag2-/- mouse Input control Input control none ProT in vitro expanded bone marrow cells transduced with Nup98-HoxB4 and grown with IL7 and DLL4 (Notch signaling) Input control Input control none HSC in vitro expanded bone marrow cells transduced with Nup98-HoxB4 RNA polymerase RNA polymerase II RNA Polymerase II (phospho S5) (Abcam ab5131) ESC stage cultures, RNA Polymerase II Others Gabpa anti-GABPalpha (sc-22810X, Santa Cruz). CD4 T cells Input control Input control None Hepa 1-6 cells Others GFP Life Technologies (A6455, rabbit anti-GFP) Neural tube Others Prdm13 Johnson lab generated rabbit polyclonal antibodies (PRDM13-Ab2 (FL) TX970, rabbit anti-mouse PRDM13) Telencephalon Others Prdm13 Johnson lab generated rabbit polyclonal antibodies (PRDM13-Ab2 (FL) TX970, rabbit anti-mouse PRDM13) Neural tube Others Rad21 Rad21 Rag1 -/- pro-B cells Others Ctcf CTCF Rag1 -/- pro-B cells Histone H3K4me3 H3K4me3 Rag1 -/- pro-B cells Histone H3K4me2 H3K4me2 Rag1 -/- pro-B cells RNA polymerase RNA polymerase II PolII Rag1 -/- pro-B cells Histone H3K27me3 H3K27me3 Rag1 -/- pro-B cells Histone H3ac H3ac Rag1 -/- pro-B cells Input control Input control MNase digested input MNase digested input DNA_differentiated ES cells Input control Input control MNase digested input MNase digested input DNA_embryonic stem cells Histone H4K16ac H4K16ac antibody (Millipore, catalog# 07-329, lot# 2073125) H4K16ac ChIP_differentiated ES cells Histone H4K16ac H4K16ac antibody (Millipore, catalog# 07-329, lot# 2073125) H4K16ac ChIP_embryonic stem cells Others Nfe2 NFE2 SC-477 from Santa Crus Ter119+ Cells Others Gata1 GATA1 ab11852 from Abcam Ter119+ Cells Others Ctcf CTCF 07-729 from Millipore Ter119+ Cells Input control Input control IGG heart ventricles from 8 week old mouse Others Dnmt3a Dnmt3a (Santa Cruz H-295) Back skin, Dnmt3a KO, DMBA/TPA, Dnmt3A ChIP Others Dnmt3a Dnmt3a (Santa Cruz H-295) Back skin, WT, DMBA/TPA, Dnmt3A ChIP Histone H3K27ac H3K27ac (Merck Millipore. Cat 07-360) Belly skin, WT, untreated, H3K27ac ChIP Histone H3K27ac H3K27ac (Merck Millipore. Cat 07-360) Back skin, WT, DMBA/TPA, H3K27ac ChIP Histone H3K4me3 H3K4me3 MEFs Input control Input control none MEFs Histone H3K27me3 H3K27me3 Millipore:07-449 H3K27me3 ChIP-seq in wt ESCs Histone H3K27me3 H3K27me3 Millipore:07-449 H3K27me3 ChIP-seq in Eed-/- ESCs Histone H3K27me3 H3K27me3 Millipore:07-449 H3K27me3 ChIP-seq in Suz12GT (aka Suz12(Bgal/Bgal)) ESCs Input control Input control none E17.5 Pancreas Input control Input control none E12.5 Neural Tube Others Ptf1a Lab generated rabbit anti-Ptf1a (AN255/256) E12.5 Telencephalon Input control Input control None Bulk forebrain Others Chd8 Chd8 (Abcam ab114126) Bulk forebrain Others Hnf4a HNF4a (ab41898, Abcam) Hnf4a_Intact Others Foxa1 FOXA1 (ab23738, Abcam) FoxA1_Intact Others Tfap2a AP2a (ab52222, Abcam) AP2a_Intact_rep2 Others Tfap2a AP2a (ab52222, Abcam) AP2a_Intact_rep1 Others Tfap2a AP2a (ab52222, Abcam) AP2a_Cast1b Others Tfap2a AP2a (ab52222, Abcam) AP2a_Cast1a Others Ar AR (Sahu et al. 2011) AR_Intact_rep2 Others Ar AR (Sahu et al. 2011) AR_Intact_rep1 Others Foxa1 FOXA1 (ab23738, Abcam) FoxA1_Cast+T Others Hnf4a HNF4a (ab41898, Abcam) Hnf4a_Cast1b Others Hnf4a HNF4a (ab41898, Abcam) Hnf4a_Cast1a Others Ar AR (Sahu et al. 2011) AR_Cast+T_rep2 Others Ar AR (Sahu et al. 2011) AR_Cast+T_rep1 Input control Input control rIgG (sc-2027, SantaCruz) rIgG1b Input control Input control rIgG (sc-2027, SantaCruz) rIgG1a Others Foxa1 FOXA1 (ab23738, Abcam) FoxA1_Cast+T_rep2 Others Foxa1 FOXA1 (ab23738, Abcam) FoxA1_Cast+T_rep1 Others Foxa1 FOXA1 (ab23738, Abcam) FoxA1_Cast Others Ar AR (Sahu et al. 2011) AR_Cast+T_rep2b Others Ar AR (Sahu et al. 2011) AR_Cast+T_rep2a Others Ar AR (Sahu et al. 2011) AR_Cast+T_rep1b Others Ar AR (Sahu et al. 2011) AR_Cast+T_rep1a Others Ar AR (Sahu et al. 2011) AR_Cast1b Others Ar AR (Sahu et al. 2011) AR_Cast1a Input control Input control nono (input) input DNA brain Histone H2A.Z H2AZ Chromatin IP against H2AZ brain Unclassified Unclassified Pro-B cell Others Biotin Dynabeads M-280 Streptavidin (Invitrogen) Pro-B cell Input control Input control none, input CLK_Input_Sonicated_WT30_ZT22 Input control Input control none, input CLK_Input_Sonicated_WT30_ZT06 Input control Input control none, input CLK_Input_Sonicated_WT29_ZT22 Input control Input control none, input CLK_Input_Sonicated_WT29_ZT06 Input control Input control none, input CLK_Input_Sonicated_WT28_ZT22 Input control Input control none, input CLK_Input_Sonicated_WT28_ZT06 Others Clock goat polyclonal anti-CLK, S-19; sc-6927; lot E3112 CLK_ChIP_Sonicated_WT30_ZT22 Others Clock goat polyclonal anti-CLK, S-19; sc-6927; lot E3112 CLK_ChIP_Sonicated_WT30_ZT06 Others Clock goat polyclonal anti-CLK, S-19; sc-6927; lot E3112 CLK_ChIP_Sonicated_WT29_ZT22 Others Clock goat polyclonal anti-CLK, S-19; sc-6927; lot E3112 CLK_ChIP_Sonicated_WT29_ZT06 Others Clock goat polyclonal anti-CLK, S-19; sc-6927; lot E3112 CLK_ChIP_Sonicated_WT28_ZT22 Others Clock goat polyclonal anti-CLK, S-19; sc-6927; lot E3112 CLK_ChIP_Sonicated_WT28_ZT06 Others Clock goat polyclonal anti-CLK, S-19; sc-6927; lot E3112 CLK_ChIP_MNase_WT30_ZT22 Others Clock goat polyclonal anti-CLK, S-19; sc-6927; lot E3112 CLK_ChIP_MNase_WT30_ZT06 Others Clock goat polyclonal anti-CLK, S-19; sc-6927; lot E3112 CLK_ChIP_MNase_WT29_ZT22 Others Clock goat polyclonal anti-CLK, S-19; sc-6927; lot E3112 CLK_ChIP_MNase_WT29_ZT06 Others Clock goat polyclonal anti-CLK, S-19; sc-6927; lot E3112 CLK_ChIP_MNase_WT28_ZT22 Others Clock goat polyclonal anti-CLK, S-19; sc-6927; lot E3112 CLK_ChIP_MNase_WT28_ZT06 Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008001 H2AZ_BM5_ZT22 Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008001 H2AZ_BM5_ZT18 Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008001 H2AZ_BM5_ZT14 Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008001 H2AZ_BM5_ZT10 Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008001 H2AZ_BM5_ZT06 Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008001 H2AZ_BM5_ZT02 Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008001 H2AZ_WT12_ZT22 Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008001 H2AZ_WT12_ZT18 Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008001 H2AZ_WT12_ZT14 Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008001 H2AZ_WT12_ZT10 Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008001 H2AZ_WT12_ZT06 Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008001 H2AZ_WT12_ZT02 Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008001 H2AZ_WT11_ZT22 Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008001 H2AZ_WT11_ZT18 Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008001 H2AZ_WT11_ZT14 Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008001 H2AZ_WT11_ZT10 Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008001 H2AZ_WT11_ZT06 Histone H2A.Z rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008001 H2AZ_WT11_ZT02 Input control Input control none Three-week cultured Th2 cells generated from primary splenic CD4_T cells Others Esrrg ERR? (Dufour et al. Cell Metab 5, 345-356 (2007)) mouse ES-cell derived neurons Input control Input control none mouse ES-cell derived neurons Input control Input control NULL shKdm5b 4TF-MEFs Input control Input control NULL shLuc 4TF-MEFs Histone H3K4me2 Anti-H3K4me2 antibody (Abcam: ab32356) shKdm5b 4TF-MEFs Histone H3K4me3 Anti-H3K4me3 antibody (Millipore: 17-614) shKdm5b 4TF-MEFs Histone H3K4me2 Anti-H3K4me2 antibody (Abcam: ab32356) shLuc 4TF-MEFs Histone H3K4me3 Anti-H3K4me3 antibody (Millipore: 17-614) shLuc 4TF-MEFs Others Tal1 Scl/Tal1 Mouse erythroleukemic cells Input control Input control N/A (input sample) Hematopoietic progenitors Histone H3K4me1 H3K4me1 Hematopoietic progenitors Input control Input control normal goat IgG ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells Input control Input control No antibody IgG control ESC Input control Input control Normal rabbit IgG (Santa Cruz Biotechnology, sc-2027) Striatal Progenitor Cells Others Runx1 Abcam; ab23980 ChIP_NKT_Runx1 Input control Input control None ChIP_NKT_Input Unclassified Unclassified ChIP CTL+ Nc1A-Bio.BirA Unclassified Unclassified ChIP CTL+ BirA Input control Input control IgG: Sigma, I8140 Haematopoietic progenitor cells Input control Input control none CD8+ cells, Foxo1tagBirA mice Input control Input control none CD8+ cells, wild-type Others Biotin Strepdavidin CD8+ cells, Foxo1tagBirA mice Others Foxo1 Foxo1 antibody (Abcam, Ab39670) CD8+ cells, wild-type Input control Input control none Junbfl/flCD4cre Th17 cells Input control Input control none Junb+/+CD4cre Th17 cells Others Junb JunB (C-11; sc-8051x) WT Th17 cells Others Junb JunB (N-17; sc-46x) WT Th17 cells RNA polymerase RNA polymerase II RNA Pol II antibody (Santa Cruz Biotechnology, N20, sc899) Murine erythroleukemia (MEL) cells Others Cdk9 CDK9 C20 antibody (Santa Cruz Biotechnology, C20, sc-484) Murine erythroleukemia (MEL) cells Input control Input control E14 ES cells, CHX, input Input control Input control E14 ES cells, control, input Input control Input control None Differentiated and FACS from NSCs Histone H3K27me3 H3K27me3 Differentiated and FACS from NSCs Histone H3K4me3 H3K4me3 Differentiated and FACS from NSCs Input control Input control None Derived from mESCs Histone H3K27me3 H3K27me3 Derived from mESCs Histone H3K4me3 H3K4me3 Derived from mESCs Others Irf4 Anti-IRF4 (M-17) (Santa Cruz Biotechnology, sc-6059x) WT murine Treg cells, Irf4 ChIP Input control Input control rabbit IgG (I5006, Sigma) IgG_TgERG_leukemia_2 Others Erg ERG-1/2/3 (clone C-17, Sc354X, Santa Cruz) ERG_TgERG_leukemia_2 Input control Input control rabbit IgG (I5006, Sigma) IgG_TgERG_leukemia_1 Others Erg ERG-1/2/3 (clone C-17, Sc354X, Santa Cruz) ERG_TgERG_leukemia_1 Input control Input control None None mouse heart Others Brd4 Brd4 A301-985A mouse heart Others Kdm6a Anti-UTX (Bethyl laboratories, A302-374A) mESC Others Ep300 Anti-p300 (Santa Cruz, sc-585) mESC Input control Input control none spleen, WT, input Histone H3K4me3 H3K4me3 (Active Motif Cat.#39159 Lot.4) spleen, RBP-J mutant, H3K4me3 ChIP Histone H3K4me3 H3K4me3 (Active Motif Cat.#39159 Lot.4) spleen, WT, H3K4me3 ChIP Histone H3K27me3 H3K27me3 (Millipore Cat.#07-449 Lot. JBC1854858) spleen, RBP-J mutant, H3K27me3 ChIP Histone H3K27me3 H3K27me3 (Millipore Cat.#07-449 Lot. JBC1854858) spleen, WT, H3K27me3 ChIP Others Foxo1 FKHR (H-128)X (sc-11350X, Santa Cruz Biotechnology), lot# F0310 spleen Histone H3K4me3 H3K4me3 Abcam AB8580 Chromatin IP against H3K4 (10^6) Histone H3K27me3 H3K27me3 Abcam AB6002 Chromatin IP against H3K27me3 Histone H3K27me3 anti-H3K27me3 E11.5 Primordial Germ Cells, H3K27me3 ChIP Histone H3K4me3 anti-H3K4me3 E11.5 Primordial Germ Cells, H3K4me3 ChIP Input control Input control none E11.5 Primordial Germ Cells, input Histone H3K27me3 anti-H3K27me3 (Millipore, 17-622, lot 1731568) BCL1 cell line transduced with Y641N EZH2 Histone H3K27me3 anti-H3K27me3 (Millipore, 17-622, lot 1731568) BCL1 cell line transduced with Y641F EZH2 Histone H3K27me3 anti-H3K27me3 (Millipore, 17-622, lot 1731568) BCL1 cell line transduced with WT EZH2 Input control Input control none CD4+ T cells_treatment with immobilized anti-CD3 mAb_input DNA Input control Input control none mouse embryo fibroblasts_background_p53-/- dox Others Trp53 CM-5 (Vector labs, VP-P956) mouse embryo fibroblasts_p53 ChIP-seq_p53-/- dox Input control Input control none mouse embryo fibroblasts_background_wt dox Others Trp53 CM-5 (Vector labs, VP-P956) mouse embryo fibroblasts_p53 ChIP-seq_wt dox Unclassified Unclassified 7438 cells + Afos Others Biotin Streptavidin Dynalbeads (Invitrogen) Beko-bioNIC cells Others Biotin Streptavidin Dynalbeads (Invitrogen) Beko-bio cells Input control Input control none (input) iWAT-derived adipocytes Input control Input control none T29 Ik1-ER cells treated with 4OHT Others Ikzf1 in house anti-Ikaros rabbit polyclonal antibody ; lot: A3 T29 Ik1-ER cells treated with 4OHT Others Pparg PPARg 3T3-F442A white adipocytes Others Nfia NFI 3T3-F442A white adipocytes DNase-seq DNase-Seq DNase Male C57BL/6, adrenalectomized Others Batf3 anti-BATF3 cultured TH2 cells Input control Input control none (input) CTCF_knockout Others Ctcf CTCF (Active Motif Cat# 61311) CTCF_knockout Input control Input control none (input) Control Others Ctcf CTCF (Active Motif Cat# 61311) Control Input control Input control none (input lysate) primary CD4+ T cells from spleen and lymph nodes Others Bach2 anti-Bach2 - rabbit antibody (generated in-house, Tohoku University) primary CD4+ T cells from spleen and lymph nodes Others Ctcf CTCF (Active motif REF# 61311) Forelimb Input control Input control anti-IgG (Abcam, Cat # ab37415, Lot # GR90135-1) murine embryonic stem cells Input control Input control none NIH3T3_Control_combined Input control Input control none NIH3T3_Control_UO Input control Input control none NIH3T3_Control_LAT Input control Input control none NIH3T3_Control_15 Input control Input control none NIH3T3_Control_03 Histone H3 Total H3 NIH3T3_TOTAL_H3_UO Histone H3 Total H3 NIH3T3_TOTAL_H3_LAT Histone H3 Total H3 NIH3T3_TOTAL_H3_15 Histone H3 Total H3 NIH3T3_TOTAL_H3_03 RNA polymerase RNA polymerase II 8WG16 NIH3T3_8WG16_UO RNA polymerase RNA polymerase II 8WG16 NIH3T3_8WG16_03 Others Elk3 anti-Net 1996 NIH3T3_NET_UO Others Elk3 anti-Net 1996 NIH3T3_NET_LAT Others Elk3 anti-Net 1996 NIH3T3_NET_15 Others Elk3 anti-Net 1996 NIH3T3_NET_03 Others Elk4 SAP-1a NIH3T3_SAP1_UO Others Elk4 SAP-1a NIH3T3_SAP1_LAT Others Elk4 SAP-1a NIH3T3_SAP1_15 Others Elk4 SAP-1a NIH3T3_SAP1_03 Others Elk1 ELK1 NIH3T3_ELK1_UO Others Elk1 ELK1 NIH3T3_ELK1_LAT Others Elk1 ELK1 NIH3T3_ELK1_15 Others Elk1 ELK1 NIH3T3_ELK1_03 Others Mkl2 MRTF-B NIH3T3_MRTFB_UO Others Mkl2 MRTF-B NIH3T3_MRTFB_LAT Others Mkl2 MRTF-B NIH3T3_MRTFB_15 Others Mkl2 MRTF-B NIH3T3_MRTFB_03 Others Mkl1 MRTF-A NIH3T3_MRTFA_UO Others Mkl1 MRTF-A NIH3T3_MRTFA_LAT Others Mkl1 MRTF-A NIH3T3_MRTFA_15 Others Mkl1 MRTF-A NIH3T3_MRTFA_03 Others Srf SRF NIH3T3_SRF_UO Others Srf SRF NIH3T3_SRF_LAT Histone H3K27me3 H3K27me3 C2C12 myoblasts Histone H3K4me3 H3K4me3 C2C12 myoblasts Others Ezh2 Ezh2 C2C12 myoblasts Input control Input control IgG C2C12 myotubes Input control Input control IgG C2C12 myoblasts Others Yy1 YY1 C2C12 myotubes Input control Input control none 3T3L1 preadipocyte cell Others Kmt2d Anti-MLL4 #3 (Home-made) 3T3L1 preadipocyte cell Input control Input control none Brown preadipocyte cell Others Crebbp CBP (D6C5) Rabbit mAb (Cell Signaling Technology, Lot 7389S, Batch 1) Brown preadipocyte cell Unclassified Unclassified ESC cells Histone H3K4me1 H3K4me1-Abcam-ab8895, GR114265-2 Cerebellar Granule Cells Histone H3K27ac H3K27Ac-Abcam-ab4729, GR184332-1 Cerebellar Granule Cells Histone H3K9me3 H3K9me3-Abcam-ab8898, GR148830-2 Cerebellar Granule Cells Histone H3K4me3 H3K4me3-Abcam-ab8580, GR273043-4 Cerebellar Granule Cells Unclassified Unclassified Synovial Fibroblasts Input control Input control none spermatogenic cells, Ezh2 mutant, input Input control Input control none spermatogenic cells, control, input Others Cebpb CEBPB C/EBP Antibody (Santa Cruz Biotech, catalog# sc-150) Others Nr3c1 NR3C1 Mix of GR Antibody (Santa Cruz Biotech, catalog# sc-1004) and Glucocorticoid Receptor Antibody (Thermo Scientific, catalog# PA1-511A) Input control Input control none Cell line Others Cbx3 Anti-Cbx3 antibody, Millipore, 05-690; clone 42s2 Cell line Others Epitope tags anti V5 (Invitrogen) Others Epitope tags anti V5 (Invitrogen) V5-TopoIIa etoposide BrgWT Input control Input control none NMuMG cells, input Unclassified Unclassified Mouse ES cells Histone H3K27me3 H3K27me3 (Abcam ab6002 Lot: GR218433-1) MC9 shRad21 Histone H3K4me1 H3K4me1 (Abcam ab8895 Lot: GR243233-1-1) MC9 shRad21 Histone H3K27ac H3K27ac (Abcam ab4729 Lot: GR243994-1) MC9 shRad21 Histone H3K4me3 H3K4me3 (Abcam ab8580 Lot: GR240214-2) MC9 shRad21 Histone H3K27me3 H3K27me3 (Abcam ab6002 Lot: GR218433-1) MC9 Histone H3K4me1 H3K4me1 (Abcam ab8895 Lot: GR243233-1-1) MC9 Histone H3K27ac H3K27ac (Abcam ab4729 Lot: GR243994-1) MC9 Histone H3K4me3 H3K4me3 (Abcam ab8580 Lot: GR240214-2) MC9 RNA polymerase RNA polymerase II Rpb1 CTD (Cell Signaling 2629S Lot: 3) MC9 Histone H3K27me3 H3K27me3 (Abcam ab6002 Lot: GR218433-1) Mast WSH Histone H3K4me1 H3K4me1 (Abcam ab8895 Lot: GR243233-1-1) Mast WSH Histone H3K27ac H3K27ac (Abcam ab4729 Lot: GR243994-1) Mast WSH Histone H3K4me3 H3K4me3 (Abcam ab8580 Lot: GR240214-2) Mast WSH RNA polymerase RNA polymerase II Rpb1 CTD (Cell Signaling 2629S Lot: 3) Mast WSH Histone H3K4me1 H3K4me1 (Abcam ab8895 Lot: GR243233-1-1) Mast wt Histone H3K27ac H3K27ac (Abcam ab4729 Lot: GR243994-1) Mast wt Histone H3K4me3 H3K4me3 (Abcam ab8580 Lot: GR240214-2) Mast wt Histone H3K27me3 H3K27me3 (Abcam ab6002 Lot: GR218433-1) 32D Histone H3K4me1 H3K4me1 (Abcam ab8895 Lot: GR243233-1-1) 32D Histone H3K27ac H3K27ac (Abcam ab4729 Lot: GR243994-1) 32D Histone H3K4me3 H3K4me3 (Abcam ab8580 Lot: GR240214-2) 32D RNA polymerase RNA polymerase II Rpb1 CTD (Cell Signaling 2629S Lot: 3) 32D Input control Input control Rabbit normal IgG IgG_ChIP Others Hexim1 ab25388 HEXIM1_ChIP Others Cdk9 mAb #2316 CDK9_ChIP RNA polymerase RNA polymerase II SC-899 Pol2_si_hnRNPB1 RNA polymerase RNA polymerase II SC-899 Pol2_si_hnRNPA1 RNA polymerase RNA polymerase II SC-899 Pol2_siNC RNA polymerase RNA polymerase II SC-899 Pol2_2meth_as7SK RNA polymerase RNA polymerase II SC-899 Pol2_2meth_asNC RNA polymerase RNA polymerase II SC-899 Pol2_SRSF2ko RNA polymerase RNA polymerase II SC-899 Pol2_SRSF2wt RNA polymerase RNA polymerase II SC-899 Pol2_SRSF1ko RNA polymerase RNA polymerase II SC-899 Pol2_SRSF1wt Others Epitope tags anti-HA (ab9110) SRSF2_ChIP_SRSF1ko Others Epitope tags anti-HA (ab9110) SRSF2_ChIP_SRSF1wt Others Epitope tags anti-HA (ab9110) SRSF1_ChIP_SRSF2ko Others Epitope tags anti-HA (ab9110) SRSF1_ChIP_SRSF2wt Unclassified Unclassified (Fu and Maniatis, 1990) SRSF2_NA_ChIP Others Srsf1 Anti-SRSF1 (32-4500) SRSF1_NA_ChIP Others Epitope tags anti-HA (ab9110) SRSF2_HA_ChIP Others Epitope tags anti-HA (ab9110) SRSF1_HA_ChIP Histone H3K27ac H3K27Ac Proximal Forelimbs E12.5 Histone H3K27ac H3K27Ac Early forelimb buds E10.5 Histone H3K27ac H3K27Ac Early forelimb buds E9.5 RNA polymerase RNA polymerase II Anti-RNAPII-Ser2P antibody (Abcam; ab5095) R1 ES cells, shKdm5b, RNAPII-Ser2P ChIP RNA polymerase RNA polymerase II Anti-RNAPII-Ser2P antibody (Abcam; ab5095) R1 ES cells, shLuc, RNAPII-Ser2P ChIP RNA polymerase RNA polymerase II Anti-RNAPII-Ser5P antibody (Abcam; ab5131) R1 ES cells, shKdm5b, RNAPII-Ser5P ChIP RNA polymerase RNA polymerase II Anti-RNAPII-Ser5P antibody (Abcam; ab5131) R1 ES cells, shLuc, RNAPII-Ser5P ChIP RNA polymerase RNA polymerase II Anti-RNAPII antibody (Abcam; ab817) R1 ES cells, shKdm5b, RNAPII ChIP RNA polymerase RNA polymerase II Anti-RNAPII antibody (Abcam; ab817) R1 ES cells, shLuc, RNAPII ChIP Input control Input control input primary T-cells Input control Input control rabbit anti-IgG Abcam,catalog #37415, lot #905012 BMiFLT3 (15-3) cells Others Runx1 rabbit anti-Runx1 generated against a C-terminal peptide (kindly provided by Y. Groner and D. Levanon (Weizmann Institute, Rehovot)) BMiFLT3 (15-3) cells Others Ep300 anti-P300 Others Runx1 anti-Runx1 Input control Input control non-immune serum Histone H3K9me3 H3K9me3 (Abcam, ab8898) E14 cells with SMARCAD1 knockdown Histone H3K4me3 H3K4me3 (Abcam, Ab8580) E14 cells with SMARCAD1 knockdown Histone H3K27me3 H3K27me3 antibody Histone H3K4me3 H3K4me3 antibody Others Biotin Streptavidin bead mESC Others Epitope tags Anti-FLAG antibody (Sigma) mESC Others Cbx5 Anti-HP1 antibody (Millipore) shSmyd5_mESC Others Cbx5 Anti-HP1 antibody (Millipore) shLuc_mESC Histone H3K9me2 Anti-H3K9me2 antibody (Abcam; ab1220) shSmyd5_mESC Histone H3K9me2 Anti-H3K9me2 antibody (Abcam; ab1220) shLuc_mESC Histone H3K9me3 Anti-H3K9me3 antibody (Abcam; ab8898) shSmyd5_mESC Histone H3K9me3 Anti-H3K9me3 antibody (Abcam; ab8898) shLuc_mESC Histone H4K20me3 Anti-H4K20me3 antibody (Abcam; ab9053) shSmyd5_mESC Histone H4K20me3 Anti-H4K20me3 antibody (Abcam; ab9053) shLuc_mESC Histone H3K36me3 anti-H3K36me3 (Diagenode, Premium, C15410192) B6spo11ko_H3K36me3_Input Histone H3K36me3 anti-H3K36me3 (Diagenode, Premium, C15410192) RJ2_H3K36me3_Input Histone H3K4me3 anti-H3K4me3 (Abcam, ab8580) RJ2_H3K4me3_Input Histone H3K4me3 anti-H3K4me3 (Abcam, ab8580) RJ2_H3K4me3_ChIPseq Histone H3K4me3 anti-H3K4me3 (Abcam, ab8580) B6_H3K4me3_Input Histone H3K4me3 anti-H3K4me3 (Abcam, ab8580) B6_H3K4me3_ChIPseq Others Prdm9 anti-PRDM9 (BdM) B6prdm9ko_PRDM9_Input Others Prdm9 anti-PRDM9 (BdM) B6prdm9ko_PRDM9_ChIPseq Input control Input control none Cerebellar granule neuron Histone H3K27ac H3K27ac (Diagenode) Cerebellar granule neuron progenitor Input control Input control none Cerebellar granule neuron progenitor Others Bhlhe41 anti-V5 antibody (clone V5-10) Bhlhe41 ChIP-seq Vh12/Vk4 Tg B-1a Others Bhlhe41 anti-V5 antibody (clone V5-10) Bhlhe41 ChIP-seq Vh12/Vk4 Tg B-1a; spike in Input control Input control ChIP-seq input pro-B cell Input control Input control anti-Rabbit IgG antibody (sc-2027, Santa Cruz) E14 cells_IgG_IP Others Zfp322a anti-ZNF322 antibody (sc-102205, Santa Cruz) E14 cells_Zfp322a_IP Input control Input control whole serum from normal nonimmunized rabbits naive_IgG_nave Input control Input control none vehicle_Input_Veh Histone H4K12ac AcH4K12 HD-82Q_AcH4K12_ChIPseq Histone H4K12ac AcH4K12 WT_AcH4K12_ChIPseq Histone H3K9K14ac AcH3K9,14 HD-82Q_AcH3K9,14_ChIPseq Histone H3K9K14ac AcH3K9,14 WT_AcH3K9,14_ChIPseq Others Epitope tags anti-V5 antibody (Cat# R960-CUS, Life Technologies, Carlsbad, CA) Klf3-/- murine embryonic fibroblasts, rescued with DBD-V5 Input control Input control none Klf3-/- murine embryonic fibroblasts, rescued with DBD-V5 Others Epitope tags anti-V5 antibody (Cat# R960-CUS, Life Technologies, Carlsbad, CA) Klf3-/- murine embryonic fibroblasts, rescued with ?DL-V5 Input control Input control none Klf3-/- murine embryonic fibroblasts, rescued with ?DL-V5 Others Klf3 anti-V5 antibody (Cat# R960-CUS, Life Technologies, Carlsbad, CA) Klf3-/- murine embryonic fibroblasts, rescued with Klf3-V5 Input control Input control none Klf3-/- murine embryonic fibroblasts, rescued with Klf3-V5 Others Ehf ESE-3A (E-15) antibody Santa Cruz Biotechnology, Catalog# sc-15450, Lot# I1704 mouse corneal epithelium Input control Input control none mouse corneal epithelium Others Nanog Nanog (Santa Cruz) Mouse embryoid bodies Others Nanog Nanog (Santa Cruz) Mouse embryonic stem cells Others Tbx3 Tbx3 (Santa Cruz) Mouse embryoid bodies Others Tbx3 Tbx3 (Santa Cruz) Mouse embryonic stem cells Unclassified Unclassified 2010-4428_101222_HWI-EAS146_0319_s_3_sequence Others Epitope tags Monoclonal ANTI-FLAG M2 antibody 2011-947_110806_SN484_0108_AD0BT3ABXX_2_sequence Others Atf4 ATF4 CREB-2 (C-20): sc-200, Lot#J2011 ATF4_ChIP-seq Others Cebpb CEBPb CEBP B:(C-19): sc-150, lot:#I1010 CEBPB_Tg_ChIP-seq Others Cebpb CEBPb CEBP B:(C-19): sc-150, lot:#I1010 CEBPB_ChIP-seq Input control Input control none none C2C12-diff-60h-1pFA+EGS-Input-60h-11132 Input control Input control none none C2C12-diff-60h-1pFA-Input-11610 Others Myog myogenin Santa Cruz; sc-12732 C2C12-diff-60h-myogenin-12152 Others Myog myogenin Santa Cruz; sc-12732 C2C12-diff-60h-myogenin-10598 Others Myog myogenin Santa Cruz; sc-12732 C2C12-diff-60h-myogenin-10158 Others Myod1 MyoD Santa Cruz; sc-32758 C2C12-diff-60h-MyoD-10480 Others Epitope tags anti-HA cultured mouse myoblasts (C2C12) Input control Input control None undifferentiated myeloid progenitor cells Input control Input control None in-vitro differentiated neutrophils Histone H3K36me3 H3K36me3 ab9050 Abcam undifferentiated myeloid progenitor cells Histone H3K36me3 H3K36me3 ab9050 Abcam in-vitro differentiated neutrophils Histone H3K9me3 H3K9me3 ab8898 Abcam undifferentiated myeloid progenitor cells Histone H3K9me3 H3K9me3 ab8898 Abcam in-vitro differentiated neutrophils Histone H3K27me3 H3K27me3 07-449 Millipore undifferentiated myeloid progenitor cells Histone H3K27me3 H3K27me3 07-449 Millipore in-vitro differentiated neutrophils Histone H3K4me3 H3K4me3 ab8580 Abcam undifferentiated myeloid progenitor cells Histone H3K4me3 H3K4me3 ab8580 Abcam in-vitro differentiated neutrophils Histone H3K4me2 H3K4me2 ab7766 Abcam undifferentiated myeloid progenitor cells Histone H3K4me2 H3K4me2 ab7766 Abcam in-vitro differentiated neutrophils Histone H3K4me1 H3K4me1 ab8895 Abcam undifferentiated myeloid progenitor cells Histone H3K4me1 H3K4me1 ab8895 Abcam in-vitro differentiated neutrophils Histone H3K27ac H3K27ac ab4729 Abcam undifferentiated myeloid progenitor cells Histone H3K27ac H3K27ac ab4729 Abcam in-vitro differentiated neutrophils Others Ctcf CTCF 07-729 Millipore undifferentiated myeloid progenitor cells Others Ctcf CTCF 07-729 Millipore in-vitro differentiated neutrophils Others Rad21 RAD21 ab992 Abcam undifferentiated myeloid progenitor cells Others Rad21 RAD21 ab992 Abcam in-vitro differentiated neutrophils Input control Input control none splenic Plasmablasts Others Ctcf CTCF splenic Plasmablasts Input control Input control none splenic B cells Others Ctcf CTCF splenic B cells Input control Input control immunoglobulin G Testes, input RNA polymerase RNA polymerase II anti-RNA polymerase II Others Mybl1 anti-A-MYB Testes, A-MYB ChIP Input control Input control E11.5 heart, Input Histone H3K79me2 H3K79me2 DP thymocytes Input control Input control none embryonic stem cells mixed with neural progenitor cells in a ratio of 10:90 Others Klf4 Klf4 (R&D AF3158) embryonic stem cells mixed with neural progenitor cells in a ratio of 10:90 Others Tcf7 Tcf1 IL-2 activated Splenic NK cells, Tcf7-/- Histone H3K4me3 H3K4me3 IL-2 activated Splenic NK cells, Tcf7+/+ Others Tcf7 Tcf1 IL-2 activated Splenic NK cells, Tcf7+/+ Unclassified Unclassified IL-2 activated Splenic NK cells, Tcf7+/+ Input control Input control IgG Thymus Histone H3K27ac H3K27ac Abcam/ab4729 Thymus Histone H3K4me1 H3K4me1 Abcam and Millipore/ab8895 and 07-436 Thymus Others Ep300 p300 (sc-585, Santa Cruz Biotechnology) AntNPC (anterior neural progenitors derived from mESC) Unclassified Unclassified macrophage Unclassified Unclassified 3T3L1 Unclassified Unclassified epididymal WAT Histone H3K27ac H3K27ac (Active Motif, 39133) Pool of epididymal and inguinal WAT Others Smc1a SMC1 (Bethyl, A300-055A) delA-L1-SMC1 Others Ctcf CTCF (Abcam ab70303 / Millipore 07-729) Mammary-delD-L1-H3K27ac Others Ctcf CTCF (Abcam ab70303 / Millipore 07-729) Mammary-delC-L1-CTCF Others Ctcf CTCF (Abcam ab70303 / Millipore 07-729) Mammary-delAB-L1-CTCF Histone H3K4me3 H3K4me3 Dnmt1-/-_MEFs_H3K4me3 Histone H3K4me3 H3K4me3 Dnmt1+/+_MEFs_H3K4me3 Histone H3K27me3 H3K27me3 Dnmt1-/-_MEFs_H3K27me3 Histone H3K27me3 H3K27me3 Dnmt1+/+_MEFs_H3K27me3 Input control Input control None Neuro 2a cells, input Input control Input control None Cortex, input Input control Input control none (input) Input Replicate 3 Input control Input control none (input) Input Replicate 2 Input control Input control none (input) Input Replicate 1 Histone H3K27ac ab4729 (abcam) H3K27ac ChIP-seq in Erk inhibitor treated 24hr condition Replicate 3 Histone H3K27ac ab4729 (abcam) H3K27ac ChIP-seq in Erk inhibitor treated 24hr condition Replicate 2 Histone H3K27ac ab4729 (abcam) H3K27ac ChIP-seq in Erk inhibitor treated 24hr condition Replicate 1 Histone H3K27ac ab4729 (abcam) H3K27ac ChIP-seq in Erk inhibitor treated 4hr condition Replicate 3 Histone H3K27ac ab4729 (abcam) H3K27ac ChIP-seq in Erk inhibitor treated 4hr condition Replicate 2 Histone H3K27ac ab4729 (abcam) H3K27ac ChIP-seq in Erk inhibitor treated 4hr condition Replicate 1 Histone H3K27ac ab4729 (abcam) H3K27ac ChIP-seq in 24hr Replicate 3 Histone H3K27ac ab4729 (abcam) H3K27ac ChIP-seq in 24hr Replicate 2 Histone H3K27ac ab4729 (abcam) H3K27ac ChIP-seq in 24hr Replicate 1 Histone H3K27ac ab4729 (abcam) H3K27ac ChIP-seq in 4hr Replicate 3 Histone H3K27ac ab4729 (abcam) H3K27ac ChIP-seq in 4hr Replicate 2 Histone H3K27ac ab4729 (abcam) H3K27ac ChIP-seq in 4hr Replicate 1 Histone H3K27ac ab4729 (abcam) H3K27ac ChIP-seq in Untreated condition (0hr) Replicate 3 Histone H3K27ac ab4729 (abcam) H3K27ac ChIP-seq in Untreated condition (0hr) Replicate 2 Histone H3K27ac ab4729 (abcam) H3K27ac ChIP-seq in Untreated condition (0hr) Replicate 1 Histone H3K9me3 Ab8898(Abcam) Embryonic stem cells Histone H3K27ac Ab4729(Abcam) Embryonic stem cells Input control Input control IgG IgG Others Gata3 anti-GATA3 Gata3 Others Gata2 anti-GATA2 Gata2 Input control Input control Mettl3_H5_37_input Others Mettl3 Mettl3_H5_HS_IP Others Mettl3 Mettl3_H5_37_IP Input control Input control Mettl3_H4_37_input Others Mettl3 Mettl3_H4_HS_IP Others Mettl3 Mettl3_H4_37_IP Input control Input control DGCR8_37_input Others Dgcr8 DGCR8_HS_IP Others Dgcr8 DGCR8_37_IP Input control Input control DGCR8_WT_input Others Dgcr8 DGCR8_Mettl3-KO_IP Others Dgcr8 DGCR8_WT_IP Input control Input control mettl3_clone2_input Input control Input control mettl3_clone1_input Input control Input control parental_input_1 Others Drosha Drosha_DSG_IP Others Dicer1 Dicer_DSG_IP Input control Input control DGCR8_input Others Dgcr8 DGCR8_DSG_IP Others Dgcr8 DGCR8_FA_IP Histone H3K4me3 H3K4me3 (Millipore 07-473, 5ul per IP) Neuro 2a cells, H3K4me3 ChIP Histone H3K27ac H3K27ac (Abcam ab4729, 10ug per IP) Neuro 2a cells, H3K27ac ChIP RNA polymerase RNA polymerase II Pol2ser5P (Abcam ab5131, 5ug per IP) Cortex, Pol2ser5P ChIP Histone H3K9me2 H3K79me2 (Abcam ab3594, 5ug per IP) Cortex, H3K79me2 ChIP Unclassified Unclassified emIE Input control Input control Rabbit normal IgG (Jackson ImmunoResearch 011-000-002) embryonic stem cells Input control Input control Rabbit gamma globulin (Jackson ImmunoResearch 011-000-002) embryonic stem cells Others Prdm13 Johnson lab generated rabbit polyclonal antibodies (PRDM13-Ab1 (ZF) PA6659, rabbit anti-mouse PRDM13) Neural tube Unclassified Unclassified MEFs expressing Sox2 from inducible system for 48h Unclassified Unclassified MEFs expressing Oct4 from inducible system for 48 Unclassified Unclassified MEFs expressing Oct4 from pMX vector for 48h Unclassified Unclassified MEFs expressing Klf4 from pMX vector for 48h Histone H3K27me3 H3K27me3 (39155, Active Motif) AntNPC (anterior neural progenitors derived from mESC) Others Biotin Dynabeads MyOne Streptavidin T1 BirA cells_mock control Others Arid3a Arid3a TS cells Others Biotin Dynabeads MyOne Streptavidin T1 OEGata3_TS+ Others Biotin Dynabeads MyOne Streptavidin T1 OEArid3a_TS+ Others Biotin Dynabeads MyOne Streptavidin T1 OECdx2_TS+ Others Biotin Dynabeads MyOne Streptavidin T1 OEGata3_ES+ Others Biotin Dynabeads MyOne Streptavidin T1 OEArid3a_ES+ Others Biotin Dynabeads MyOne Streptavidin T1 OECdx2_ES+ Others Arid3a Arid3a ES cells Others Satb1 SATB1 peripheral CD4 T cell Others Satb1 SATB1 CD4 thymocyte Others Satb1 SATB1 DP thymocyte Input control Input control IgG liver RNA polymerase RNA polymerase II rabbit polyclonal anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (Abcam ab5131) whole testis 16dpp RNA polymerase RNA polymerase II rabbit polyclonal anti-RNA polymerase II (N-20) (santa cruz sc-899) whole testis 10dpp Input control Input control none, input whole testis 16dpp Input control Input control none, input whole testis 6dpp Histone H3K4me1 H3K4me1 WT_GCps_K4me1_ChIP-seq Input control Input control None None WCE myotubes Others Cdk9 Cdk9 Santa Cruz SC-8338,SC-484 Embryonic stem cells Others Suz12 Suz12 Abcam AB12073 Embryonic stem cells Histone H3K4me3 H3K4me3 Abcam AB8580 Embryonic stem cells Input control Input control None Input INPUT Embryonic stem cells Others Nanog Nanog Bethyl A300-397A Embryonic stem cells Others Sox2 Sox2 R&D Systems MAB2018 Embryonic stem cells Others Pou5f1 Oct4 Santa Cruz SC-8628X Embryonic stem cells Input control Input control none Mouse adult hybrid brain RNA polymerase RNA polymerase II PolII-S5p, Abcam ab5131 Mouse adult hybrid brain Input control Input control none Myoblasts Pax7-flag C2C12 cells Histone H3K27me3 H3K27me3 (Millipore 07-449, 2.5 ug for ChIP) Myoblasts Pax7-flag C2C12 cells Histone H3K4me3 H3K4me3 (Active Motif 39159, 2.5 ug for ChIP) Myoblasts Pax7-flag C2C12 cells Histone H3K4me1 H3K4me1 (Abcam ab8895, 2.5 ug for ChIP) Myoblasts Pax7-flag C2C12 cells Histone H3K27ac H3K27Ac (Abcam ab4729, 2.5 ug for ChIP) Myoblasts Pax7-flag C2C12 cells Input control Input control none Myoblasts flag control C2C12 cells Histone H3K27me3 H3K27me3 (Millipore 07-449, 2.5 ug for ChIP) Myoblasts flag control C2C12 cells Histone H3K4me3 H3K4me3 (Active Motif 39159, 2.5 ug for ChIP) Myoblasts flag control C2C12 cells Histone H3K4me1 H3K4me1 (Abcam ab8895, 2.5 ug for ChIP) Myoblasts flag control C2C12 cells Histone H3K27ac H3K27Ac (Abcam ab4729, 2.5 ug for ChIP) Myoblasts flag control C2C12 cells Input control Input control none 2% HS from iPax7 myogenic progenitors Histone H3K27me3 H3K27me3 (Millipore 07-449, 2.5 ug for ChIP) 2% HS from iPax7 myogenic progenitors Histone H3K4me3 H3K4me3 (Active Motif 39159, 2.5 ug for ChIP) 2% HS from iPax7 myogenic progenitors Histone H3K4me1 H3K4me1 (Abcam ab8895, 2.5 ug for ChIP) 2% HS from iPax7 myogenic progenitors Histone H3K27ac H3K27Ac (Abcam ab4729, 2.5 ug for ChIP) 2% HS from iPax7 myogenic progenitors Histone H3K27me3 H3K27me3 (Millipore 07-449, 2.5 ug for ChIP) iPax7 myogenic progenitors -dox 3d Histone H3K27me3 H3K27me3 (Millipore 07-449, 2.5 ug for ChIP) iPax7 myogenic progenitors +dox Histone H3K4me3 H3K4me3 (Active Motif 39159, 2.5 ug for ChIP) iPax7 myogenic progenitors -dox 3d Histone H3K4me3 H3K4me3 (Active Motif 39159, 2.5 ug for ChIP) iPax7 myogenic progenitors +dox Histone H3K4me1 H3K4me1 (Abcam ab8895, 2.5 ug for ChIP) iPax7 myogenic progenitors -dox 3d Histone H3K4me1 H3K4me1 (Abcam ab8895, 2.5 ug for ChIP) iPax7 myogenic progenitors +dox Histone H3K27ac H3K27Ac (Abcam ab4729, 2.5 ug for ChIP) iPax7 myogenic progenitors -dox 3d Histone H3K27ac H3K27Ac (Abcam ab4729, 2.5 ug for ChIP) iPax7 myogenic progenitors +dox Others Pax7 Pax7 (DSHB, 3 ug for ChIP) Pax7 in iPax7 myogenic progenitors -dox 3d Others Pax7 Pax7 (DSHB, 3 ug for ChIP) Pax7 in iPax7 myogenic progenitors +dox Histone H3K27me3 H3K27me3 derived from J1 ESC Others Ezh2 Ezh2 derived from J1 ESC Histone H2Aub H2AUb derived from J1 ESC Others Cbx2 Cbx2 derived from J1 ESC Others Cbx8 Cbx8 derived from J1 ESC Others Rnf2 Ring1b derived from J1 ESC Histone H3K27me3 H3K27me3 J1 ESC Others Ezh2 Ezh2 J1 ESC Histone H2Aub H2AUb J1 ESC Others Cbx2 Cbx2 J1 ESC Others Cbx7 Cbx7 J1 ESC Others Phc1 Phc1 J1 ESC Others Rnf2 Ring1b J1 ESC Histone H3K4me3 anti-H3K4me3 Suprabasal Keratinocytes Others Dlx3 anti-Dlx3 Suprabasal Keratinocytes Input control Input control IgG Suprabasal Keratinocytes Input control Input control none (input) mouse pre-iPSC input Input control Input control none (input) mouse ESC input Others Cbx3 Cbx3- Millipore- 05-690; clone 42s2 mouse pre-iPSC / Cbx3 IP Others Cbx3 Cbx3- Millipore- 05-690; clone 42s2 mouse ESC / Cbx3 IP Input control Input control WCE V6.5 embryonic stem cells Others Foxp3 FoxP3 (affinity purified rabbit polyclonal antibody, generated in house) Treg cells from FoxP3WT:hCD2 mice RNA polymerase RNA polymerase II Anti-Pol II antibody, sc-56767 Cell line_PolII_ChIP_Cbx_siRNA RNA polymerase RNA polymerase II Anti-Pol II antibody, sc-56767 Cell line_PolII_ChIP_control_siRNA Others Cdk8 Anti-Cdk8 antibody, sc-1521 Cell line_Cdk8_ChIP_Cbx3_siRNA Others Cdk8 Anti-Cdk8 antibody, sc-1521 Cell line_Cdk8_ChIP_control_siRNA Others Med26 Anti-Med26 antibody, sc-48776 Cell line_Med26_ChIP_Cbx3_siRNA Others Med26 Anti-Med26 antibody, sc-48776 Cell line_Med26_ChIP_control_siRNA RNA polymerase RNA polymerase II Anti-Pol II antibody, sc-56767 Cell line_PolII_ChIP_no treatment Others Cbx3 Anti-Cbx3 antibody, Millipore, 05-690; clone 42s2 Cell line_Cbx3_ChIP_no treatment Input control Input control none MLL knockout MEF Input control Input control none MLL wild-type MEF Unclassified Unclassified MLL D2N1D MLL knockout MEF Unclassified Unclassified MLL D2N1D MLL wild-type MEF Unclassified Unclassified MLL D2M7U MLL knockout MEF Unclassified Unclassified MLL D2M7U MLL wild-type MEF Unclassified Unclassified MLL NT86 MLL wild-type MEF RNA polymerase RNA polymerase II Pol II N20 MLL knockout MEF RNA polymerase RNA polymerase II Pol II N20 MLL wild-type MEF RNA polymerase RNA polymerase II PolII antibody (Millipore,CTD4H8,05-623B,2691697) CD8+ T cell Others Ezh2 Ezh2 antibody (Santa Cruz H-80,sc-25383,H0213) CD8+ T cell Input control Input control none Mouse ESCs and mouse extended PSCs, input Histone H3K27me3 anti-H3K27me3 (Millipore, cat. no. 07-449, lot# 2194165) Mouse extended PSCs, H3K27me3 ChIP Histone H3K4me3 anti-H3K4me3 (Millipore, cat. no. 07-473, lot# 2152225) Mouse extended PSCs, H3K4me3 ChIP Histone H3K27me3 anti-H3K27me3 (Millipore, cat. no. 07-449, lot# 2194165) Mouse ESCs, H3K27me3 ChIP Histone H3K4me3 anti-H3K4me3 (Millipore, cat. no. 07-473, lot# 2152225) Mouse ESCs, H3K4me3 ChIP Histone H3K4me3 H3K4me3 (39159, Active Motif) mESC Input control Input control none AntNPC (anterior neural progenitors derived from mESC) Input control Input control none (sonicated chromatin that is directly de-crosslinked without any IP) Others Trim28 KAP1 affinity-purified rabbit polyclonal antibody raised against KAP1 aa 20418, RBCC (F. R. Santoni de Sio et al.,. Blood 119, 4675 (2012)) RNA polymerase RNA polymerase II Pol II antibody from Santa Cruz (sc-899) Primary bone marrow-derived macrophages (BMDM); 7th day of differentiation Input control Input control not needed Primary bone marrow-derived macrophages (BMDM); 7th day of differentiation Others Elf1 Elf1 antibody from Santa Cruz (sc-631X) Primary bone marrow-derived macrophages (BMDM); 7th day of differentiation Others Fli1 Fli1 antibody from Santa Cruz (sc-356X) Primary bone marrow-derived macrophages (BMDM); 7th day of differentiation Input control Input control Goat IgG (Jackson Immuno 005-000-003) Kidney Others Tfcp2l1 Tfcp2l1 (RnD, AF5726) Kidney Input control Input control Total input n MEFs Kap1 WT cells Input control Input control Total input n MEFs Kap1 KO cells Input control Input control Total input Hepa 1.6 cells Histone H3K9me3 antiH3K9me3 (Diagenode, C15410056) H3K9me3 ChIP-Seq in MEF WT cells Histone H3K27ac antiH3K27ac (Abcam, ab4729) H3K27ac ChIP-Seq in MEF WT cells Histone H3K9me3 antiH3K9me3 (Diagenode, C15410056) H3K9me3 ChIP-Seq in MEFs Kap1 KO cells Histone H3K27ac antiH3K27ac (Abcam, ab4729) H3K27ac ChIP-Seq in MEFs Kap1 KO cells Others Setdb1 antiSETDB1 (Sripathy, Stevens et al. 2006) SETDB1 ChIP-Seq in Hepa 1.6 cells Others Trim28 antiKAP1 (Trono laboratory, rabbit polyclonal S23470) KAP1 ChIP-Seq inHepa 1.6 cells Histone H3.3 Millipore 09-838 Sperm Input control Input control none Th17 cells Others Tsc22d3 TSC22D3 Th17 cells Input control Input control none Intestinal epithelium stem cells Input control Input control none Pancreatic beta cell Histone H3K9me3 ab8898 (Abcam) Pancreatic beta cell Others Nfe2 NF-E2 p18(c-16) pre-pro B cells Others Bach1 Bach1 (A1-6) pre-pro B cells Others Pparg PPARg Epididymal White Adipose Tissue Others Pparg PPARg Brown Adipose Tissue Input control Input control none olfactory bulb Histone H3K4me2 H3K4me2 Spermatids Histone H3K4me2 H3K4me2 Spermatocytes Histone H3K4me2 H3K4me2 Testis Histone H3K4me2 H3K4me2 Liver Histone H3K4me2 H3K4me2 Brain Input control Input control anti-rabbit IgG antibody Embryonic fibroblasts Others Nfe2l2 rabbit-anti-Nrf2 polyclonal Embryonic fibroblasts Others Nfe2l2 rabbit-anti-Nrf2 monoclonal Embryonic fibroblasts Others Trim33 TRIM33 (A301-059A, Bethyl, lot: A301-059A1) bone marrow derived macrophages Others Trim33 TRIM33 (A301-059A, Bethyl, lot: A301-059A1) RAW Others Duxbl1 S-20 (anti-mDUX) cultured mouse myoblasts (C2C12) Input control Input control anti-IgG cultured mouse myoblasts (C2C12) Others Duxbl1 A-19 (anti-mDUX) cultured mouse myoblasts (C2C12) Unclassified Unclassified cultured mouse myoblasts (C2C12) Input control Input control Santa Cruz Tech. rIgG (sc-2027) Others Esrra Epitomics ERR (2131-1) Others Mtor Abcam mTOR ChIP grade (ab32028) Others Epitope tags anti-FLAG mouse embryonic stem cells Input control Input control Input_ChIRP-seq Unclassified Unclassified Snord116del_brain_NSC_ChIRP-seq Unclassified Unclassified Snord116del_brain_116HG_ChIRP-seq Unclassified Unclassified WT_brain_NSC_ChIRP-seq Histone H3K4me1 ab8995 (lot#GR61280-1) C3H10T1/2 cells Unclassified Unclassified DHS Splenic B Cells Others Mbd2 anti-Flag M2 (Sigma, catalog# F1804, lot# 080M6035) Mbd2KD, Mbd2FLAG, ChIP, murine embryonic stem cells Others Mbd2 anti-Flag M2 (Sigma, catalog# F1804, lot# 080M6035) Mbd3KD, Mbd2FLAG, ChIP, murine embryonic stem cells Others Mbd2 anti-Flag M2 (Sigma, catalog# F1804, lot# 080M6035) EGFPKD, Mbd2FLAG, ChIP, murine embryonic stem cells Others Mbd2 anti-Flag M2 (Sigma, catalog# F1804, lot# 080M6035) Untagged, Mbd2FLAG, ChIP, murine embryonic stem cells Others Mbd3 anti-Flag M2 (Sigma, catalog# F1804, lot# 080M6035) Mbd2KD, Mbd3FLAG, ChIP, murine embryonic stem cells Others Mbd3 anti-Flag M2 (Sigma, catalog# F1804, lot# 080M6035) Mbd3KD, Mbd3FLAG, ChIP, murine embryonic stem cells Others Mbd3 anti-Flag M2 (Sigma, catalog# F1804, lot# 080M6035) EGFPKD, Mbd3FLAG, ChIP, murine embryonic stem cells Others Mbd3 anti-Flag M2 (Sigma, catalog# F1804, lot# 080M6035) Untagged, Mbd3FLAG, ChIP, murine embryonic stem cells Input control Input control whole serum from normal nonimmunized rabbits Unclassified Unclassified Veh Histone H3K4me3 H3K4me3; Anti-trimethyl-Histone H3 (Lys4) Antibody nave_H3K4me3_ChIPseq Input control Input control IgG (Santa Cruz, sc-2027, lot J2909) STHdhQ111 Input control Input control IgG (Santa Cruz, sc-2027, lot J2909) STHdhQ7 Others Sox2 Sox2 (R&D, MAB2018, lot KGQ0311111) STHdhQ7 Others Jund Jund (Santa Cruz, sc-74x, lot B0111) STHdhQ111 Others Jund Jund (Santa Cruz, sc-74x, lot B0111) STHdhQ7 Others Fosl2 Fra-2 (Santa Cruz, sc-604x, lot I0210) STHdhQ111 Others Fosl2 Fra-2 (Santa Cruz, sc-604x, lot I0210) STHdhQ7 Others Tead1 BD Transduction Laboratories/610923 stromal adherent WT pre-B cell progenitors derived from WT mice Others Tead1 BD Transduction Laboratories/610923 stromal adherent IKDN pre-B cell progenitors derived from IKDN CD2 Cre mice RNA polymerase RNA polymerase II Abcam/Ab5131 stromal adherent WT pre-B cell progenitors derived from WT mice RNA polymerase RNA polymerase II Abcam/Ab5131 stromal adherent IKDN pre-B cell progenitors derived from IKDN CD2 Cre mice Others Med1 Bethyl Labs/A300-793A stromal adherent WT pre-B cell progenitors derived from WT mice Others Med1 Bethyl Labs/A300-793A stromal adherent IKDN pre-B cell progenitors derived from IKDN CD2 Cre mice Others Lmo2 Novus Biologicals/NB110-78626 stromal adherent IKDN pre-B cell progenitors derived from IKDN CD2 Cre mice Input control Input control none (input) stromal adherent WT pre-B cell progenitors derived from WT mice Input control Input control none (input) stromal adherent IKDN pre-B cell progenitors derived from IKDN CD2 Cre mice Others Ikzf1 EMD Millipore/MABE912 & MABE913 stromal adherent WT pre-B cell progenitors derived from WT mice Histone H3K36me3 Abcam/ab9050 stromal adherent WT pre-B cell progenitors derived from WT mice Histone H3K36me3 Abcam/ab9050 stromal adherent IKDN pre-B cell progenitors derived from IKDN CD2 Cre mice Histone H3K27me3 EMD Millipore/07-449 stromal adherent WT pre-B cell progenitors derived from WT mice Histone H3K27me3 EMD Millipore/07-449 stromal adherent IKDN pre-B cell progenitors derived from IKDN CD2 Cre mice Histone H3K27ac Abcam/ab4729 stromal adherent WT pre-B cell progenitors derived from WT mice Histone H3K27ac Abcam/ab4729 stromal adherent IKDN pre-B cell progenitors derived from IKDN CD2 Cre mice Histone H3K27me3 Active Motif/AM39155 stromal adherent WT pre-B cell progenitors derived from WT mice Histone H3K4me2 EMD Millipore/07-030 stromal adherent WT pre-B cell progenitors derived from WT mice Histone H3K4me2 EMD Millipore/07-030 stromal adherent IKDN pre-B cell progenitors derived from IKDN CD2 Cre mice Histone H3K4me1 Active Motif/AM39297 stromal adherent WT pre-B cell progenitors derived from WT mice Others Ets1 Santa Cruz Biotech/sc-350x stromal adherent WT pre-B cell progenitors derived from WT mice Others Ebf1 Abnova/H00001879-M01 stromal adherent WT pre-B cell progenitors derived from WT mice Others Ebf1 Abnova/H00001879-M01 stromal adherent IKDN pre-B cell progenitors derived from IKDN CD2 Cre mice Others Tcf3 Santa Cruz Biotech/sc-349x stromal adherent WT pre-B cell progenitors derived from WT mice Others Ikzf3 EMD Millipore/MABE911 stromal adherent WT pre-B cell progenitors derived from WT mice Others Ikzf3 EMD Millipore/MABE911 stromal adherent IKDN pre-B cell progenitors derived from IKDN CD2 Cre mice Input control Input control none (input) ChIP-Seq_STAT5_input Others Stat5a anti-STAT5 antibody (Santa Cruz, sc-835 (C-17)) ChIP-Seq_STAT5 Unclassified Unclassified C57BL/6J mouse mammary gland Others Esr1 ERalpha C57BL/6J mouse mammary gland Others Kmt2b Mll2 (Homemade, #9172) mouse embryonic stem cells Input control Input control none (input) melan-Ink4a-Arf-null Others Sox17 Sox17 none F9+RA cells Others Pou5f1 Pou5f1/Oct4 none F9+RA cells Others Pou5f1 Pou5f1/Oct4 none F9 cells Histone H3K27ac Abcam ab4729 lung adenocarcinoma Others Supt5 Spt5 (H-300) (sc-28678), Santa Cruz Biotechnology Jmjd2c KD mESCs RNA polymerase RNA polymerase II RNA Pol II Ser5p, CTD4H8 (MMS-128P), Covance Jmjd2c KD mESCs RNA polymerase RNA polymerase II RNA Pol II Ser2p, clone 3E10 (04-1571), Millipore Jmjd2c KD mESCs RNA polymerase RNA polymerase II RNA Pol II 8WG16 (MMS-126R), Covance Jmjd2c KD mESCs Others Pou5f1 Oct4(N-19)(sc-8628), Santa Cruz Biotechnology Jmjd2c KD mESCs Others Nanog Nanog (A300-397A), Bethyl Laboratories Jmjd2c KD mESCs Others Myc cMyc (9402), Cell signaling Jmjd2c KD mESCs Histone H3K9me3 H3K9me3 (ab8898), Abcam Jmjd2c KD mESCs Histone H3K4me3 H3K4me3 (ab1012), Abcam Jmjd2c KD mESCs Histone H3K36me3 H3K36me3 (ab9050), Abcam Jmjd2c KD mESCs Histone H3K27me3 H3K27me3 (ab6002), Abcam Jmjd2c KD mESCs Others Ezh2 ChIPAb+ Ezh2, clone AC22 (17-662), Millipore Jmjd2c KD mESCs Others Ctr9 Ctr9 (A301-395A), Bethyl Laboratories Jmjd2c KD mESCs Others Pou5f1 Oct4(N-19)(sc-8628), Santa Cruz Biotechnology Jmjd2b KD mESCs Others Myc cMyc (9402), Cell signaling Jmjd2b KD mESCs Histone H3K9me3 H3K9me3 (ab8898), Abcam Jmjd2b KD mESCs Histone H3K4me3 H3K4me3 (ab1012), Abcam Jmjd2b KD mESCs Histone H3K36me3 H3K36me3 (ab9050), Abcam Jmjd2b KD mESCs Histone H3K27me3 H3K27me3 (ab6002), Abcam Jmjd2b KD mESCs Histone H3K27ac H3K27ac (ab4729), Abcam Jmjd2b KD mESCs Others Supt5 Spt5 (H-300) (sc-28678), Santa Cruz Biotechnology Anti-GFP KD mESCs RNA polymerase RNA polymerase II RNA Pol II Ser5p, CTD4H8 (MMS-128P), Covance Anti-GFP KD mESCs RNA polymerase RNA polymerase II RNA Pol II Ser2p, clone 3E10 (04-1571), Millipore Anti-GFP KD mESCs RNA polymerase RNA polymerase II RNA Pol II 8WG16 (MMS-126R), Covance Anti-GFP KD mESCs Others Pou5f1 Oct4(N-19)(sc-8628), Santa Cruz Biotechnology Anti-GFP KD mESCs Others Nanog Nanog (A300-397A), Bethyl Laboratories Anti-GFP KD mESCs Others Myc cMyc (9402), Cell signaling Anti-GFP KD mESCs Histone H3K9me3 H3K9me3 (ab8898), Abcam Anti-GFP KD mESCs Histone H3K4me3 H3K4me3 (ab1012), Abcam Anti-GFP KD mESCs Histone H3K36me3 H3K36me3 (ab9050), Abcam Anti-GFP KD mESCs Histone H3K27me3 H3K27me3 (ab6002), Abcam Anti-GFP KD mESCs Histone H3K27ac H3K27ac (ab4729), Abcam Anti-GFP KD mESCs Others Ezh2 ChIPAb+ Ezh2, clone AC22 (17-662), Millipore Anti-GFP KD mESCs Others Ctr9 Ctr9 (A301-395A), Bethyl Laboratories Anti-GFP KD mESCs Histone H3K4me3 H3K4me3 (ab1012), Abcam Mouse ES cells Histone H3K27me3 H3K27me3 (ab6002), Abcam Mouse ES cells Input control Input control None Mouse ES cells Others Biotin ChIP-ed with Streptavidin beads Mouse ES cells with BirA ligase Others Kdm4c Biotinylated protein ChIP-ed with Streptavidin beads Biotinylated Jmjd2c mouse ES cells, with BirA ligase Others Biotin Biotinylated protein ChIP-ed with Streptavidin beads Biotinylated Jmjd2b mouse ES cells, with BirA ligase Input control Input control Mef2Da2 antibody control (antibody blocked with peptide) C2C12 Input control Input control Mef2Da1 antibody control (antibody blocked with peptide) C2C12 Others Mef2d Mef2Da2 C2C12 Others Mef2d Mef2Da1 C2C12 Histone H3K9me2 Histone H3 dimethyl Lys9 Others Ascl1 Mash1 spinal cord at embryonic day 12.5 Input control Input control MNase digested input differentiated ES cells Input control Input control MNase digested input embryonic stem cells Histone H4K16ac H4K16ac ChIP differentiated ES cells Histone H4K16ac H4K16ac ChIP embryonic stem cells Others Ldb1 anti-Ldb1 antibody N-18, Santa Cruz hemangioblast equivalent cells Input control Input control IgG, Sigma, I8140 Hematopoietic Stem Cells Others Cebpa Cebpa, Santa Cruz 14-AA Hematopoietic Stem Cells Others Ep300 acCBP/p300 (rabbit polyclonal, Cell Signaling Technology, catalog number mouse postnatal (P0) cortex Others Ep300 p300 (rabbit polyclonal antip300 (C20), Santa Cruz Biotechnology, catalog number Mouse embryonic day 11.5 (e11.5) forebrain Others Tal1 Scl/Tal1 Others Ldb1 Ldb1 Histone H3K4me1 H3K4me1 Day2 differentiating rtta ESCs, H3K4me1 ChIP Histone H3K4me1 H3K4me1 Day2 differentiating Teto-Brn2 ESCs, H3K4me1 ChIP Others Sox2 Sox2 Embryonic stem cells, Sox2 ChIP Input control Input control none ES-derived neural progenitor cells, WCE Histone H3K9me3 H3K9me3 Millipore #CS200604 NAc dissection from 3-5 animals Histone H2A.Z mouse ES cells, shMLL4, H2AZ ChIP Histone H2A.Z mouse ES cells, shluc control, H2AZ ChIP Others Rara mouse ES cells, shH2A.Z, RARa-ChIP Others Rara mouse ES cells, shluc control, RARa-ChIP Unclassified Unclassified Van Der Heijden et al. Nature Genetics, 2007, pubmed ID:17237782 Round spermatids Histone H3.3 Millipore 17-10245 Round spermatids Unclassified Unclassified Sperm Histone H3.3 Millipore 17-10245 Sperm Input control Input control none pancreas Others Leo1 Leo1 antibody, serum purified Myotubes shPhf5a Others Leo1 Leo1 antibody, serum purified Myotubes shControl Others Leo1 Leo1 antibody, serum purified Myoblasts shControl Input control Input control Input Myotubes shPhf5a Input control Input control Input Myotubes shControl Input control Input control Input Myoblasts shControl Unclassified Unclassified E13.5 embryos derived Mouse Embryonic Fibroblasts Input control Input control NA Mouse Embryonic Fibroblasts 4 days post SLHR induction Others Lmo2 anti- hLmo2, AF2726, R&D Systems Mouse Embryonic Fibroblasts 4 days post SLHR induction Input control Input control none (Input) Liver tissue Others Gfi1 Gfi1 MAST Others Gata2 Gata2 MAST Others Rybp Millipore, #3637 Embryonic stem cells (E14) Others Suz12 Abcam, ab12073 Embryonic stem cells (E14) Others Cbx7 Abcam, ab21873 Embryonic stem cells (E14) Unclassified Unclassified Ab generated in Di Croces lab Embryonic stem cells (E14) Others Med1 Med1/TRAP220 (Bethyl, Catalog No.A300-793A) pro-B cell Others Rpa1 RPA MEF Histone H3K27ac H3K27ac mouse_E11.5_HL Histone H3K27ac H3K27ac mouse_E11.5_FL Histone H3K27ac H3K27ac mouse_E10.5_HL Histone H3K27ac H3K27ac mouse_E10.5_FL Unclassified Unclassified mouse_E11.5_HL Unclassified Unclassified mouse_E11.5_FL Unclassified Unclassified mouse_E10.5_HL Unclassified Unclassified mouse_E10.5_FL Others Cbx2 CBX2 (Bethyl Laboratories Inc. A302-524A) ESC_WT Input control Input control none ESC_WT Others Xbp1 anti-XBP1 M-186 (sc-7160-X, Santa Cruz, Heidelberg, Germany) liver: 48h after sham operation Others Xbp1 anti-XBP1 M-186 (sc-7160-X, Santa Cruz, Heidelberg, Germany) liver: 6h after sham operation Others Xbp1 anti-XBP1 M-186 (sc-7160-X, Santa Cruz, Heidelberg, Germany) liver: 7d after XBP1 silencing and 48h after partial hepatectomy Others Xbp1 anti-XBP1 M-186 (sc-7160-X, Santa Cruz, Heidelberg, Germany) liver: 48h after partial hepatectomy Others Xbp1 anti-XBP1 M-186 (sc-7160-X, Santa Cruz, Heidelberg, Germany) liver: 7d after XBP1 silencing and 6h after partial hepatectomy Others Xbp1 anti-XBP1 M-186 (sc-7160-X, Santa Cruz, Heidelberg, Germany) liver: 6h after partial hepatectomy Others Xbp1 anti-XBP1 M-186 (sc-7160-X, Santa Cruz, Heidelberg, Germany) liver: 7d after XBP1 silencing Others Xbp1 anti-XBP1 M-186 (sc-7160-X, Santa Cruz, Heidelberg, Germany) normal liver Others Egr1 Egr1 Egr1 36h Input control Input control IgG Mock IgG Mock 0h RNA polymerase RNA polymerase II RNA Polymerase II RNA Polymerase II 168h RNA polymerase RNA polymerase II RNA Polymerase II RNA Polymerase II 48h RNA polymerase RNA polymerase II RNA Polymerase II RNA Polymerase II 36h RNA polymerase RNA polymerase II RNA Polymerase II RNA Polymerase II 24h RNA polymerase RNA polymerase II RNA Polymerase II RNA Polymerase II 16h RNA polymerase RNA polymerase II RNA Polymerase II RNA Polymerase II 8h RNA polymerase RNA polymerase II RNA Polymerase II RNA Polymerase II 3h RNA polymerase RNA polymerase II RNA Polymerase II RNA Polymerase II 0h Others Cebpb C/EBPbeta C/EBPbeta 168h Others Cebpb C/EBPbeta C/EBPbeta 48h Others Cebpb C/EBPbeta C/EBPbeta 36h Others Cebpb C/EBPbeta C/EBPbeta 24h Others Cebpb C/EBPbeta C/EBPbeta 16h Others Cebpb C/EBPbeta C/EBPbeta 8h Others Cebpb C/EBPbeta C/EBPbeta 3h Others Cebpb C/EBPbeta C/EBPbeta 0h Others Cebpa C/EBPalpha C/EBPalpha 168h Others Cebpa C/EBPalpha C/EBPalpha 48h Others Cebpa C/EBPalpha C/EBPalpha 36h Others Cebpa C/EBPalpha C/EBPalpha 24h Others Cebpa C/EBPalpha C/EBPalpha 16h Others Cebpa C/EBPalpha C/EBPalpha 8h Others Cebpa C/EBPalpha C/EBPalpha 3h Others Cebpa C/EBPalpha C/EBPalpha 0h Histone H3K4me3 H3K4me3 Bone Marrow Tet2 Ko Histone H3K4me3 H3K4me3 Bone Marrow Tet2 Wt Input control Input control No-Antibody IgG control sample Seq ES cell Input control Input control none primary megakaryocytes Others Nfe2 anti-p45 antibody by Bresnick EH primary megakaryocytes Input control Input control None TT2 mES cells treated with shRNA of Tet2 (shTet2#3). Others Sall4 Monoclonal antibody against SALL4A was generated with the immunogenic peptide TSGPNSRDLM in mice at Abmart. TT2 mES cells treated with shRNA of Tet2 (shTet2#3). Input control Input control None TT2 mES cells treated with scrambled shRNA (shScr-2nd) Others Sall4 Monoclonal antibody against SALL4A was generated with the immunogenic peptide TSGPNSRDLM in mice at Abmart. TT2 mES cells treated with scrambled shRNA (shScr-2nd) Histone H3K4me2 H3K4me2(Millipore, Cat. No. 07-030, Lot No. DAM1724042) Embryonic cortex Histone H3K27ac H3K27ac (Abcam, Cat. No. ab4729, Lot No. GR46123) Embryonic cortex Others Smc1a Smc1a (Bethyl, Cat. No. A300-055A, Lot No. A300-055A-3) Embryonic cortex Others Ctcf CTCF (Millipore, Cat. No. 07-729, Lot No. JCB1881349) Limb bud Histone H3K27me3 H3K27me3 (Millipore, Cat. No. 07-449, Lot No. JCB1873477) Limb bud Histone H3K4me2 H3K4me2(Millipore, Cat. No. 07-030, Lot No. DAM1724042) Limb bud Others Cdx2 Cdx2 (Bethyl Labs, A300-691-A, lot A300-691-A1) Trophoblast stem cells Histone H3K4me1 H3K4me1 (Abcam, ab8895, lot 962583) Trophoblast stem cells Histone H3K4me3 H3K4me3 (ActiveMotif, 39159, lot 1609004) Trophoblast stem cells Unclassified Unclassified Mature Megakaryocytes Others Runx1 Runx1, antibody vendor, cat#, lot #: Abcam, ab23980, gr25538-1 Mature Megakaryocytes Others Fli1 Fli-1, antibody vendor, cat#, lot #: Abcam, ab15289, gr1478-2 Mature Megakaryocytes Input control Input control input chromatin Thymocytes Input control Input control input chromatin Mature granulocytes Input control Input control input chromatin Immature granulocytes Input control Input control input chromatin Mature Erytrhoid Input control Input control input chromatin Immature Erythroid Input control Input control input chromatin Mature Megakaryocytes Input control Input control input chromatin Immature Megakaryocytes Input control Input control input chromatin HSC Histone H3K4me2 H3K4me2, antibody vendor, cat#, lot #: Millipore, 07-030, DAM1724042 Thymocytes Others Spi1 PU.1, antibody vendor, cat #, lot #: Santa Cruz, sc-352, D2011 Immature granulocytes Histone H3K27ac H3K427ac, antibody vendor, cat #, lot #: Abcam, ab4729, 509313 Immature granulocytes Histone H3K4me2 H3K4me2, antibody vendor, cat#, lot #: Millipore, 07-030, DAM1724042 Mature granulocytes Unclassified Unclassified Immature granulocytes Histone H3K4me2 H3K4me2, antibody vendor, cat#, lot #: Millipore, 07-030, DAM1724042 Immature granulocytes Histone H3K27ac H3K427ac, antibody vendor, cat #, lot #: Abcam, ab4729, 509313 Immature Erythroid Others Nfe2 NF-E2 TB16+TB17, home made Immature Erythroid Histone H3K4me2 H3K4me2, antibody vendor, cat#, lot #: Millipore, 07-030, DAM1570816 Mature Erytrhoid Histone H3K4me2 H3K4me2, antibody vendor, cat#, lot #: Millipore, 07-030, DAM1570816 Immature Erythroid Others Nfe2 NF-E2 TB16+TB17, home made Mature Megakaryocytes Others Nfe2 NF-E2 TB16+TB17, home made Immature Megakaryocytes Histone H3K4me2 H3K4me2, antibody vendor, cat#, lot #: Millipore, 07-030, DAM1570816 Mature Megakaryocytes Histone H3K4me2 H3K4me2, antibody vendor, cat#, lot #: Millipore, 07-030, DAM1570816 Immature Megakaryocytes Histone H3K4me2 H3K4me2, antibody vendor, cat#, lot #: Millipore, 07-030, DAM1724042 MEP Histone H3K4me2 H3K4me2, antibody vendor, cat#, lot #: Millipore, 07-030, DAM1724042 GMP Histone H3K4me2 H3K4me2, antibody vendor, cat#, lot #: Millipore, 07-030, DAM1724042 CMP Histone H3K4me2 H3K4me2, antibody vendor, cat#, lot #: Millipore, 07-030, DAM1724042 HSC Histone H3K27me3 H3K27me3 (Millipore, 07-449) Th17 cells Histone H3K27me3 H3K27me3 (Millipore, 07-449) Th1 cells Histone H3K4me2 H3K4me2 (Millipore, 07-030) Th17 cells Histone H3K4me2 H3K4me2 (Millipore, 07-030) Th1 cells Histone H3K27me3 H3K27me3 (Millipore, 07-449) CD27-CCR6+ gd T cells Histone H3K27me3 H3K27me3 (Millipore, 07-449) CD27+ gd T cells Histone H3K4me2 H3K4me2 (Millipore, 07-030) CD27-CCR6+ gd T cells Histone H3K4me2 H3K4me2 (Millipore, 07-030) CD27+ gd T cells Input control Input control none Adipocite Others Spi1 rabbit anti-PU.1 antibody (sc-352, Santa Cruz) Tot2 cells, MSCV-IRF8 transduced, Day3 Others Tbp anti-TBP (abcam 62126) C3H10T1/2 mouse cells Others Tbp anti-TBP (abcam 62126) adipocytes differentiated from C3H10T1/2 mouse cells Others Taf7l TAF7L (in-house) C3H10T1/2 mouse cells Others Taf7l TAF7L (in-house) adipocytes differentiated from C3H10T1/2 mouse cells Others Pparg PPAR (sc-7196) C3H10T1/2 mouse cells Others Pparg PPAR (sc-7196) adipocytes differentiated from C3H10T1/2 mouse cells RNA polymerase RNA polymerase II Pol II (monoclonal 8GW16, protein-A purified) C3H10T1/2 mouse cells RNA polymerase RNA polymerase II Pol II (monoclonal 8GW16, protein-A purified) adipocytes differentiated from C3H10T1/2 mouse cells Input control Input control IgG (in-house) C3H10T1/2 mouse cells Input control Input control IgG (in-house) adipocytes differentiated from C3H10T1/2 mouse cells Others Usp7 USP7, Bethyl, A300-033A Embryonic stem cell Others Usp7 USP7, Bethyl, A300-033A Embryonic stem cells RNA polymerase RNA polymerase II PolII S5; BioLegend, 904001 Embryonic stem cells RNA polymerase RNA polymerase II PolII S5, BioLegend, 904001 Embryonic stem cells Input control Input control none MEF MLL3(+/+) Histone H3K4me1 (rb) -H3K4me1 (39297;Active Motif) MEF MLL3(+/+) Histone H3K27me3 (rb) -H3K27me3 (39155; Active Motif) MEF MLL3(+/+) Input control Input control none MEF MLL3(-/-) Histone H3K4me1 (rb) -H3K4me1 (39297;Active Motif) MEF MLL3(-/-) Histone H3K27me3 (rb) -H3K27me3 (39155; Active Motif) MEF MLL3(-/-) Input control Input control none MEF MLL1(+/+) Histone H3K4me1 (rb) -H3K4me1 (39297;Active Motif) MEF MLL1(+/+) Histone H3K27me3 (rb) -H3K27me3 (39155; Active Motif) MEF MLL1(+/+) Input control Input control none MEF MLL1(-/-) Histone H3K4me1 (rb) -H3K4me1 (39297;Active Motif) MEF MLL1(-/-) Histone H3K27me3 (rb) -H3K27me3 (39155; Active Motif) MEF MLL1(-/-) Unclassified Unclassified MC3T3-E1 cells differentiated for 15 days Unclassified Unclassified MC3T3-E1 cells Histone H2AK119Ub H2AK119 ubiquitination (Cell signaling D27C4, catalog 8240S and lot2 MLL-AF9 leukemic cells Unclassified Unclassified Rag1 -/- with TCRb transgene, thymocytes Others Ctcf Anti-CTCF Antibody Rag1 -/- with TCRb transgene, thymocytes Others Ctcf Anti-CTCF Antibody Rag1 -/- pro-B cells Unclassified Unclassified Rag1 -/- CD4-CD8- (DN) thymocytes Others Ctcf Anti-CTCF Antibody Rag1 -/- CD4-CD8- (DN) thymocytes Input control Input control none Liver tumor cell line, sgMll3/Cas9, input Input control Input control none Liver tumor cell line, sgp53/Cas9, input Histone H3K4me1 H3K4me1 (Abcam; ab8895, Lot:GR114265-2) Liver tumor cell line, sgMll3/Cas9, H3K4me1 ChIP Input control Input control none Mouse Fetal Placenta Input control Input control none Mouse Stem Cells Others Epitope tags anti-HA polyclonal antibody (ChIP-grade ab 9110; Abcam) Mouse Stem Cells Histone H3K27ac H3K27ac Ab (ab4729) pro-B Histone H3K4me3 H3K4me3 Ab (Abcam ab8580-100) pro-B Histone H3K4me2 H3K4me2 Ab (Upstate 07-030) pro-B Histone H3K9ac H3K9ac Ab (Upstate 07-352) pro-B Histone H3K27me3 H3K27me3 Ab (T.Jenuwein) pro-B Histone H3K4me3 Rabbit anti-H3K4me3 (07-473) spermatids Histone H3K4me3 Rabbit anti-H3K4me3 (07-473) spermatocytes Others Biotin Streptavidin (BioChIP using a Streptavidin pulldown; PMID:21552207) Total Thymocytes Histone H2S112GlcNAc H2B S112 GlcNAc antibody Mouse ES cell Others Ogt OGT antibody Mouse ES cell Others Tet2 in-house made mouse TET2 antibody Mouse ES cell Input control Input control None Embryonic stem cells Input control Input control none (input) Input DNA from postnatal cortex Others GFP GFP antibody (Santa Cruz, sc-8334, H0612) GFP ChIP-SEQ from postnatal cortex Others Neurod2 NeuroD2 antibody (Abcam, ab109406, YK010204CS) NeuroD2 ChIP-SEQ from postnatal cortex Others Neurod2 NeuroD2 antibody (Abcam, ab104430, GR94291-1) NeuroD2 ChIP-SEQ from postnatal cortex Others Neurod2 NeuroD2 antibody (Abcam, ab168932, GR161014-2) NeuroD2 ChIP-SEQ from postnatal cortex Histone H3K4me1 H3K4me1 (Abcam: 8898) Embryonic Midbrain Input control Input control none Isolated whole islets Others Isl1 Anti-Islet 1 antibody EP4182 (Abcam, ab109517) Isolated whole islets Others Ldb1 CLIM-2 Antibody (N-18)-X (Santa Cruz, sc11198 X) Isolated whole islets Others Stat1 anti-Stat1 Primary bone marrow-derived macrophages, IFNg for 4hrs, Stat1 ChIP Others Junb anti-JunB Primary bone marrow-derived macrophages, LPS for 4hrs, JunB ChIP Others Junb anti-JunB Primary bone marrow-derived macrophages, no treatment, JunB ChIP Others Stat1 anti-Stat1 Primary bone marrow-derived macrophages, IFNg for 2hrs, Stat1 ChIP Others Stat1 anti-Stat1 Primary bone marrow-derived macrophages, IFNg for 1hrs, Stat1 ChIP Others Stat1 anti-Stat1 Primary bone marrow-derived macrophages, IFNg for 30min, Stat1 ChIP Others Spi1 anti-PU.1 (rabbit polyclonal against the N-terminus (aa. 1-100)) Primary bone marrow-derived macrophages, IFNg for 2hrs, PU.1 ChIP Others Spi1 anti-PU.1 (rabbit polyclonal against the N-terminus (aa. 1-100)) Primary bone marrow-derived macrophages, IFNg for 1hrs, PU.1 ChIP Others Spi1 anti-PU.1 (rabbit polyclonal against the N-terminus (aa. 1-100)) Primary bone marrow-derived macrophages, IFNg for 30min, PU.1 ChIP Histone H3K4me1 anti-H3K4me1 Primary bone marrow-derived macrophages, IFNg for 2hrs, H3K4me1 ChIP Histone H3K4me1 anti-H3K4me1 Primary bone marrow-derived macrophages, IFNg for 1hrs, H3K4me1 ChIP Histone H3K4me1 anti-H3K4me1 Primary bone marrow-derived macrophages, IFNg for 30min, H3K4me1 ChIP Others Stat6 anti-Stat6 Primary bone marrow-derived macrophages, IL4 for 4hrs, Stat6 ChIP Others Stat6 anti-Stat6 Primary bone marrow-derived macrophages, IL4 for 2hrs, Stat6 ChIP Others Stat6 anti-Stat6 Primary bone marrow-derived macrophages, IL4 for 1hrs, Stat6 ChIP Others Stat6 anti-Stat6 Primary bone marrow-derived macrophages, IL4 for 30min, Stat6 ChIP Others Stat6 anti-Stat6 Primary bone marrow-derived macrophages, IL4 for 15min, Stat6 ChIP Others Stat6 anti-Stat6 Primary bone marrow-derived macrophages, no treatment, Stat6 ChIP Histone H3K27ac anti-H3K27ac Primary bone marrow-derived macrophages, IL4 for 2hrs, H3K27ac ChIP Histone H3K27ac anti-H3K27ac Primary bone marrow-derived macrophages, IL4 for 1hrs, H3K27ac ChIP Histone H3K27ac anti-H3K27ac Primary bone marrow-derived macrophages, IL4 for 30min, H3K27ac ChIP Histone H3K27ac anti-H3K27ac Primary bone marrow-derived macrophages, IL4 for 15min, H3K27ac ChIP Histone H3K4me1 anti-H3K4me1 Primary bone marrow-derived macrophages, IL4 for 2hrs, H3K4me1 ChIP Histone H3K4me1 anti-H3K4me1 Primary bone marrow-derived macrophages, IL4 for 1hrs, H3K4me1 ChIP Histone H3K4me1 anti-H3K4me1 Primary bone marrow-derived macrophages, IL4 for 30min, H3K4me1 ChIP Histone H3K4me1 anti-H3K4me1 Primary bone marrow-derived macrophages, IL4 for 15min, H3K4me1 ChIP Histone H3K4me1 anti-H3K4me1 Primary bone marrow-derived macrophages, IFNg for 24hrs, then washed, H3K4me1 ChIP Histone H3K4me1 anti-H3K4me1 Primary bone marrow-derived macrophages, IFNg for 72hrs, H3K4me1 ChIP Histone H3K4me1 anti-H3K4me1 Primary bone marrow-derived macrophages, IL4 for 24hrs, then washed, H3K4me1 ChIP Histone H3K4me1 anti-H3K4me1 Primary bone marrow-derived macrophages, IL4 for 72hrs, H3K4me1 ChIP Others Phf19 custom produced rabbit polyclonal PHF19 Embryonic stem cells Histone H3K27me3 H3K27me3 - Millipore, #07450 H3K27me3-ShPhf19_ChIPSeq Histone H3K27me3 H3K27me3 - Millipore, #07449 H3K27me3-ShRd_ChIPSeq Others Suz12 Suz12 - Abcam, #12073 Suz12_ChIPSeq Histone H3K36me2 H3K36me2 - Abcam, #9049 H3K36me2_ChIPSeq Histone H3K36me3 H3K36me3 - Abcam, #9050 H3K36me3_ChIPSeq Input control Input control 3T3-L1_Input Input control Input control 3T3-L1_Input virus Others Tal1 Tal1 (Santa Cruz, cat no. sc-12984x, lot B2511) Multipotent haematopoietic progenitor, Tal1 ChIP Others Spi1 Spi1 (Santa Cruz, cat no. sc-352x, lot B0314) Multipotent haematopoietic progenitor, Spi1 ChIP Others Runx1 Runx1 (Abcam, cat no. ab23980, lot GR37372-1) Multipotent haematopoietic progenitor, Runx1 ChIP Others Meis1 Meis1 (Santa Cruz, cat no. sc-10599x, lot D2310) Multipotent haematopoietic progenitor, Meis1 ChIP Others Lyl1 Lyl1 (Abcam, cat no. ab30334-200, lot 383134) Multipotent haematopoietic progenitor, Lyl1 ChIP Others Lmo2 Lmo2 (R&D Systems, cat no. AF2726, lot VHX0110111) Multipotent haematopoietic progenitor, Lmo2 ChIP Input control Input control IgG Rabbit Multipotent haematopoietic progenitor, IgG ChIP Others Gfi1b Gfi1b (Santa Cruz, cat no. sc8559x, lot E1409) Multipotent haematopoietic progenitor, Gfi1b ChIP Others Gfi1 Gfi1 (Abcam, cat no. ab21061, lot 151880) Multipotent haematopoietic progenitor, Gfi1 ChIP Others Gata2 Gata2 (Santa Cruz, cat no. sc-9008x, lot I0109) Multipotent haematopoietic progenitor, Gata2 ChIP Others Fli1 Fli1 (Abcam, cat no. ab15289-500, lot 775077) Multipotent haematopoietic progenitor, Fli1 ChIP Others Erg Erg (Santa Cruz, cat no. sc-354x, lot A2510) Multipotent haematopoietic progenitor, Erg ChIP Others Cebpb Cebpb (Santa Cruz, cat no. sc-150x, lot F0711) Multipotent haematopoietic progenitor, Cebpb ChIP Others Cebpa Cebpa (Santa Cruz, cat no. sc-61x, lot F2811) Multipotent haematopoietic progenitor, Cebpa ChIP Input control Input control none intestinal villus cells Histone H3K79me2 H3K79me2 antibody: Abcam ab3594 (lot number 121826) intestinal villus cells Input control Input control none intestinal Lgr5(hi) stem cells Histone H3K79me2 H3K79me2 antibody: Abcam ab3594 (lot number 121826) intestinal Lgr5(hi) stem cells Others Pparg anti-PPAR (sc-7196; Santa Cruz) BAT-derived adipocytes Others Pparg anti-PPAR (sc-7196; Santa Cruz) iWAT-derived adipocytes Others Pparg anti-PPAR (sc-7196; Santa Cruz) eWAT-derived adipocytes Histone H3K9me2 H3K9me2 3T3-L1 preadipocytes Input control Input control none Striatal MSN nuclei RNA polymerase RNA polymerase II Pol II (Abcam AB5408) Striatal MSN nuclei Histone H3K27ac H3k27ac (Abcam AB4729) Striatal MSN nuclei Histone H3K27me3 H3k27me3 (Millipore 07-449) Striatal MSN nuclei Histone H3K4me3 H3k4me3 (Abcam AB8580) Striatal MSN nuclei Input control Input control none Embryonic stem cell (ESC) Histone H3 anti-H3 ChIP DNA TS cells_H3 M Histone H3 anti-H3 ChIP DNA TS cells_H3 S Histone H3 anti-H3 ChIP DNA TS cells_H3 G1 Others Ctcf anti-CTCF ChIP DNA TS cells_CTCF M Others Ctcf anti-CTCF ChIP DNA TS cells_CTCF S Others Ctcf anti-CTCF ChIP DNA TS cells_CTCF G1 Input control Input control Input DNA TS cells_Input M Input control Input control Input DNA TS cells_Input S Input control Input control Input DNA TS cells_Input G1 Histone H2A anti-H2A ChIPreChIP DNA TS cells_reChIP H2A M Histone H2A anti-H2A ChIPreChIP DNA TS cells_reChIP H2A S Histone H2A anti-H2A ChIPreChIP DNA TS cells_reChIP H2A G1 Histone H2A.Z H2A.Z antibodies produced in-house PMID:12660166 ChIP DNA TS cells_H2A.Z M Histone H2A.Z H2A.Z antibodies produced in-house PMID:12660166 ChIP DNA TS cells_H2A.Z S Histone H2A.Z H2A.Z antibodies produced in-house PMID:12660166 ChIP DNA TS cells_H2A.Z G1 Others Gata4 BD pharmingen, L97-56, lot 17576 ES_Dex-_DKO_ChIPSeq Others Gata4 BD pharmingen, L97-56, lot 17576 ES_Dex-_Wild-type_ChIPSeq Others Gata4 BD pharmingen, L97-56, lot 17576 Flk1+Dex+DKO_ChIPSeq Others Gata4 BD pharmingen, L97-56, lot 17576 Flk1+Dex+Wild-type_ChIPSeq Others Stat6 STAT6 (Santa Cruz, M-20, sc-981) Th9 cells, STAT6 ChIP Others Stat5b STAT5B (R&D Systems) Th9 cells, STAT5B ChIP Input control Input control Rabbit IgG (R&D Systems) Th9 cells Others Rnf2 Ring1b 5694 Kdm2b knockdown mouse ES cells Others Rnf2 Ring1b 5694 Control mouse ES cells Others Epitope tags Flag F7425 Kdm2b knockdown mouse ES cells Others Epitope tags Flag F7425 Control mouse ES cells Input control Input control IgG Kdm2b knockdown mouse ES cells Input control Input control IgG Control mouse ES cells Others Ezh2 Ezh2 5246 Kdm2b knockdown mouse ES cells Others Ezh2 Ezh2 5246 Control mouse ES cells Histone H3K4me2 Histone H3 dimethyl Lys4 antibody (ACTIVE MOTIF, 39141) Neural progenitor like cells Unclassified Unclassified mouse_e11.5_heart_control Others Smarca4 mouse_e11.5_heart_smarca4-flag Others Smarca4 mouse_e11.5_hindbrain_smarca4-flag Others Smarca4 mouse_ESC_smarca4-flag Others Sp1 Anti-Sp1 (home-made, antigen purified) STHdh Q7/Q7, Sp1 ChIP Input control Input control Rabbit IgG, sigma E8.5 head Input control Input control none embryonic stem cells, vitamin C, input Histone H3K9me2 H3K9me2 (Abcam, ab1220) embryonic stem cells, vitamin C, H3K9me2 ChIP Input control Input control none embryonic stem cells, untreated, input Histone H3K9me2 H3K9me2 (Abcam, ab1220) embryonic stem cells, untreated, H3K9me2 ChIP Unclassified Unclassified Stomach Others Zc3h11a ZC3H11A_(NB100-74650) NB100-74650 ZC3H11A is a C3H1-type zinc finger protein. ZC3H11A has been identified as a protein that is phosphorylated upon DNA damage by ATM or ATR. The function of ZC3H11A remains uncharacterized. Rabbit polyclonal antibody. The immunogen recognized by this antibody maps to a region between residue 250 and 300 of human zinc finger CCCH-type containing 11A. ES-E14 Others Mafk MafK_(ab50322) ab50322 NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. Rabbit polyclonal. Raised against synthetic peptide: TTNPKPNKALKVKKEA conjugated to KLH by a C-terminal Cysteine residue linker, corresponding to amino acids 2-17 of Human MAFK. Antibody Target: MafK ES-E14 Others Zfp384 ZNF384_(HPA004051) HPA004051 This gene encodes a C2H2-type zinc finger protein, which may function as a transcription factor. This gene also contains long CAG trinucleotide repeats that encode consecutive glutamine residues. The protein appears to bind and regulate the promoters of the extracellular matrix genes MMP1, MMP3, MMP7 and COL1A1. Studies in mouse suggest that nuclear matrix transcription factors (NP/NMP4) may be part of a general mechanical pathway that couples cell construction and function during extracellular matrix remodeling. Alternative splicing results in multiple transcript variants. Recurrent rearrangements of this gene with the Ewing's sarcoma gene, EWSR1 on chromosome 22, or with the TAF15 gene on chromosome 17, or with the TCF3 (E2A) gene on chromosome 19, have been observed in acute leukemia. A related pseudogene has been identified on chromosome 7. Rabbit polyclonal generated using the immunogen: Zinc finger protein 384 recombinant protein epitope signature tag (PrEST) ES-E14 Others Chd1 CHD1_(NB100-60411) NB100-60411 ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. Also required to maintain a specific chromatin configuration across the genome. Is also associated with histone deacetylase (HDAC) activity (By similarity). Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Required for maintaining open chromatin and pluripotency in embryonic stem cells Rabbit polyclonal, The epitope recognized by this antibody maps to a region between residue 1660 and 1710 of human chromodomain helicase DNA binding protein 1 using the numbering given in entry NP_001261.2 (GeneID 1105). Antibody Target: CHD1 MEL Others Kat2a GCN5 Missing KAT2A, or GCN5, is a histone acetyltransferase (HAT) that functions primarily as a transcriptional activator. Acetylation of histones gives a specific tag for epigenetic transcription activation. In case of HIV-1 infection, it is recruited by the viral protein Tat. Regulates Tat's transactivating activity and may help inducing chromatin remodeling of proviral genes. Component of the SAGA and ATAC complexes, complexes with histone acetyltransferase activities on histones H3 and H4 Rabbit polyclonal anti-GCN5 antibody (2676), Immunogen : synthetic peptide coupled to Ovalbumin (sequence-MAEPSQAPTPAPAAQPRPLC). Antibody Target: GCN5 MEL Others Chd1 CHD1_(NB100-60411) NB100-60411 ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. Also required to maintain a specific chromatin configuration across the genome. Is also associated with histone deacetylase (HDAC) activity (By similarity). Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Required for maintaining open chromatin and pluripotency in embryonic stem cells Rabbit polyclonal, The epitope recognized by this antibody maps to a region between residue 1660 and 1710 of human chromodomain helicase DNA binding protein 1 using the numbering given in entry NP_001261.2 (GeneID 1105). Antibody Target: CHD1 CH12 Others Kat2a GCN5 Missing KAT2A, or GCN5, is a histone acetyltransferase (HAT) that functions primarily as a transcriptional activator. Acetylation of histones gives a specific tag for epigenetic transcription activation. In case of HIV-1 infection, it is recruited by the viral protein Tat. Regulates Tat's transactivating activity and may help inducing chromatin remodeling of proviral genes. Component of the SAGA and ATAC complexes, complexes with histone acetyltransferase activities on histones H3 and H4 Rabbit polyclonal anti-GCN5 antibody (2676), Immunogen : synthetic peptide coupled to Ovalbumin (sequence-MAEPSQAPTPAPAAQPRPLC). Antibody Target: GCN5 CH12 Others Maz MAZ_(ab85725) ab85725 May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. Rabbit polyclonal, immunogen is synthetic peptide, corresponding to a region within amino acids 427-477 of Human MAZ, GenBank BAA33064.1. Antibody Target: MAZ CH12 Others Gabpa Nrf2 sc-22810 epitope corresponding to amino acids 1-180 mapping at the N-terminus of GABP-alpha of human origin Rabbit polyclonal IgG. Antibody Target: Nrf2 CH12 Others Hcfc1 HCFC1_(NB100-68209) NB100-68209 The epitope recognized by this antibody maps to a region between residue 1700 and 1750 of human host cell factor C1 (VP16-accessory protein). Rabbit polyclonalantibody against residue 1700 and 1750 of human host cell factor C1 ES-E14 Others Zmiz1 ZNF-MIZD-CP1_(ab65767) ab65767 Zinc finger MIZ domain-containing protein 1 that increases ligand-dependent transcriptional activity of AR and promotes AR sumoylation. The stimulation of AR activity is dependent upon sumoylation. Rabbit Polyclonal against synthetic peptide conjugated to KLH derived from within residues 200 - 300 of Human Zinc finger MIZ domain-containing protein 1. MEL Others Zfp384 ZNF384_(HPA004051) HPA004051 This gene encodes a C2H2-type zinc finger protein, which may function as a transcription factor. This gene also contains long CAG trinucleotide repeats that encode consecutive glutamine residues. The protein appears to bind and regulate the promoters of the extracellular matrix genes MMP1, MMP3, MMP7 and COL1A1. Studies in mouse suggest that nuclear matrix transcription factors (NP/NMP4) may be part of a general mechanical pathway that couples cell construction and function during extracellular matrix remodeling. Alternative splicing results in multiple transcript variants. Recurrent rearrangements of this gene with the Ewing's sarcoma gene, EWSR1 on chromosome 22, or with the TAF15 gene on chromosome 17, or with the TCF3 (E2A) gene on chromosome 19, have been observed in acute leukemia. A related pseudogene has been identified on chromosome 7. Rabbit polyclonal generated using the immunogen: Zinc finger protein 384 recombinant protein epitope signature tag (PrEST) MEL Others Zfp384 ZNF384_(HPA004051) HPA004051 This gene encodes a C2H2-type zinc finger protein, which may function as a transcription factor. This gene also contains long CAG trinucleotide repeats that encode consecutive glutamine residues. The protein appears to bind and regulate the promoters of the extracellular matrix genes MMP1, MMP3, MMP7 and COL1A1. Studies in mouse suggest that nuclear matrix transcription factors (NP/NMP4) may be part of a general mechanical pathway that couples cell construction and function during extracellular matrix remodeling. Alternative splicing results in multiple transcript variants. Recurrent rearrangements of this gene with the Ewing's sarcoma gene, EWSR1 on chromosome 22, or with the TAF15 gene on chromosome 17, or with the TCF3 (E2A) gene on chromosome 19, have been observed in acute leukemia. A related pseudogene has been identified on chromosome 7. Rabbit polyclonal generated using the immunogen: Zinc finger protein 384 recombinant protein epitope signature tag (PrEST) CH12 Others Hcfc1 HCFC1_(NB100-68209) NB100-68209 The epitope recognized by this antibody maps to a region between residue 1700 and 1750 of human host cell factor C1 (VP16-accessory protein). Rabbit polyclonalantibody against residue 1700 and 1750 of human host cell factor C1 CH12 Others Bhlhe40 BHLHE40_(NB100-1800) NB100-1800 This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. Rabbit polyclonal, maps to a region between residues 350 and the C-terminus (residue 412). Antibody Target: BHLHE40 MEL Others Zmiz1 ZNF-MIZD-CP1_(ab65767) ab65767 Zinc finger MIZ domain-containing protein 1 that increases ligand-dependent transcriptional activity of AR and promotes AR sumoylation. The stimulation of AR activity is dependent upon sumoylation. Rabbit Polyclonal against synthetic peptide conjugated to KLH derived from within residues 200 - 300 of Human Zinc finger MIZ domain-containing protein 1. CH12 Others Zc3h11a ZC3H11A_(NB100-74650) NB100-74650 ZC3H11A is a C3H1-type zinc finger protein. ZC3H11A has been identified as a protein that is phosphorylated upon DNA damage by ATM or ATR. The function of ZC3H11A remains uncharacterized. Rabbit polyclonal antibody. The immunogen recognized by this antibody maps to a region between residue 250 and 300 of human zinc finger CCCH-type containing 11A. CH12 Others Gabpa Nrf2 sc-22810 epitope corresponding to amino acids 1-180 mapping at the N-terminus of GABP-alpha of human origin Rabbit polyclonal IgG. Antibody Target: Nrf2 MEL Others Maz MAZ_(ab85725) ab85725 May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. Rabbit polyclonal, immunogen is synthetic peptide, corresponding to a region within amino acids 427-477 of Human MAZ, GenBank BAA33064.1. Antibody Target: MAZ MEL Others Rcor1 COREST_(sc-30189) sc-30189 Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. Rabbit polyclonal, epitope corresponding to amino acids 246-310 mapping within an internal region of CoREST of human origin recommended for detection of CoREST of mouse, rat and human origin. Antibody Target: COREST (sc30189) MEL Others Ubtf UBF_(sc-13125) sc-13125 Upstream binding factor (UBF) is a transcription factor required for expression of the 18S, 5.8S, and 28S ribosomal RNAs, along with SL1 (a complex of TBP (MIM 600075) and multiple TBP-associated factors or 'TAFs'). Two UBF polypeptides, of 94 and 97 kD, exist in the human (Bell et al., 1988 (PubMed 3413483)). UBF is a nucleolar phosphoprotein with both DNA binding and transactivation domains. Sequence-specific DNA binding to the core and upstream control elements of the human rRNA promoter is mediated through several HMG boxes UBF (F-9) is a mouse monoclonal antibody raised against amino acids 1-220 of UBF of human origin. Antibody Target: UBF MEL Others Rcor1 COREST_(sc-30189) sc-30189 Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. Rabbit polyclonal, epitope corresponding to amino acids 246-310 mapping within an internal region of CoREST of human origin recommended for detection of CoREST of mouse, rat and human origin. Antibody Target: COREST (sc30189) CH12 Others Ubtf UBF_(sc-13125) sc-13125 Upstream binding factor (UBF) is a transcription factor required for expression of the 18S, 5.8S, and 28S ribosomal RNAs, along with SL1 (a complex of TBP (MIM 600075) and multiple TBP-associated factors or 'TAFs'). Two UBF polypeptides, of 94 and 97 kD, exist in the human (Bell et al., 1988 (PubMed 3413483)). UBF is a nucleolar phosphoprotein with both DNA binding and transactivation domains. Sequence-specific DNA binding to the core and upstream control elements of the human rRNA promoter is mediated through several HMG boxes UBF (F-9) is a mouse monoclonal antibody raised against amino acids 1-220 of UBF of human origin. Antibody Target: UBF CH12 Others Zkscan1 ZKSCAN1_(HPA006672) HPA006672 The ZKSCAN1 gene encodes a transcriptional regulator of the KRAB (Kruppel-associated box) subfamily of zinc finger proteins, which contain repeated Cys2-His2 (C2H2) zinc finger domains that are connected by conserved sequences, called H/C links. Transcriptional regulatory proteins containing tandemly repeated zinc finger domains are thought to be involved in both normal and abnormal cellular proliferation and differentiation. Rabbit polyclonal, Immunogen: Zinc finger with KRAB and SCAN domain-containing protein 1 recombinant protein epitope signature tag (PrEST). Antibody Target: ZKSCAN1 CH12 Others Sin3a SIN3A_(NB600-1263) NB600-1263 Mammalian Sin 3 (mSin 3) is closely related to the yeast SIN3 repressor protein involved in the transcriptional repression of many genes. Containing 4 paired amphipathic helix domains (PAH domains), mSin 3A and mSin 3B have been shown to directly interact with several other transcriptional repressor proteins including HDAC 1, HDAC 2, RbAp 46, the methyl CpG binding protein MeCP 2, the Mad/Max heterodimer, and the corepressors silencing mediator of retinoic acid & thyroid hormone receptor (SMRT) and nuclear receptor corepressor (N-CoR). Rabbit polyclonal, Immunogen: Synthetic peptide: MKRRLDDQESDVYAAQQRR, corresponding to amino acids 1-19 of Mouse mSin3A. Antibody Target: SIN3A (NB600-1263) CH12 Others Sin3a SIN3A_(NB600-1263) NB600-1263 Mammalian Sin 3 (mSin 3) is closely related to the yeast SIN3 repressor protein involved in the transcriptional repression of many genes. Containing 4 paired amphipathic helix domains (PAH domains), mSin 3A and mSin 3B have been shown to directly interact with several other transcriptional repressor proteins including HDAC 1, HDAC 2, RbAp 46, the methyl CpG binding protein MeCP 2, the Mad/Max heterodimer, and the corepressors silencing mediator of retinoic acid & thyroid hormone receptor (SMRT) and nuclear receptor corepressor (N-CoR). Rabbit polyclonal, Immunogen: Synthetic peptide: MKRRLDDQESDVYAAQQRR, corresponding to amino acids 1-19 of Mouse mSin3A. Antibody Target: SIN3A (NB600-1263) MEL Others Zkscan1 ZKSCAN1_(HPA006672) HPA006672 The ZKSCAN1 gene encodes a transcriptional regulator of the KRAB (Kruppel-associated box) subfamily of zinc finger proteins, which contain repeated Cys2-His2 (C2H2) zinc finger domains that are connected by conserved sequences, called H/C links. Transcriptional regulatory proteins containing tandemly repeated zinc finger domains are thought to be involved in both normal and abnormal cellular proliferation and differentiation. Rabbit polyclonal, Immunogen: Zinc finger with KRAB and SCAN domain-containing protein 1 recombinant protein epitope signature tag (PrEST). Antibody Target: ZKSCAN1 MEL Others Hcfc1 HCFC1_(NB100-68209) NB100-68209 The epitope recognized by this antibody maps to a region between residue 1700 and 1750 of human host cell factor C1 (VP16-accessory protein). Rabbit polyclonalantibody against residue 1700 and 1750 of human host cell factor C1 MEL Others Ets1 ETS1 sc-350 ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis Rabbit polyclonal IgG. Antibody Target: ETS1 MEL Others Zc3h11a ZC3H11A_(NB100-74650) NB100-74650 ZC3H11A is a C3H1-type zinc finger protein. ZC3H11A has been identified as a protein that is phosphorylated upon DNA damage by ATM or ATR. The function of ZC3H11A remains uncharacterized. Rabbit polyclonal antibody. The immunogen recognized by this antibody maps to a region between residue 250 and 300 of human zinc finger CCCH-type containing 11A. MEL Others Ets1 ETS1 sc-350 ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis Rabbit polyclonal IgG. Antibody Target: ETS1 CH12 Unclassified Unclassified Th2 polarized cells Input control Input control none islet Others Nkx6-1 Nkx-6.1 islet Input control Input control none A172LoxP ESC line Others Vsx2 rabbit anti-Chx10 A172LoxP ESC line Others Tead4 TEAD4 ChIP DNA Histone H3K9me3 H3K9me3 (Abcam ab8898) Embryonic stem cells Histone H3K9ac H3K9ac (Abcam, ab4441) Embryonic stem cells Histone H3K27ac H3K27ac (Abcam, ab4729) Embryonic stem cells Others Stat3 STAT3 Th0 in vitro Others Rorc RORg Th0 in vitro Others Jmjd6 Jmjd6 Th17 in vitro Others Kdm6b Jmjd3 Th17 in vitro Others Fosl2 Fosl2 Th0 in vitro Others Maf c-Maf Th0 in vitro Others Batf BATF Th17 in vitro Histone H3K4me3 H3K4me3 ab8580; 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal. Antibody Target: H3K4me3 ES-E14 Histone H3K9me3 H3K9me3 ab8898 Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. rabbit polyclonal, ChIP grade. Antibody Target: H3K9me3 ES-E14 Histone H3K36me3 H3K36me3B 9763S Histone H3 (tri-methyl K36) marks actively transcribed chromatin regions rabbit polyclonal. Antibody Target: H3K36me3 MEL Histone H3K27me3 H3K27me3B 9733S Histone H3 (tri-methyl K27) marks repressed chromatin regions rabbit monoclonal. Antibody Target: H3K27me3 MEL Input control Input control none Embryonic stem cells, Kdm2b shRNA, input Others Kdm2b KDM2B Embryonic stem cells, Kdm2b shRNA, Kdm2b ChIP Others Rnf2 RING1B Embryonic stem cells, Kdm2b shRNA, Ring1b ChIP Input control Input control none Embryonic stem cells, control shRNA, input Others Kdm2b KDM2B Embryonic stem cells, control shRNA, Kdm2b ChIP Others Rnf2 RING1B Embryonic stem cells, control shRNA, Ring1b ChIP Input control Input control none Embryonic stem cells, WT, input Others Kdm2b KDM2B Embryonic stem cells, WT, Kdm2b ChIP Others Kdm2a KDM2A Embryonic stem cells, WT, Kdm2a ChIP Histone H3K4me3 custom-made H3K4Me3 antibody Sperm Others Yy1 YY1 YY1 Rag1 -/- pro-B cells Histone H3K79me2 H3K79me2 39143 H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). Rabbit polyclonal antibody raised against a peptide containing K79 di-methylation. Antibody Target: H3K79me2 MEL Histone H3K36me3 H3K36me3 ab9050 Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts. rabbit polyclonal. Antibody Target: H3K36me3 MEL Histone H3K27me3 H3K27me3 07-449 Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. rabbit polyclonal. Antibody Target: H3K27me3 MEL Histone H3K27ac H3K9ac ab4441 Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K9ac Liver Histone H3K79me2 H3K79me2 39143 H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). Rabbit polyclonal antibody raised against a peptide containing K79 di-methylation. Antibody Target: H3K79me2 Liver Histone H3K36me3 H3K36me3 ab9050 Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts. rabbit polyclonal. Antibody Target: H3K36me3 Liver Histone H3K27me3 H3K27me3 07-449 Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. rabbit polyclonal. Antibody Target: H3K27me3 Liver Histone H3K27ac H3K9ac ab4441 Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K9ac Heart Histone H3K36me3 H3K36me3 ab9050 Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts. rabbit polyclonal. Antibody Target: H3K36me3 B-cell_(CD43-) Histone H3K9me3 H3K9me3 ab8898 Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. rabbit polyclonal, ChIP grade. Antibody Target: H3K9me3 ES-Bruce4 Histone H3K27me3 H3K27me3 07-449 Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. rabbit polyclonal. Antibody Target: H3K27me3 Spleen Histone H3K27me3 H3K27me3 07-449 Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. rabbit polyclonal. Antibody Target: H3K27me3 Testis Histone H3K27me3 H3K27me3 07-449 Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. rabbit polyclonal. Antibody Target: H3K27me3 Thymus Histone H3K27me3 H3K27me3 07-449 Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. rabbit polyclonal. Antibody Target: H3K27me3 WholeBrain Histone H3K27ac H3K27ac ab4729 Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K27ac MEL Histone H3K27ac H3K9ac ab4441 Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K9ac MEL Histone H3K27ac H3K27ac ab4729 Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K27ac MEF Histone H3K27ac H3K27ac ab4729 Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K27ac Spleen Histone H3K27me3 anti-H3K27me3 (17-622, Lot 2213948, Millipore) 5uM_GSK126_H3K27me3_DNA Input control Input control none 5uM_GSK126_Input_DNA Histone H3K27me3 anti-H3K27me3 (17-622, Lot 2213948, Millipore) Vehicle_H3K27me3_DNA Input control Input control none Vehicle_Input_DNA Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal. Antibody Target: H3K4me1 Heart Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal. Antibody Target: H3K4me3 Heart Histone H3K27ac H3K27ac ab4729 Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K27ac Placenta Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal. Antibody Target: H3K4me1 Placenta Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal. Antibody Target: H3K4me3 Placenta Histone H3K27me3 H3K27me3 07-449 Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. rabbit polyclonal. Antibody Target: H3K27me3 Heart Histone H3K36me3 H3K36me3 ab9050 Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts. rabbit polyclonal. Antibody Target: H3K36me3 Heart Histone H3K79me2 H3K79me2 39143 H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). Rabbit polyclonal antibody raised against a peptide containing K79 di-methylation. Antibody Target: H3K79me2 Heart Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal. Antibody Target: H3K4me3 OlfactBulb Histone H3K9ac H3K9ac ab4441 Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K9ac ES-Bruce4 Histone H3K27ac H3K27ac ab4729 Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K27ac ES-E14 Histone H3K36me3 H3K36me3 ab9050 Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts. rabbit polyclonal. Antibody Target: H3K36me3 ES-E14 Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal. Antibody Target: H3K4me3 ES-E14 Histone H3K9ac H3K9ac ab4441 Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K9ac ES-E14 Histone H3K79me2 H3K79me2 39143 H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). Rabbit polyclonal antibody raised against a peptide containing K79 di-methylation. Antibody Target: H3K79me2 CH12 Input control Input control Input Control signal which may be subtracted from experimental raw signal before peaks are called. B-cell_(CD43-) Histone H3K27ac H3K27ac ab4729 Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K27ac CH12 Histone H3K4me2 H3K4me2 ab7766 Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. rabbit polyclonal. Antibody Target: H3K4me2 CH12 Histone H3K9ac H3K9ac ab4441 Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K9ac CH12 Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal. Antibody Target: H3K4me1 Liver Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal. Antibody Target: H3K4me3 Liver Histone H3K36me3 H3K36me3 ab9050 Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts. rabbit polyclonal. Antibody Target: H3K36me3 ES-Bruce4 Histone H3K27ac H3K27ac ab4729 Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K27ac BoneMarrow Histone H3K27ac H3K27ac ab4729 Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K27ac Limb Histone H3K9me3 H3K9me3 ab8898 Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. rabbit polyclonal, ChIP grade. Antibody Target: H3K9me3 WholeBrain Histone H3K27ac H3K27ac ab4729 Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K27ac OlfactBulb Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal. Antibody Target: H3K4me1 OlfactBulb Histone H3K27ac H3K27ac ab4729 Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K27ac Thymus Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal. Antibody Target: H3K4me1 Thymus Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal. Antibody Target: H3K4me3 Thymus Histone H3K27ac H3K27ac ab4729 Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K27ac Cortex Histone H3K27ac H3K27ac ab4729 Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K27ac ES-Bruce4 Histone H3K27ac H3K27ac ab4729 Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K27ac Cerebellum Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal. Antibody Target: H3K4me1 WholeBrain Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal. Antibody Target: H3K4me3 WholeBrain Histone H3K27ac H3K27ac ab4729 Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K27ac WholeBrain Histone H3K27ac H3K27ac ab4729 Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K27ac Kidney Histone H3K27me3 H3K27me3 07-449 Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. rabbit polyclonal. Antibody Target: H3K27me3 Cerebellum Histone H3K27me3 H3K27me3 07-449 Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. rabbit polyclonal. Antibody Target: H3K27me3 ES-Bruce4 Histone H3K27me3 H3K27me3 07-449 Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. rabbit polyclonal. Antibody Target: H3K27me3 B-cell_(CD43-) Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal. Antibody Target: H3K4me3 MEL Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal. Antibody Target: H3K4me3 Limb Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal. Antibody Target: H3K4me1 Limb Histone H3K27ac H3K27ac ab4729 Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K27ac SmIntestine Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal. Antibody Target: H3K4me3 SmIntestine Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal. Antibody Target: H3K4me1 SmIntestine Histone H3K27ac H3K27ac ab4729 Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K27ac Testis Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal. Antibody Target: H3K4me3 Testis Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal. Antibody Target: H3K4me1 Testis Histone H3K27me3 H3K27me3 07-449 Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. rabbit polyclonal. Antibody Target: H3K27me3 Kidney Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal. Antibody Target: H3K4me1 BAT Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal. Antibody Target: H3K4me3 BAT Histone H3K27ac H3K27ac ab4729 Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K27ac BMDM Histone H3K36me3 H3K36me3 ab9050 Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts. rabbit polyclonal. Antibody Target: H3K36me3 WholeBrain Histone H3K27ac H3K27ac ab4729 Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. rabbit polyclonal. Antibody Target: H3K27ac BAT Histone H3K36me3 H3K36me3 ab9050 Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts. rabbit polyclonal. Antibody Target: H3K36me3 Spleen Histone H3K36me3 H3K36me3 ab9050 Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts. rabbit polyclonal. Antibody Target: H3K36me3 SmIntestine Histone H3K36me3 H3K36me3 ab9050 Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts. rabbit polyclonal. Antibody Target: H3K36me3 Thymus Histone H3K36me3 H3K36me3 ab9050 Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts. rabbit polyclonal. Antibody Target: H3K36me3 Testis Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal. Antibody Target: H3K4me1 BMDM Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal. Antibody Target: H3K4me3 BMDM Histone H3K27me3 H3K27me3 07-449 Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. rabbit polyclonal. Antibody Target: H3K27me3 SmIntestine Histone H3K36me3 H3K36me3 ab9050 Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts. rabbit polyclonal. Antibody Target: H3K36me3 Kidney Input control Input control none Input Genomic DNA mK4 Cells Input control Input control none Input Genomic DNA mK3 Cells Histone H3K27me3 H3K27 mK4 Cells Histone H3K27me3 H3K27 mK3 Cells Unclassified Unclassified H3K4 mK4 Cells Unclassified Unclassified H3K4 mK3 Cells Unclassified Unclassified Bone marrow derived dendritic cells stimulated with LPS Unclassified Unclassified Th0 polarized cells Unclassified Unclassified Th17 polarized cells Others Irf4 IRF-4 Antibody (M-17) Bone marrow derived dendritic cells stimulated with LPS Others Irf4 IRF-4 Antibody (M-17) Th0 polarized cells Others Irf4 IRF-4 Antibody (M-17) Th2 polarized cells Others Batf BATF Th17 polarized cells Others Irf4 IRF-4 Antibody (M-17) Th17 polarized cells Input control Input control none (input control) bone marrow progenitors Others Ogt anti-OGT1 Sigma, catalog# 06264 bone marrow progenitors Others Hcfc1 anti-HCF1 Bethyl Laboratories, catalog# A301-399A bone marrow progenitors Others Epitope tags anti-FLAG Sigma, catalog# A2220 bone marrow progenitors Others Cbfb CD4 Cbfb ChIP Others Cbfb Treg Cbfb ChIP Others Ets1 CD4 Ets1 ChIP Others Ets1 Treg Ets1 ChIP Others Elf1 CD4 Elf1 ChIP Others Elf1 Treg Elf1 ChIP Others Tbx21 T-bet (Lab produced (Szabo et al., Nature 2000)) Tbet -/- Th1 cells Others Tbx21 T-bet (Lab produced (Szabo et al., Nature 2000)) Th1 cells Input control Input control None T cells Histone H3K27ac anti-H3K27Ac (Abcam; Cat #: ab4729; Lot: GR117011-1) rTr_H3K27Ac Unclassified Unclassified primary CD4+ T cells from spleen and lymph nodes Others Stat1 anti-STAT1 primary CD4+ T cells from spleen and lymph nodes RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 776_AsyncUninduced_Pol2 Input control Input control input 725_AsyncUninduced_input RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 646_AsyncUninduced_Pol2 Input control Input control input 638_AsyncUninduced_input RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 523_AsyncUninduced_Pol2 RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 775_Async_Pol2 RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 774_6h_Pol2 RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 773_4h_Pol2 RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 772_3h_Pol2 RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 771_1.5h_Pol2 RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 769_1h_Pol2 RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 768_0h_Pol2 Input control Input control input 724_Async_input Input control Input control input 723_6h_input Input control Input control input 722_4h_input Input control Input control input 721_3h_input Input control Input control input 720_1.5h_input Input control Input control input 719_1h_input Input control Input control input 718_40min_input Input control Input control input 717_0h_input RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 709_40min_Pol2 RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 645_Async_Pol2 Others Gata2 GATA2 Mouse uterus RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 644_6h_Pol2 RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 643_4h_Pol2 RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 642_3h_Pol2 RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 641_1.5h_Pol2 RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 640_1h_Pol2 RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 639_0h_Pol2 Input control Input control input 637_Async_input Input control Input control input 636_6h_input Input control Input control input 635_4h_input Input control Input control input 634_3h_input Input control Input control input 633_1.5h_input Input control Input control input 632_1h_input Input control Input control input 631_0h_input Input control Input control input 528_6h_input Input control Input control input 527_3h_input Input control Input control input 526_1.5h_input Input control Input control input 525_1h_input Input control Input control input 524_0h_input RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 522_Async_Pol2 RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 521_6h_Pol2 RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 520_3h_Pol2 RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 519_1.5h_Pol2 RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 518_1h_Pol2 RNA polymerase RNA polymerase II anti-Pol II N-20 (Santa Cruz, cat# sc899) 517_0h_Pol2 Histone H3K27ac anti-H3K27Ac antibody (ActiveMotif, cat# 39685, lot# 30615010) 989_NocMPM2pos_H3K27Ac Histone H3K27ac anti-H3K27Ac antibody (ActiveMotif, cat# 39685, lot# 30615010) 988_AsyncMPM2neg_H3K27Ac Input control Input control none nTreg cells, Foxo1tagBirA mice Input control Input control none nTreg cells Others Foxo1 Strepdavidin nTreg cells, Foxo1tagBirA mice Others Foxo1 Foxo1 antibody (Abcam, Ab39670, lot#GR16346-7) nTreg cells Others Kmt2a anti-MLL1 (MO453, provide by James Hsieh lab) cultured NUP98-HOXA9 transformed mouse bone marrow LSK cells Unclassified Unclassified anti-FS2 (Gift from Prof.Rob Klose; reference: Elife. 2012 Dec 18;1:e00205. doi: 10.7554/eLife.00205) ESCs Others Tet2 anti-Tet2, ProteinTech, 21207-1-AP RA-treated P19 EC cells, Tet2 ChIP Others Pbx1 anti-Pbx1, Abnova, H00005087-M01 RA-treated P19 EC cells, Pbx1 ChIP Others Meis1 anti-Meis1, Abcam, ab19867 untreated P19 EC cells, Meis1 ChIP Unclassified Unclassified untreated P19 EC cells Histone H3K27ac anti-H3K27ac, Abcam, ab4729 untreated P19 EC cells, H3K27ac ChIP Others Foxa1 anti-FoxA1, Abcam, ab5089 RA-treated P19 EC cells, FoxA1 ChIP Others Foxa1 anti-FoxA1, Abcam, ab5089 untreated P19 EC cells, FoxA1 ChIP Histone H3K4me1 anti-H3K4me1, Abcam, ab8895 untreated P19 EC cells, H3K4me1 ChIP Input control Input control ESC time-ChIP input (for replicate 2) Others Nr3c1 anti-GR (ThermoFisher, PA1-511A) ChIPSeq_GR_Mut_p13 Histone H3K27ac anti-H3K27ac (Abcam, ab4729) ChIPSeq_H3K27ac_Mut_p13 Histone H3K27ac anti-H3K27ac (Abcam, ab4729) ChIPSeq_H2K27ac_Mut_L1 Others Stat5a anti-STAT5A (Santa Cruz, sc-1081) ChIPSeq_STAT5_Mut_p13 Others Stat5a anti-STAT5A (Santa Cruz, sc-1081) ChIPSeq_STAT5_Mut_L1 Input control Input control none 32D granuolocytic progenitor cells (bone marrow) Others Kdm1a Lsd1 32D granuolocytic progenitor cells (bone marrow) Others Tead4 TEAD4 Aviva muscle Others Tal1 TAL1_(SC-12984) sc-12984 TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis. goat polyclonal antibody; epitope mapping at the C-terminus of TAL1 of human origin, recommended for detection of TAL1 of mouse, rat and human origin. Antibody Target: TAL1 Megakaryo RNA polymerase RNA polymerase II Pol II muscle Input control Input control No antibody muscle Others Fli1 FLI1_(sc-356) sc-356 Fli1 (Friend leukemia virus integration 1) is a member of a family of genes identified on the basis of their homology to the v-Ets oncogene isolated from the E26 erythoblastosis virus. FLI1 (C-19) is an affinity purified rabbit polyclonal antibody raised against a peptide mapping at the C-terminus of FLI1 of mouse origin. Megakaryo Others Ep300 Santa Cruz, sc-585 resting B cell Others Wdr5 Bethy Laboratories, A302-429A resting B cell Others Kmt2a Bethy Laboratories, A300-086A resting B cell Others Hdac2 Bethy Laboratories, A300-705A resting B cell Others Kat2a Santa Cruz, sc-20698 resting B cell Others Chd4 abcam, ab72418 resting B cell Others Smarca4 abcam, ab110641 resting B cell Others Ep300 Santa Cruz, sc-585 activated B cell Others Wdr5 Bethy Laboratories, A302-429A activated B cell Others Kmt2a Bethy Laboratories, A300-086A activated B cell Others Hdac2 Bethy Laboratories, A300-705A activated B cell Others Kat2a Santa Cruz, sc-20698 activated B cell Others Chd4 abcam, ab72418 activated B cell Others Smarca4 abcam, ab110641 activated B cell Histone H4K91ac abcam, ab4627 resting B cell Histone H4K8ac Millipore, 07-328 resting B cell Histone H4K5ac Millipore, 07-327 resting B cell Histone H4K20me3 Diagenode, C15410207 resting B cell Histone H4K20me1 abcam, ab9051-100 resting B cell Histone H4K16ac Millipore, 07-329 resting B cell Histone H4K12ac Millipore, 07-595 resting B cell Histone H3K9me3 abcam, ab8898 resting B cell Histone H3K9me2 abcam, ab1220 resting B cell Histone H3K9me1 abcam, ab9045 resting B cell Histone H3K9ac abcam, ab4441 resting B cell Histone H3K79me3 abcam, ab2621 resting B cell Histone H3K79me2 abcam, ab3594 resting B cell Histone H3K79me1 Diagenode, C15410082 resting B cell Histone H3K4me3 Millipore, 04-745 resting B cell Histone H3K4me2 Millipore, 07-030 resting B cell Histone H3K4me1 abcam, ab8895 resting B cell Histone H3K4ac Millipore, 07-539 resting B cell Histone H3K36me3 abcam, ab9050 resting B cell Histone H3K36me2 abcam, ab9049 resting B cell Histone H3K36me1 abcam, ab9048 resting B cell Histone H3K36ac Millipore, 07-540 resting B cell Histone H3K27me3 Millipore, 07-449 resting B cell Histone H3K27me1 Millipore, 07-448 resting B cell Histone H3K23ac Millipore, 07-355 resting B cell Histone H3K18ac Diagenode, C15410139 resting B cell Histone H2BK20ac Millipore, 07-347 resting B cell Histone H2BK5ac Active motif, 39123 resting B cell Histone H3K14ac Millipore, MABE351 resting B cell Histone H2BK12ac Diagenode, C15410212 resting B cell Histone H2BK120ac active motif, 39119 resting B cell Histone H2A.Z abcam, ab4174 resting B cell Histone H2AK9ac Millipore, 07-289 resting B cell Histone H4K91ac abcam, ab4627 activated B cell Histone H4K8ac Millipore, 07-328 activated B cell Histone H4K5ac Millipore, 07-327 activated B cell Histone H4K20me3 Diagenode, C15410207 activated B cell Histone H4K20me1 abcam, ab9051-100 activated B cell Histone H4K16ac Millipore, 07-329 activated B cell Histone H4K12ac Millipore, 07-595 activated B cell Histone H3K9me3 abcam, ab8898 activated B cell Histone H3K9me2 abcam, ab1220 activated B cell Histone H3K9me1 abcam, ab9045 activated B cell Histone H3K9ac abcam, ab4441 activated B cell Histone H3K79me3 abcam, ab2621 activated B cell Histone H3K79me2 abcam, ab3594 activated B cell Histone H3K79me1 Diagenode, C15410082 activated B cell Histone H3K4me3 Millipore, 04-745 activated B cell Histone H3K4me2 Millipore, 07-030 activated B cell Histone H3K4me1 abcam, ab8895 activated B cell Histone H3K4ac Millipore, 07-539 activated B cell Histone H3K36me3 abcam, ab9050 activated B cell Histone H3K36me2 abcam, ab9049 activated B cell Histone H3K36me1 abcam, ab9048 activated B cell Histone H3K36ac Millipore, 07-540 activated B cell Histone H3K27me3 Millipore, 07-449 activated B cell Histone H3K27me1 Millipore, 07-448 activated B cell Histone H3K23ac Millipore, 07-355 activated B cell Histone H3K18ac Diagenode, C15410139 activated B cell Histone H2BK20ac Millipore, 07-347 activated B cell Histone H2BK5ac Active motif, 39123 activated B cell Histone H3K14ac Millipore, MABE351 activated B cell Histone H2BK12ac Diagenode, C15410212 activated B cell Histone H2BK120ac active motif, 39119 activated B cell Histone H2A.Z abcam, ab4174 activated B cell Histone H2AK9ac Millipore, 07-289 activated B cell Others Foxa2 Foxa2 Definitive endoderm cells Others Srf anti-SRF Santa Cruz Biotechnology/sc-335 10T1/2 cells knockdown Med23 Others Srf anti-SRF Santa Cruz Biotechnology/sc-335 10T1/2 cells knockdown control Unclassified Unclassified SC differentiating murine hematopoietic cells Others Fli1 FLI1 differentiating murine hematopoietic cells RNA polymerase RNA polymerase II RNA Pol II differentiating murine hematopoietic cells Others Cebpb CEBPb differentiating murine hematopoietic cells Input control Input control none differentiating murine hematopoietic cells Input control Input control none CD4+ T cells, input RNA polymerase RNA polymerase II anti-Pol II (N20) sc-899 CD4+ T cells, FLAG-FoxP3+GATA1, Pol II ChIP Others Foxp3 anti-FLAG, clone M2 F1804 CD4+ T cells, FLAG-FoxP3, FLAG ChIP Others Foxp3 anti-FLAG, clone M2 F1804 CD4+ T cells, FLAG-FoxP3+GATA1, FLAG ChIP Input control Input control NKT Input Input control Input control Tg thy Input Unclassified Unclassified NKT Streptavidin ChIP-seq Others Biotin Tg thy Streptavidin ChIP-seq Input control Input control None multipotent progenitor Others Myc c-Myc (sc764x, Santa Cruz), lot# H0107 progenitor B Histone H3K27me3 H3K27me3 (07-449, Millipore), lot# DAM1588246 progenitor B Others Ep300 p300 (sc-585x, Santa Cruz), lot# H2610 progenitor B Histone H3K36me3 H3K36me3 (ab9050, Abcam), lot# 947467 progenitor B Others Rad21 Rad21 (ab992, Abcam), lot# GR12688-4 progenitor B Others Ctcf CTCF (07-729, Millipore), lot# DAM1772428 progenitor B Histone H3K4me2 H3K4me2 (07-030, Millipore), lot# DAM1570816 progenitor B Histone H3K36me3 H3K36me3 (ab9050, Abcam), lot# 947467 multipotent progenitor Others Rad21 Rad21 (ab992, Abcam), lot# GR12688-4 multipotent progenitor Others Ctcf CTCF (07-729, Millipore), lot# DAM1772428 multipotent progenitor Histone H3K4me2 H3K4me2 (07-030, Millipore), lot# DAM1570816 multipotent progenitor Histone H3K4me3 H3K4me3 BM pre-B cells Histone H3K27ac H3K27ac BM pre-B cells Input control Input control none (input) Input#1+2+3 Others Kdm1a LSD1 (20752, homemade, Schle lab) Differentiated primary brown adipocytes Input control Input control None Differentiated primary brown adipocytes Unclassified Unclassified fetal testis Histone H3K27me1 H3K27me1 Cell Signaling/No 07-448/Lot 24439 E14 ES cells Histone H3K27me2 H3K27me2 Cell Signaling/No 9728S/Lot 1 E14 ES cells Histone H3 H3 Abcam/No 1791/GR50122-1 E14 ES cells Histone H3K27me3 H3K27me3 (Millipore:07-449) ES cells Histone H3K27me3 anti-H3K27me3 H3K27me3 ChIP DNA fromMx1-Cre; Dpy30F/- Lineage negative bone marrow cells Histone H3K27me3 anti-H3K27me3 H3K27me3 ChIP DNA fromMx1-Cre; Dpy30F/+ Lineage negative bone marrow cells Histone H3K4me3 anti-H3K4me3 H3K4me3 ChIP DNA from Mx1-Cre; Dpy30F/- Lineage negative bone marrow cells Histone H3K4me3 anti-H3K4me3 H3K4me3 ChIP DNA from Mx1-Cre; Dpy30F/+ Lineage negative bone marrow cells Input control Input control none Input DNA from Mx1-Cre; Dpy30F/- Lineage negative bone marrow cells Input control Input control none Input DNA from Mx1-Cre; Dpy30F/+ Lineage negative bone marrow cells Histone H3K27me3 anti-H3K27me3 (Cell Signaling, #9733) embryonic forelmb bud, H3K27me3 ChIP Others Hoxd13 anti-HoxD13 (in-house, affinity purified) embryonic forelmb bud, HoxD13 ChIP Others Hoxa13 anti-HoxA13 (in-house, affinity purified) embryonic forelmb bud, HoxA13 ChIP Others Nfib Nfib antibody (Sigma, #HPA003956) Nfib pulldown KP1-PD2 Others Nfib Nfib antibody (Sigma, #HPA003956) Nfib pulldown KP1-PD1 RNA polymerase RNA polymerase II Pol2-S5P (Abcam, ab5131) Day2+8hrs post-RA exposure Others Nfatc1 NFATc1 NFATc1-ChIP-Seq-shSTAT3 Others Nfatc1 NFATc1 NFATc1-ChIP-Seq-scramble Input control Input control Rabbit IgG (ab37415, Abcam) FDC-P1 RUNX1-ERt2 Others Runx1 Runx1, rabbit (Aziz-Aloya R, 1998) FDC-P1 RUNX1-ERt2 Input control Input control Rabbit IgG (ab37415, Abcam) FDC-P1 wt Others Runx1 Runx1, rabbit (Aziz-Aloya R, 1998) FDC-P1 wt Histone H3 anti-H3 (Abcam ab1791) ESCs, Jmjd2abc, OHT, H3 ChIP Histone H3 anti-H3 (Abcam ab1791) ESCs, Jmjd2abc, Control, H3 ChIP Histone H3 anti-H3 (Abcam ab1791) ESCs, Jmjd2ac, OHT, H3 ChIP Histone H3 anti-H3 (Abcam ab1791) ESCs, Jmjd2ac, Control, H3 ChIP Histone H3K4me3 anti-H3K4me3 (C42D8) (Cell Signaling #9751) ESCs, Jmjd2abc, OHT, H3K4me3 ChIP Histone H3K4me3 anti-H3K4me3 (C42D8) (Cell Signaling #9751) ESCs, Jmjd2abc, Control, H3K4me3 ChIP Histone H3K4me3 anti-H3K4me3 (C42D8) (Cell Signaling #9751) ESCs, Jmjd2ac, OHT, H3K4me3 ChIP Histone H3K4me3 anti-H3K4me3 (C42D8) (Cell Signaling #9751) ESCs, Jmjd2ac, Control, H3K4me3 ChIP Others Kdm4a anti-Jmjd2a (Cell Signaling Technology, #5328) ESCs, Jmjd2a, OHT, Jmjd2a ChIP Others Kdm4a anti-Jmjd2a (Cell Signaling Technology, #5328) ESCs, Jmjd2a, Control, Jmjd2a ChIP Others Fam60a Fam60a NIH3T3 Others Sin3a Sin3a NIH3T3 Others Fam60a Fam60a Embryonic stem cells Others Sin3a Sin3a Embryonic stem cells Input control Input control none F3_Testis_Atrazine_Input_DNA Input control Input control none F3_Testis_Control_Input_DNA Input control Input control none F1_Testis_Input_DNA Others Zfp281 Zfp281 (Abcam #ab101318) Embryonic stem cells Unclassified Unclassified Described in Garcia-Tuon I et al. Stem Cell Res.(2011)7(1), 1-16. and in Prez-Palacios et al., 2016. Trophectoderm Stem cells Others Yy2 In house aYY2 polyclonal rabbit serum Trophectoderm Stem cells Input control Input control IgG antibodies (Santa Cruz, sc-2025) ctrl.2, 2i Others Tfe3 Tfe3 (Santa Cruz, sc-5958) Tfe3.3, 2i Others Tfe3 Tfe3 (Santa Cruz, sc-5958) Flcn.4, 2i Others Tfe3 Tfe3 (Santa Cruz, sc-5958) ctrl.2, 2i Histone H2A.XS139ph Anti-gamma H2A.X (phospho S139) (ab2893, Abcam) Doxycycline-treated BCR-ABL1-transformed primary B cell precursors that carry the empty vector (EV) respective to the DOX-inducible CEBPA vector used in the other experimens. Cells are succesfully transformed cells. Input control Input control none Untreated BCR-ABL1-transformed primary B cell precursors that carry a DOX-inducible CEBPA vector. Cells are succesfully transformed cells. Input control Input control none Doxycycline (DOX) treated BCR-ABL1-transformed primary B cell precursors that carry a DOX-inducible CEBPA vector. Cells were enriched for CD11B+ myeloid phenotype by MACS. Cells are succesfully transformed cells. Histone H2A.XS139ph Anti-gamma H2A.X (phospho S139) (ab2893, Abcam) Untreated BCR-ABL1-transformed primary B cell precursors that carry a DOX-inducible CEBPA vector. Cells are succesfully transformed cells. Histone H2A.XS139ph Anti-gamma H2A.X (phospho S139) (ab2893, Abcam) Doxycycline (DOX) treated BCR-ABL1-transformed primary B cell precursors that carry a DOX-inducible CEBPA vector. Cells were enriched for CD11B+ myeloid phenotype by MACS. Cells are succesfully transformed cells. Histone H3K27ac Anti-Histone H3 (acetyl K27) (ab4729, Abcam) C-MYC expressing primary B cell precursors (D7-9 post transduction) Histone H3K27ac Anti-Histone H3 (acetyl K27) (ab4729, Abcam) BCR-ABL1 expressing primary B cell precursors (D7-9 post transduction) Input control Input control none C-MYC expressing primary B cell precursors (D7-9 post transduction) Input control Input control none BCR-ABL1 expressing primary B cell precursors (D7-9 post transduction) Histone H2A.XS139ph Anti-gamma H2A.X (phospho S139) (ab2893, Abcam) BCR-ABL1 expressing primary B cell precursors that were cultured for >50 days (>D50) in cell culture with IL7 post transduction. Cells were also treated with 10mM hydroxyurea (HU) for 2 hours before harvest. Input control Input control polyclonal rabbit IgG (sc2027, Santa Cruz Biotechnologies) BCR-ABL1 expressing primary B cell precursors (D7-9 post transduction) Others Myc Anti-c-MYC (Santa cruz sc-764) Splenic B cells activated in vitro Unclassified Unclassified Germinal center light zone cells Unclassified Unclassified Germinal center dark zone cells Others Tfap4 anti-AP4 (in house) Germinal center light zone cells Others Tfap4 anti-AP4 (in house) Germinal center dark zone cells Histone H3K4me3 H3K4me3 Cell Signaling, 9751 Embryonic Stem Cell Input control Input control none Embryonic Stem Cell Others Stat1 STAT3 (Invitrogen, 13-7000) Th17 Cells Others Jund JunD (Santa Cruz, sc-74, J-1411) Th17 Cells Others Jun cJUN (Abcam, ab31419, GR30-33) Th17 Cells Others Junb JunB (Santa Cruz, sc-73, k0311) Th17 Cells Others Irf4 IRF4 (Santa Cruz, sc-6059, k1209) Th17 Cells Others Batf BATF (from Ken Murphy rabbit , not commercial available) Th17 Cells Input control Input control Rabbit IgG (R&D, AB-105-C, ER11) Th17 Cells Input control Input control Rabbit IgG (R&D, AB-105-C, ER11) CD4+ T Cells Input control Input control Rabbit IgG (R&D, AB-105-C, ER11) B cells Input control Input control none (chromatin processed without incubation with the antibody) Embryonic Stem cells mESCs Histone H3K27me3 H3K27me3 Crypt Others Suz12 Suz12 Crypt Input control Input control none Crypt Input control Input control C2C12 myotubes, WCE Others Esrra C2C12 myotubes, IP ERRalpha Unclassified Unclassified post mitotic neuronal cells Others Pbx1 Pbx1 (4342 CST) E11.5 Embryo Trunk Others Pknox1 Prep1/2 (N15 Santa Cruz) E11.5 Embryo Trunk Others Meis1 Meis1/2 (K830, K844) E11.5 Embryo Trunk Others Nanog antibody: calbiochem (SC1000) mESCs Others Nanog antidoby: calbiochem (SC1000) mESCs Histone H3K9me3 antibody: active motif (39161) mESCs Others Smc3 antibody: abcam (ab9263) mESCs Others Ctcf antibody: millipore (07-729) mESCs Unclassified Unclassified CD19+IgD-B220+IgM-CD25+ckit- pre-B cells Unclassified Unclassified CD19+IgD-B220+IgM+ immature B cells Unclassified Unclassified CD4-CD8- double negative (CD25+CD44-/+) T cells Histone H3K27me3 anti-trimethyl-histone H3 (Lys27) (Millipore, Cat# 07-449, Lot# 2607758) H3K27me3_WT_embryonic cerebellum Histone H3K27me3 anti-trimethyl-histone H3 (Lys27) (Millipore, Cat# 07-449, Lot# 2607758) H3K27me3_Ezh2KO_embryonic cerebellum Input control Input control none Neuroblastoma cells Others Nacc1 Nacc1 antibody (abcam ab29047) Neuroblastoma cells Histone H3K4me3 H3K4me3 (Millipore, cat# 07-473, lot# 2207275) brain tumor, Olig2cKO, H3K4me3 ChIP Histone H3K4me3 H3K4me3 (Millipore, cat# 07-473, lot# 2207275) brain tumor, control, H3K4me3 ChIP Histone H3K27ac H3K27Ac (Active Motif, cat# 39133, lot# 1613007) brain tumor, Olig2cKO, H3K27Ac ChIP Histone H3K27ac H3K27Ac (Active Motif, cat# 39133, lot# 1613007) brain tumor, control, H3K27Ac ChIP Others Olig2 Olig2 (Millipore, cat# AB9610) brain tumor, control, Olig2 ChIP Others Cebpb Cebpb Bone Marrow Histone H3K27me3 H3K27me3 mouse embryonic stem cells (E14) Input control Input control input inputs Rap1 Input control Input control input inputs RAP1 Others Terf2ip RAP1 G3 Rap1 KO2 Others Terf2ip RAP1 G3 Rap1 KO1 Others Terf2ip RAP1 G3 Rap1 wt2 Others Terf2ip RAP1 G3 Rap1 wt1 Others Terf2ip RAP1 G1 Rap1 ko2 Others Terf2ip RAP1 G1 Rap1 ko1 Others Terf2ip RAP1 G1 RAP1 wt2 Others Terf2ip RAP1 G1 RAP1 wt1 Others Terf2ip RAP1 RAP1 ko2 Others Terf2ip RAP1 RAP1 ko1 Others Terf2ip RAP1 RAP1 wt2 Others Terf2ip RAP1 RAP1 wt1 Histone H3K27me3 anti-H3K27me3 (Diagenode, catalog# C15410069 (pAb-069-050)) Preimplantation embryo Histone H3K27ac anti-H3K27ac (ActivMotif, catalog# 39133, lot# 16612005) Preimplantation embryo Input control Input control none mouse embryonic stem cell Others Epitope tags Flag(Sigma, F3165) mouse embryonic stem cell Others Epitope tags HA Abcam ab9110 Cardiac progenitor cells Others Isl1 ISL1 Abcam ab109517 Cardiac progenitor cells Input control Input control Non Cardiac progenitor cells Histone H3K4me3 custom-made H3K4Me3 antibody (Abmart) Sperm Histone H3K4me3 H3K4Me3 (04-745, Millipore) testis TRF2 -/- Histone H3K4me3 H3K4Me3 (04-745, Millipore) testis wt RNA polymerase RNA polymerase II PolII (sc-9001X, Santa Cruz) testis TRF2 -/- RNA polymerase RNA polymerase II PolII (sc-9001X, Santa Cruz) testis TRF2 tag/tag Others Tbp TBP (ab28175, Abcam), TBP (ab51841, Abcam) testis TRF2 -/- Others Tbp TBP (ab28175, Abcam), TBP (ab51841, Abcam) testis TRF2 tag/tag Others Tbpl1 Flag (M2 affinity gel, Sigma), TRF2 (in house) testis TRF2 -/- Others Tbpl1 Flag (M2 affinity gel, Sigma), TRF2 (in house) testis TRF2 tag/tag Input control Input control abcam 46540 (Lot GR172884-2) Undifferentiated ES cells Others Ep300 p300 (Santa Cruz, catalog# sc-584, lot# I2712) Postmitotic motor neurons day 6 Others Ep300 p300 (Santa Cruz, catalog# sc-584, lot# I2712) Postmitotic motor neurons day 5 Histone H3K27ac H3K27ac (Abcam, catalog# ab4729, lot# GR00563-2) Postmitotic motor neurons day 6 Histone H3K27ac H3K27ac (Abcam, catalog# ab4729, lot# GR00563-2) Postmitotic motor neurons day 5 Others Epitope tags V5 (Invitrogen, catalog# R960, lot# 1652168) Motor neurons progenitors day 4 Input control Input control none (WCE) Postmitotic motor neurons day 5 Input control Input control IgG (R&D, catalog# AB-108-C, lot# ES3411101) Postmitotic motor neurons day 6 Input control Input control IgG (R&D, catalog# AB-108-C, lot# ES3411101) Postmitotic motor neurons day 5 Others Epitope tags V5 (Invitrogen, catalog# R960, lot# 1652168) Postmitotic motor neurons day 4 Others Onecut1 Onecut1 (Santa Cruz, catalog# sc-13050, lot# J0405) Postmitotic motor neurons day 6 Others Onecut1 Onecut1 (Santa Cruz, catalog# sc-13050, lot# J0405) Postmitotic motor neurons day 5 Histone H3K27me3 Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9738 Day 7 of Activin/FGF2 treatment E14 mouse embryonic stem cells Histone H3K27me3 Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9737 Day 4 of Activin/FGF2 treatment E14 mouse embryonic stem cells Histone H3K27me3 Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9736 Cultured in 2i+vitc E14 mouse embryonic stem cells Histone H3K27me3 Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9735 Day 7 of Activin/FGF2 treatment E14 mouse embryonic stem cells Histone H3K27me3 Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9734 Day 4 of Activin/FGF2 treatment E14 mouse embryonic stem cells Histone H3K27me3 Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9733 Cultured in 2i+vitc E14 mouse embryonic stem cells Input control Input control none pro-B Ba/F3_input DNA Input control Input control none Murine PDAC Input control Input control MEL-FLAG Control Cells Others Brd9 Brd9 (ab66443; Abcam) RN2 Others Epop EPOP (Ab3), Active Motif #61753 Embryonic stem cells Others Epop EPOP (Ab3) , Active Motif #61753 Embryonic stem cells Others Tead4 TEAD4 (Abcam, catalog# ab58310) TEAD4 HE1 WT Others Tead4 TEAD4 (Abcam, catalog# ab58310) TEAD4 d1BC plus dox Others Tead4 TEAD4 (Abcam, catalog# ab58310) TEAD4 d1BC minus dox Others Jun c-Jun (Santa Cruz Biotechnology, catalog# sc-1694-X) Jun d1BC WT Others Crebbp c-Fos (Santa Cruz Biotechnology, catalog# sc-253-X) Fos d1BC minus dox Input control Input control none Sperm Histone H3 ab1791, Abcam Sperm Input control Input control none sonicated chromatin from on control, non-induced iBN cells Input control Input control none sonicated chromatin from iBN cells induced for 72 hours with doxycyclin Input control Input control Input Epididymal white adipose tissue Others Nr1d1 Rev-erb alpha (Cell Signaling, catalog number CS2124, rabbit antibody) Epididymal white adipose tissue Input control Input control none E15.5 cortex, input Others Pbx1 Pbx1/2/3 (Santa Cruz, sc-888) mixed with the PBX blocking peptide (Santa Cruz, sc-888P) at 1:400 molar ratio E15.5 cortex, negative control Others Pbx1 Pbx1/2/3 (Santa Cruz, sc-888) E15.5 cortex, Pbx1/2/3 ChIP Histone H3K4me1 H3K4me1: Abcam ab8895 Primary bone marrow-derived mast cells (BMMCs) Input control Input control none RAG-/-+ pre-B cells Histone H3K4me1 H3K4me1 (Abcam (Ab8895)) RAG-/-+ pre-B cells Others GFP abcam ab290 mouse embryonic stem cells Input control Input control none anterior trunk Histone H3K27ac H3K27ac (Abcam, catalog# ab4729, lot# GR184558-1) anterior trunk Histone H3K27me3 H3K27me3 EZH2_Y641F_855D_MEL_JQEZ5_H3K27_IP Histone H3K27me3 H3K27me3 EZH2_Y641F_855D_MEL_H3K27_IP Histone H3K27me3 H3K27me3 EZH2_Y641F_480D_MEL_JQEZ5_H3K27_IP Histone H3K27me3 H3K27me3 EZH2_Y641F_480D_MEL_H3K27_IP Histone H3K27me3 H3K27me3 EZH2_WT_855_MEL_JQEZ5_H3K27_IP Histone H3K27me3 H3K27me3 EZH2_WT_855_MEL_H3K27_IP Input control Input control EZH2_WT_855_MEL_H3K27_input Histone H3K27me3 H3K27me3 EZH2_WT_480_MEL_JQEZ5_ H3K27_IP Histone H3K27me3 H3K27me3 EZH2_WT_480_MEL_H3K27_IP Input control Input control EZH2_WT_480_MEL_H3K27_input Others Gli2 Gli2 antibody (Abcam, 26056, lot GR223520-2) Gli2 chromatin binding in pri-NPC Others Gli2 Gli2 antibody (Abcam, 26056, lot GR223520-2) Gli2 chromatin binding in ciNSLCs Others Gli2 Gli2 antibody (Abcam, 26056, lot GR223520-2) Gli2 chromatin binding at day 8 of M9-induced reprogramming Others Gli2 Gli2 antibody (Abcam, 26056, lot GR223520-2) Gli2 chromatin binding at day 4 of M9-induced reprogramming Others Gli2 Gli2 antibody (Abcam, 26056, lot GR223520-2) Gli2 chromatin binding at day 0 of M9-induced reprogramming Others Elk1 Elk1 antibody (Epitomics, 1277-1, lot GR106696-8) Elk1 chromatin binding in pri-NPC Others Elk1 Elk1 antibody (Epitomics, 1277-1, lot GR106696-8) Elk1 chromatin binding in ciNSLCs Others Elk1 Elk1 antibody (Epitomics, 1277-1, lot GR106696-8) Elk1 chromatin binding at day 8 of M9-induced reprogramming Others Elk1 Elk1 antibody (Epitomics, 1277-1, lot GR106696-8) Elk1 chromatin binding at day 4 of M9-induced reprogramming Others Elk1 Elk1 antibody (Epitomics, 1277-1, lot GR106696-8) Elk1 chromatin binding at day 0 of M9-induced reprogramming Histone H3K27ac H3K27ac (Millipore, 17-683, lot 2510209) H3K27Ac of pri-NPC Histone H3K27me3 H3K27me3 (Millipore, 17-622, lot 2135434) H3K27me3 of pri-NPC Histone H3K4me3 H3K4me3 (Millipore, 17-614, lot 2109590) H3K4me3 of pri-NPC Histone H3K4me1 H3K4me1 (Abcam, ab8895, lot GR193727-1) H3K4me1 of pri-NPC Input control Input control None Input genomic DNA of pri-NPCs Histone H3K27ac H3K27ac (Millipore, 17-683, lot 2510209) H3K27Ac of ciNSLCs Histone H3K27me3 H3K27me3 (Millipore, 17-622, lot 2135434) H3K27me3 of ciNSLCs Histone H3K4me3 H3K4me3 (Millipore, 17-614, lot 2109590) H3K4me3 of ciNSLCs Histone H3K4me1 H3K4me1 (Abcam, ab8895, lot GR193727-1) H3K4me1 of ciNSLCs Input control Input control None Input genomic DNA of ciNSLCs Histone H3K27ac H3K27ac (Millipore, 17-683, lot 2510209) H3K27Ac at day 8 of M9-induced reprogramming Histone H3K27me3 H3K27me3 (Millipore, 17-622, lot 2135434) H3K27me3 at day 8 of M9-induced reprogramming Histone H3K4me3 H3K4me3 (Millipore, 17-614, lot 2109590) H3K4me3 at day 8 of M9-induced reprogramming Histone H3K4me1 H3K4me1 (Abcam, ab8895, lot GR193727-1) H3K4me1 at day 8 of M9-induced reprogramming Input control Input control None Input genomic DNA of tdMEFs at day 8 of M9-induced reprogramming Histone H3K27ac H3K27ac (Millipore, 17-683, lot 2510209) H3K27Ac at day 4 of M9-induced reprogramming Histone H3K27me3 H3K27me3 (Millipore, 17-622, lot 2135434) H3K27me3 at day 4 of M9-induced reprogramming Histone H3K4me3 H3K4me3 (Millipore, 17-614, lot 2109590) H3K4me3 at day 4 of M9-induced reprogramming Histone H3K4me1 H3K4me1 (Abcam, ab8895, lot GR193727-1) H3K4me1 at day 4 of M9-induced reprogramming Input control Input control None Input genomic DNA of tdMEFs at day 4 of M9-induced reprogramming Histone H3K27ac H3K27ac (Millipore, 17-683, lot 2510209) H3K27Ac at day 0 of M9-induced reprogramming Histone H3K27me3 H3K27me3 (Millipore, 17-622, lot 2135434) H3K27me3 at day 0 of M9-induced reprogramming Histone H3K4me3 H3K4me3 (Millipore, 17-614, lot 2109590) H3K4me3 at day 0 of M9-induced reprogramming Histone H3K4me1 H3K4me1 (Abcam, ab8895, lot GR193727-1) H3K4me1 at day 0 of M9-induced reprogramming Input control Input control None Input genomic DNA of tdMEFs at day 0 of M9-induced reprogramming Input control Input control none mouse trophoblast stem cells Input control Input control none MII oocyte Input control Input control none isolated mouse islet Others Rnf2 anti-RNF2 (Bethyl, A302-869A) NSC Ring1b ChIP Others Rnf2 anti-RNF2 (Bethyl, A302-869A) ESC Ring1b ChIP Input control Input control none NSC input for Ring1b ChiP Input control Input control none ESC input for Ring1b ChIP Histone H3K27me3 anti-H3K27me3 (Millipore, 07-449) NSC ChIP for H3K27me3 Others Ezh2 anti-Ezh2(D2C9) (Cell Signaling, 5246S) ESC ChIP for Ezh2 Others Cbx2 anti-Cbx2 (Santa Cruz, sc-19297) ESC ChIP for Cbx2 Histone H3K27me3 anti-H3K27me3 (Millipore, 07-449) ESC ChIP for H3K27me3 Input control Input control none NSC input for ChIP (H3K27me3) Input control Input control none ESC input for ChIP (H3K27me3, Cbx2, Ezh2) Input control Input control non ESC input for HA ChIP Others Epitope tags ChIP with anti-HA (Abcam, ab9110) ESC HA ChIP Input control Input control NSC time-ChIP input (for replicates 2 and 3) Input control Input control NSC time-ChIP input (for replicate 1) Input control Input control ESC time-ChIP input (for replicates 2 and 3) Others Ep300 p300 (sc-586, Santa Cruz) Pre-activated CD8+ T cells Input control Input control IgG (Santa Cruz Biotechnology, Sc-2027) Differentiated mouse ES cells Others Ctcf CTCF (Millipore, 07-729, lot DAM1682158) Differentiated mouse ES cells Others Ctcf CTCF (Millipore, 07-729, lot DAM1682158) Undifferentiated mouse ES cells Histone H3K27ac H3K27ac E36 ES cells Histone H3K27ac H3K27ac (Abcam, cat No:4729, Lot: GR55451-1) E36 ES cells Input control Input control none, input MEF Input control Input control C2C12 myotubes_input Others Epitope tags anti-Flag (Sigma, F1804-200UG) embryonic stem cells Others Epitope tags anti-V5 (Abcam, ab15828) embryonic stem cells RNA polymerase RNA polymerase II anti-Pol2 antibody 8WG16 (Covance MMS-126R) progenitor motor neurons Histone H3K79me2 anti-H3K79me2 antibody (Abcam ab3594) progenitor motor neurons Histone H3K4me3 anti-H3K4me3 antibody (Abcam ab8580) progenitor motor neurons Histone H3K27me3 anti-H3K27me3 (Abcam, ab6002) progenitor motor neurons Histone H3K27me3 anti-H3K27me3 (Abcam, ab6002) Day 5 cells Others Tbp TBP (Abcam ab818) F1 C/B trophoblast stem cells Others Sp1 SP1 (Santa Cruz sc-17824) F1 C/B trophoblast stem cells Histone H3K4me1 H3K4me1 (Abcam ab8895) F1 C/B trophoblast stem cells Histone H3K27ac H3K27ac (Abcam 4729) F1 C/B trophoblast stem cells Histone H3K27me3 H3K27me3, B/C (Abcam ab6002) F1 B/C trophoblast stem cells Histone H3K27me3 H3K27me3, C/B #2 (Abcam ab6002) F1 C/B trophoblast stem cells Histone H3K27me3 H3K27me3 (Abcam ab6002) F1 C/B trophoblast stem cells Histone H4K20me1 H4K20me1 (Active Motif 39175) F1 C/B trophoblast stem cells Histone H3 Total H3 (Abcam ab1791) F1 C/B trophoblast stem cells Histone H3K36me3 H3K36me3 (Abcam ab9050) F1 C/B trophoblast stem cells Histone H3K4me2 H3K4me2 (Millipore 07-030) F1 C/B trophoblast stem cells RNA polymerase RNA polymerase II Pol II (Santa Cruz sc-899) F1 C/B trophoblast stem cells Input control Input control none E12.5 cortex, input Others Pbx1 Pbx1/2/3 (Santa Cruz, sc-888) mixed with the PBX blocking peptide (Santa Cruz, sc-888P) at 1:400 molar ratio E12.5 cortex, negative control Others Pbx1 Pbx1/2/3 (Santa Cruz, sc-888) E12.5 cortex, Pbx1/2/3 ChIP Others Kmt2b Mll2 (Homemade, #9175) mouse embryonic stem cells Others Men1 Menin (Bethyl, A300-105A, Lot A300-105A-5) mouse embryonic stem cells Input control Input control none (input) Trophoblast stem cells Unclassified Unclassified 20752 Trophoblast stem cells Histone H3K27me3 H3K27me3 (Abcam ab6002) mouse embryonic fibroblast (MEF) Histone H3K4me3 H3K4me3 (Abcam ab8580) mouse embryonic fibroblast (MEF) Input control Input control none mouse embryonic fibroblast (MEF) Histone H3K27me3 H3K27me3 (Abcam ab6002) macrophage Histone H3K4me3 H3K4me3 (Abcam ab8580) macrophage Input control Input control none macrophage Input control Input control none haematopoietic stem and progenitor cell (HSC) Histone H3K27ac H3K27ac (Abcam ab4729) Spermatogonial stem and progenitor cell (SSC) Histone H3K27ac H3K27ac (Abcam ab4729) multipotent adult spermatogonial-derived stem cell (MASC) Input control Input control none multipotent adult spermatogonial-derived stem cell (MASC) Others Zfp143 ZNF143, rabbit polyclonal raised against a C-terminal epitope of ZNF143 (Myslinski et al JBC 2006) Mouse Embryonic Stem cells Input control Input control None Sall4/- (Sall4 KO) mES cells with Bio-tagged TET2 Others Tet2 Dynabeads M-280 Streptavidin (Life Technologies) Sall4/- (Sall4 KO) mES cells with Bio-tagged TET2 Input control Input control None Sall4flox/- (Sall4 het) mES Cells with Bio-tagged TET2 Others Tet2 Dynabeads M-280 Streptavidin (Life Technologies) Sall4flox/- (Sall4 het) mES Cells with Bio-tagged TET2 Input control Input control None TT2 mES cells with Biotin-tagged TET2 Others Tet2 Dynabeads M-280 Streptavidin (Life Technologies) TT2 mES cells with Biotin-tagged TET2 Histone H2A.Z Acetyl-H2A.Z (Abcam ab18262) acH2AZ_mNP_ChIPSeq Histone H2A.Z H2A.Z (Millipore 07-594) H2AZ_mNP_ChIPSeq RNA polymerase RNA polymerase II RNAPII (CTD4H8) (Covance MMS-128P) RNAPII_mES_ChIPSeq Others Tbp TFIID(TBP) (Santa Cruz sc-273X) TFIID_mES_ChIPSeq Histone H2A.Z Acetyl-H2A.Z (Abcam ab18262) acH2AZ_mES_ChIPSeq Histone H2A.Z H2A.Z (Millipore 07-594) H2AZ_mES_ChIPSeq Input control Input control none Whole lung Histone H3K27ac H3K27ac (Abcam ab4729) Forelimb Input control Input control IgG control Ab (SantaCruz, sc-2028) Primary bone marrow-derived macrophages (BMDM) Input control Input control Anti-IgG (IgG from rabbit serum, Sigma-Aldrich, catalog# I5006) E14 ES cells Others Ogt Anti-OGT (O-Linked N-Acetylglucosamine Transferase antibody sold, Abcam, catalog# ab50273) E14 ES cells Histone H3K9me3 anti-H3K9me3 Mouse embryonic fibroblasts RNA polymerase RNA polymerase II anti-Pol2 Mouse embryonic fibroblasts Input control Input control none, Input Mouse embryonic fibroblasts Input control Input control None Mouse heart Others Sap130 Sap130 (A302-491A: Bethyl laboratories) Mouse heart Input control Input control n.a. Mature B cell Unclassified Unclassified mouse_liver Histone H3K27me3 Anti H3K27me3 - Millipore (cat # 07-449) Mouse Liver tumour tissue Others Tbx21 Santa Cruz sc21003 Natural killer cells Input control Input control input Input_STAT5AB_CD4_Th0_IL2_48h_rpt2 Input control Input control input Input_STAT5AA_CD4_Th0_IL2_48h_rpt2 Input control Input control input Input_STAT5BB_CD4_Th0_IL2_48h_rpt2 Input control Input control input Input_WT_CD4_Th0_IL2_48h_rpt2 Others Stat5a pan-STAT5 (polyclonal rabbit anti-human/mouse antibody purchased from Abcam; ab7969)(Lot #GR93813-4) panSTAT5_STAT5AB_CD4_Th0_IL2_48h_rpt2 Others Stat5a pan-STAT5 (polyclonal rabbit anti-human/mouse antibody purchased from Abcam; ab7969)(Lot #GR93813-4) panSTAT5_STAT5AA_CD4_Th0_IL2_48h_rpt2 Others Stat5a pan-STAT5 (polyclonal rabbit anti-human/mouse antibody purchased from Abcam; ab7969)(Lot #GR93813-4) panSTAT5_STAT5BB_CD4_Th0_IL2_48h_rpt2 Others Stat5a pan-STAT5 (polyclonal rabbit anti-human/mouse antibody purchased from Abcam; ab7969)(Lot #GR93813-4) panSTAT5_WT_CD4_Th0_IL2_48h_rpt2 Input control Input control input Input_STAT5AB_CD4_Th0_IL2_48h_rpt1 Input control Input control input Input_STAT5AA_CD4_Th0_IL2_48h_rpt1 Input control Input control input Input_WT_CD4_Th0_IL2_48h_rpt1 Others Stat5a pan-STAT5 (polyclonal rabbit anti-human/mouse antibody purchased from Abcam; ab7969)(Lot #GR93813-4) panSTAT5_STAT5AB_CD4_Th0_IL2_48h_rpt1 Others Stat5a pan-STAT5 (polyclonal rabbit anti-human/mouse antibody purchased from Abcam; ab7969)(Lot #GR93813-4) panSTAT5_STAT5BB_CD4_Th0_IL2_48h_rpt1 Others Stat5a pan-STAT5 (polyclonal rabbit anti-human/mouse antibody purchased from Abcam; ab7969)(Lot #GR93813-4) panSTAT5_STAT5AA_CD4_Th0_IL2_48h_rpt1 Others Stat5a pan-STAT5 (polyclonal rabbit anti-human/mouse antibody purchased from Abcam; ab7969)(Lot #GR93813-4) panSTAT5_WT_CD4_Th0_IL2_48h_rpt1 Others Setdb1 Setdb1 Themo Scientific PA5-30334 pro-B cells Histone H3K9ac H3K9ac Millipore #07-352 pro-B cells Input control Input control none C2C12 cell line Input control Input control none mESC-derived neuron Histone H3K27ac H3K27ac (Active Motif, Cat. 39133) mESC-derived neuron Histone H3K27me3 H3K27me3 (Active Motif, Cat. 39155) mESC-derived neuron Histone H3K4me3 H3K4me3 (Active Motif, Cat. 39159) mESC-derived neuron Histone H3K27ac H3K27ac (Active Motif, Cat. 39133) mESCs Histone H3K27me3 H3K27me3 (Active Motif, Cat. 39155) mESCs Histone H3K4me3 H3K4me3 (Active Motif, Cat. 39159) mESCs Histone H3K9me3 H3K9me3 (Abcam, 8898) E14 Others Trim28 KAP1 (Abcam, ab10483) E14 Others Zfp57 ZFP57 (Abcam, ab45341) E14 Histone H3K9me3 H3K9me3 (Abcam, 8898) A3_Zfp57-/- Others Trim28 KAP1 (Abcam, ab10483) A3_Zfp57-/- Others Zfp57 ZFP57 (Abcam, ab45341) A3_Zfp57-/- Input control Input control none A3_Zfp57-/- Histone H3K9me3 H3K9me3 (Abcam, 8898) A3 Others Trim28 KAP1 (Abcam, ab10483) A3 Others Zfp57 ZFP57 (Abcam, ab45341) A3 Input control Input control none A3 Input control Input control none ChIPSeq Input LT2i Input control Input control none ChIPSeq Input 24h2i Input control Input control none ChIPSeq Input Ser Histone H3K9me2 anti-H3K9me2; Abcam ab1220 ChIPSeq H3K9me2 LT2i 2 Histone H3K9me2 anti-H3K9me2; Abcam ab1220 ChIPSeq H3K9me2 LT2i 1 Histone H3K9me2 anti-H3K9me2; Abcam ab1220 ChIPSeq H3K9me2 24h2i 2 Histone H3K9me2 anti-H3K9me2; Abcam ab1220 ChIPSeq H3K9me2 24h2i 1 Histone H3K9me2 anti-H3K9me2; Abcam ab1220 ChIPSeq H3K9me2 Ser 2 Histone H3K9me2 anti-H3K9me2; Abcam ab1220 ChIPSeq H3K9me2 Ser 1 Others Irf8 goat anti-IRF8 antibody (C-19; Santa Cruz Biotechnology) Tot2 cells, MSCV-IRF8 transuced, Day3 Histone H3K4me1 rabbit anti-H3K4me1 antibody (Ab8895, Abcam) Tot2 cells, MSCV-IRF8 transuced, Day3 Input control Input control none Tot2 cells, MSCV-IRF8 transuced, Day3 Histone H3K4me1 rabbit anti-H3K4me1 antibody (Ab8895, Abcam) Tot2 cells, MSCV transuced, Day3 Input control Input control none Tot2 cells, MSCV transuced, Day3 Input control Input control none mpkDCT4a Histone H3K4me3 rabbit H3K4me3 (Abcam, AB8580) mpkDCT4a Others Hnf1b rabbit anti-Hnf1 (Santa Cruz, H-85, SC-22840) mpkDCT4a Others Tbx21 anti-T-bet antibody (sc-21749, Santa Cruz) Th1 Unclassified Unclassified Clontech, 632460 Quiescent B cells, lipopolysaccharide (LPS) and 10058-F4 treatments for 4hrs RNA polymerase RNA polymerase II Abcam, ab5408 Quiescent B cells, lipopolysaccharide (LPS) and 10058-F4 treatments for 4hrs RNA polymerase RNA polymerase II Abcam, ab5408 Quiescent B cells, lipopolysaccharide (LPS) treatment for 4hrs Input control Input control Santa Cruz SC-2025 Quiescent B cells Unclassified Unclassified Clontech, 632460 Quiescent B cells Input control Input control input DNA pituitary cell line Others Biotin streptavidin beads pituitary cell line Histone H4K8bu H4K8bu (PTM biolabs) Spermatogenic cells (spermatocytes) Histone H4K8ac H4K8ac (gift from Dr H. Kimura) Spermatogenic cells (spermatocytes) Histone H4K5bu H4K5bu (PTM biolabs) Spermatogenic cells (spermatocytes) Histone H4K5ac H4K5ac (gift from Dr H. Kimura) Spermatogenic cells (spermatocytes) Input control Input control none Spermatogenic cells (spermatocytes) Histone H4K8bu H4K8bu (PTM biolabs) Spermatogenic cells (round spermatids) Histone H4K8ac H4K8ac (gift from Dr H. Kimura) Spermatogenic cells (round spermatids) Histone H4K5bu H4K5bu (PTM biolabs) Spermatogenic cells (round spermatids) Histone H4K5ac H4K5ac (gift from Dr H. Kimura) Spermatogenic cells (round spermatids) Input control Input control none Spermatogenic cells (round spermatids) Input control Input control input Mouse embriyonic stem cell Input control Input control input Mouse neural progenitor cells Input control Input control none Input control Others Satb2 Anti-V5 (Abcam, catalog# 15828, lot# GR195596-1) Satb2-ChIP Others Arntl Bmal1 (Santa Cruz, catalog# sc-8550, lot# J1211 ) mouse embryonic fibroblast cells Input control Input control none mouse embryonic fibroblast cells Others Zfp281 ZFP281 murine embryonic stem cells Histone H3K27me3 H3K27Me3 Somatic liver Histone H3K27me3 H3K27Me3 Somatic cortex Histone H3K27me3 H3K27Me3 primordial germ cell Histone H3K27me3 H3K27Me3 E5.5 epiblast Histone H3K27me3 H3K27Me3 GV oocyte Histone H3K27me3 H3K27Me3 Mature sperm Histone H3K9me3 H3K9me3 ab8898 Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. rabbit polyclonal, ChIP grade. Antibody Target: H3K9me3 Erythrobl Histone H3K9me3 H3K9me3 ab8898 Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. rabbit polyclonal, ChIP grade. Antibody Target: H3K9me3 CH12 Histone H3K27me3 H3K27me3 07-449 Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. rabbit polyclonal. Antibody Target: H3K27me3 Erythrobl Histone H3K9me3 H3K9me3 ab8898 Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. rabbit polyclonal, ChIP grade. Antibody Target: H3K9me3 G1E-ER4 Histone H3K36me3 H3K36me3 ab9050 Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts. rabbit polyclonal. Antibody Target: H3K36me3 Erythrobl Histone H3K9me3 H3K9me3 ab8898 Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. rabbit polyclonal, ChIP grade. Antibody Target: H3K9me3 G1E Histone H3K9me3 H3K9me3 ab8898 Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. rabbit polyclonal, ChIP grade. Antibody Target: H3K9me3 Megakaryo Histone H3K36me3 H3K36me3 ab9050 Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts. rabbit polyclonal. Antibody Target: H3K36me3 Megakaryo Histone H3K27me3 H3K27me3 07-449 Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. rabbit polyclonal. Antibody Target: H3K27me3 G1E-ER4 Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal. Antibody Target: H3K4me1 Erythrobl Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal. Antibody Target: H3K4me1 G1E Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal. Antibody Target: H3K4me1 G1E-ER4 Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal. Antibody Target: H3K4me3 G1E Histone H3K27me3 H3K27me3 07-449 Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. rabbit polyclonal. Antibody Target: H3K27me3 CH12 Histone H3K27me3 H3K27me3 07-449 Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. rabbit polyclonal. Antibody Target: H3K27me3 G1E Histone H3K36me3 H3K36me3 ab9050 Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts. rabbit polyclonal. Antibody Target: H3K36me3 G1E Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal. Antibody Target: H3K4me3 Megakaryo Histone H3K36me3 H3K36me3 ab9050 Histone H3 (tri-methyl K36). Marks regions of RNAPII elongation, including coding and non-coding transcripts. rabbit polyclonal. Antibody Target: H3K36me3 G1E-ER4 Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal. Antibody Target: H3K4me1 Megakaryo Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal. Antibody Target: H3K4me3 Erythrobl Histone H3K27me3 H3K27me3 07-449 Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. rabbit polyclonal. Antibody Target: H3K27me3 Megakaryo Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal. Antibody Target: H3K4me3 G1E-ER4 Others Epitope tags FLAG non-proliferating, tagged WT-AR Others Epitope tags FLAG proliferating, tagged WT AR Others Epitope tags FLAG proliferating, non-tagged WT AR Histone H3K4me2 H3K4Me2 - Abcam, ab8895 H3K4Me2.FC/FC Input control Input control none Mouse ES-cells Histone H3 HistoneH3 DP T-cells Others Rybp DEDAF (Millipore, AB3637, lot 2426983) MPI-II_wild type Input control Input control none MPI-II_DDX5 knock-out Input control Input control none MPI-II_wild type Histone H2AK119Ub H2AK119ub (Cell signaling, D27C4, lot 8240) MPI-II_DDX5 knock-out Histone H2AK119Ub H2AK119ub (Cell signaling, D27C4, lot 8240) MPI-II_wild type Input control Input control non-immunoprecipitated DNA lung tumors Others Zmynd8 Bethyl, A302-090A mES cell Histone H3K9me3 H3K9me3 Total thymocytes, KAP1 KO, H3K9me3 ChIP Histone H3K9me3 H3K9me3 Total thymocytes, WT, H3K9me3 ChIP Others Trim28 RBCC (KAP1 amino acids 20418) Total thymocytes, KAP1 KO, KAP1 ChIP Others Trim28 RBCC (KAP1 amino acids 20418) Total thymocytes, WT, KAP1 ChIP RNA polymerase RNA polymerase II PolII S5; Covance, MMS-128P Embryonic stem cells RNA polymerase RNA polymerase II PolII S5, Covance, MMS-128P Embryonic stem cells Others GFP GFP (Santa Cruz, lot #F2508, sc8334) retina Input control Input control WCE_p20 Input control Input control WCE_p3 Unclassified Unclassified preB_p3 Unclassified Unclassified preB_p20 Unclassified Unclassified NSC_p3 Unclassified Unclassified NSC_p20 Unclassified Unclassified MEF_p3 Unclassified Unclassified MEF_p20 Unclassified Unclassified macrophage_p3 Unclassified Unclassified macrophage_p20 Input control Input control None Bone Marrow Others Klf4 KLF4 Bone Marrow Input control Input control input Mouse primary chodrnocytes Histone H3K27me3 H3K27me3 Mouse primary chodrnocytes Histone H3K4me2 Anti-H3K4me2 RA-treated P19.6_H3K4me2 ChIP-seq Histone H3K4me2 Anti-H3K4me2 P19.6_H3K4me2 ChIP-seq Others Tet1 Anti-Tet1 RA-treated P19.6_Tet1 ChIP-seq Others Tet1 Anti-Tet1 P19.6_Tet1 ChIP-seq Others Rxra pan-RXR sc-774x lot #F1609 C17.2a neural progenitor cells, RXR ChIP Others Thrb C17.2b neural progenitor cells, TRb ChAP Others Thra C17.2a neural progenitor cells, TRa ChAP Input control Input control ChIP_MNase_din_cereb_INPUT Unclassified Unclassified ChIP_MNase_din_cereb_MECP2 Input control Input control ChIP_MNase_monon_cereb_INPUT Others Mecp2 ChIP_MNase_monon_cereb_MECP2 Input control Input control ChIP_MNase_monon_WB_INPUT Others Mecp2 ChIP_MNase_monon_WB_MECP2 Input control Input control ChIP_sonicate_WB_INPUT Others Mecp2 ChIP_sonicate_WB_MECP2 Others Hdac2 HDAC2 ChIP TAP-tagged HDAC2 in Myoblasts Others Hdac1 HDAC1 ChIP TAP-tagged HDAC1 in Myoblasts Others Tcf3 E47 ChIP TAP-tagged E47 in 2d differentiating Myoblasts Input control Input control empty vector control Empty Vector control, Myoblast (for Snai1) Others Snai1 Snai1 ChIP TAP-tagged Snai1 in Myoblasts Histone H3K4me2 H3K4me2 (Abcam, ab7766, lot# GR160184-1) newborn lens, H3K4me2 ChIP Histone H3K4me3 H3K4me3 (Abcam, ab8580, lot# GR152121-1) TN4, Pax6 shRNA, H3K4me3 ChIP Histone H3K4me2 H3K4me2 (Abcam, ab7766, lot# GR160184-1) TN4, Pax6 shRNA, H3K4me2 ChIP Histone H3K4me1 H3K4me1 (Abcam, ab8895, lot# GR61036-1) TN4, Pax6 shRNA, H3K4me1 ChIP Input control Input control none TN4, Pax6 shRNA, input Histone H3K4me3 H3K4me3 (Abcam, ab8580, lot# GR152121-1) TN4, control shRNA, H3K4me3 ChIP Histone H3K4me2 H3K4me2 (Abcam, ab7766, lot# GR160184-1) TN4, control shRNA, H3K4me2 ChIP Histone H3K4me1 H3K4me1 (Abcam, ab8895, lot# GR61036-1) TN4, control shRNA, H3K4me1 ChIP Others Pax6 Pax6 (Millipore, AB2237, lot# 2506390) TN4, control shRNA, Pol2 ChIP RNA polymerase RNA polymerase II RNA polymerase II (Abcam, ab817, lot# GR153063-402) TN4, control shRNA, Pax6 ChIP Input control Input control none TN4, control shRNA, input Others Nipbl Nipbl (Sanova A301-779A) mouse embryonic fibroblasts (E13.5d) Input control Input control none Tumor (glioma) Histone H3K27me3 polyclonal rabbit trimethyl H3K27 Millipore, 07449 neural stem cells RNA polymerase RNA polymerase II polyclonal rabbit RNAPII Phospho S2 ChIP grade Abcam, ab5095 neural stem cells Others Kdm6b affinity purified antibody against mouse JMJD3 Dr. K. Helin neural stem cells RNA polymerase RNA polymerase II RNA Pol II (8WG16) Covance MMS-126R Embryonic stem cells Others Stag2 SA2 Bethyl A300-158A-1 Embryonic stem cells Others Stag1 SA1 Bethyl A300-157A-1 Embryonic stem cells Others Brd4 Brd4 Bethyl A301-985A Embryonic stem cells Others Epitope tags FLAG M2 antibody (Sigma, F1804) Primary osteoblasts Input control Input control None Input data from HA-Ikaros transduced B3 cells Others Ell3 A fragment of human ELL3 (aa 1-248) was expressed as His-tag fusion protein in pET-16b, purified on NTA-agarose according to Qiagens protocol and sent to Pocono Rabbit Farm and Labs for immunization into rabbits. murine embryonic stem cells Histone H3K4me1 H3K4me1 (Abcam ab8895) Pro-B Others Ctcf bone marrow_day7_CTCF Input control Input control none (input) HPC7 Unclassified Unclassified STHdhQ111/Q111 striatal cells Unclassified Unclassified STHdhQ7/Q7 striatal cells Input control Input control Rabbit IgG (Abcam, ab171870) C2C12 cell line Histone H3K27me3 anti-trimethyl-histone H3 (Lys27) (Cat# 07-449, Lot# 2607758) C2C12 cell line Histone H4K16ac anti-H4K16ac (Active Motif, 39167, lot 33311003) cultured NUP98-HOXA9 transformed mouse bone marrow LSK cells Histone H3K4me3 anti-H3K4me3 (abcam, ab8580, lot GR224370-2) cultured NUP98-HOXA9 transformed mouse bone marrow LSK cells Others Kmt2a anti-MLL1 (BETHYL, A300-086A, lot 4) cultured NUP98-HOXA9 transformed mouse bone marrow LSK cells Input control Input control sigmal Aldrich-i5006 3T3-L1 cells Histone H3K27ac H3K27ac (Abcam,ab4729, lot GA104852-2) Placenta Histone H3K4me3 H3K4me3 (Millipore, 07-473, lot 2384705) Mammary gland (during lactation) Histone H3K4me3 H3K4me3 (Millipore, 07-473, lot 2384705) Tongue Histone H3K4me3 H3K4me3 (Millipore, 07-473, lot 2384705) Placenta Others Epitope tags FLAG (Sigma, A2220) and HA (Sigma, A2095) embryonic stem cells Input control Input control none E14 mouse embryonic stem cells Others Zic3 Zic3 E14 mouse embryonic stem cells Others Tead4 Abcam ab58310 Hemangioblast Others Tfe3 TFE3: Sigma, Catalog: HPA023881-100ul, Lot: E96562 RAW_LPS_ChIPSeq_activated_macrophage Others Tfe3 TFE3: Sigma, Catalog: HPA023881-100ul, Lot: E96562 RAW_Starvation_ChIPSeq_activated_macrophage Others Tfe3 TFE3: Sigma, Catalog: HPA023881-100ul, Lot: E96562 RAW_Control_ChIPSeq_macrophage Input control Input control Rabbit IgG (Santa Cruz, Catalog# sc-806, Lot# F0908) RAW_Background Control_ChIPSeq_macrophage Others Isl1 anti-Isl1/2 (gift from Dr. T. Jessell) Isl1 induced cells (Day4 iI differentiation) Others Isl1 anti-Isl1/2 (gift from Dr. T. Jessell) induced cortical motor neurons (Day4 iNIP differentiation) Others Epitope tags anti-V5 (Abcam, ab15828) induced cortical motor neurons (Day4 iNIP differentiation) Input control Input control Rabbit IgG (Santa Cruz, Catalog# sc-806, Lot# F0908) MEF Unclassified Unclassified alveaolar macrophages Unclassified Unclassified Maf-DKO macrophages Others Mafb MafB (Bethyl IHC-101) bone marrow derived macrophages Others Epitope tags Flag M2 antibody (Sigma) Maf-DKO+MafB macrophages Others Spi1 PU.1 (Santa Cruz Biotechnology, sc-352) alveaolar macrophages Others Spi1 PU.1 (Santa Cruz Biotechnology, sc-352) bone marrow derived macrophages Others Spi1 PU.1 (Santa Cruz Biotechnology, sc-352) Maf-DKO macrophages Others Ep300 P300 (Santa Cruz Biotechnology, sc-585) Maf-DKO+MafB macrophages Others Ep300 P300 (Santa Cruz Biotechnology, sc-585) alveaolar macrophages Others Ep300 P300 (Santa Cruz Biotechnology, sc-585) bone marrow derived macrophages Others Ep300 P300 (Santa Cruz Biotechnology, sc-585) Maf-DKO macrophages Histone H3K27ac H3K27ac (Abcam, ab4729) Maf-DKO+MafB macrophages Histone H3K27ac H3K27ac (Abcam, ab4729) bone marrow derived macrophages Histone H3K27ac H3K27ac (Abcam, ab4729) Maf-DKO macrophages Histone H3K4me3 H3K4m3 (Abcam ab8580) bone marrow derived macrophages Histone H3K4me3 H3K4m3 (Abcam ab8580) Maf-DKO macrophages Histone H3K4me1 H3K4me1 (Abcam, ab8895) bone marrow derived macrophages Histone H3K4me1 H3K4me1 (Abcam, ab8895) Maf-DKO macrophages Input control Input control none Mouse V19-OSKM Aberrant iPS cells, Utx-/Y, Clone #2 Histone H3K27me3 H3K27me3; ChIP grade, 07-449, Millipore Mouse V19-OSKM Aberrant iPS cells, Utx-/Y, Clone #2 Histone H3K4me3 H3K4me3; ChIP grade, ab8580, abcam Mouse V19-OSKM Aberrant iPS cells, Utx-/Y, Clone #2 Input control Input control none Mouse V19-OSKM Aberrant iPS cells, Utx-/Y, Clone #1 Histone H3K27me3 H3K27me3; ChIP grade, 07-449, Millipore Mouse V19-OSKM Aberrant iPS cells, Utx-/Y, Clone #1 Histone H3K4me3 H3K4me3; ChIP grade, ab8580, abcam Mouse V19-OSKM Aberrant iPS cells, Utx-/Y, Clone #1 Input control Input control none Mouse V6.5 ESCs, Utx-/Y Histone H3K4me3 H3K4me3; ChIP grade, ab8580, abcam Mouse V6.5 ESCs, Utx-/Y Histone H3K27me3 H3K27me3; ChIP grade, 07-449, Millipore Mouse V6.5 ESCs, Utx-/Y Input control Input control none Mouse V6.5 ESCs Others Kdm6a UTX Ab-UTX 5/1, PID 17178841 Mouse V6.5 ESCs Histone H3K4me3 H3K4me3; ChIP grade, ab8580, abcam Mouse V6.5 ESCs Histone H3K27me3 H3K27me3; ChIP grade, 07-449, Millipore Mouse V6.5 ESCs Others Six1 10709-1-AP C3H10T1/2 cells Others Aff4 Bethyl Laboratories (A302-539A) In vitro differentiated Th1 cells, T-bet-/- Others Aff4 Bethyl Laboratories (A302-539A) In vitro differentiated Th1 cells, wild-type Others Med1 Bethyl Laboratories (A300-793A) In vitro differentiated Th1 cells, T-bet-/- Others Med1 Bethyl Laboratories (A300-793A) In vitro differentiated Th1 cells, wild-type Others Brd4 Bethyl Laboratories (A301-985A100) In vitro differentiated Th1 cells, T-bet-/- Others Brd4 Bethyl Laboratories (A301-985A100) In vitro differentiated Th1 cells, wild-type Others Rela Santa Cruz C-20 (sc-372) In vitro differentiated Th1 cells, T-bet-/- Others Rela Santa Cruz C-20 (sc-372) In vitro differentiated Th1 cells, wild-type Others Aff4 Bethyl Laboratories (A302-539A) EL4-T-bet cell line, stimulated Others Aff4 Bethyl Laboratories (A302-539A) EL4-GFP cell line, stimulated Others Med1 Bethyl Laboratories (A300-793A) EL4-T-bet cell line, stimulated Others Med1 Bethyl Laboratories (A300-793A) EL4-GFP cell line, stimulated Others Brd4 Bethyl Laboratories (A301-985A100) EL4-GFP cell line, stimulated Others Brd4 Bethyl Laboratories (A301-985A100) EL4-T-bet cell line, stimulated Others Rela Santa Cruz C-20 (sc-372) EL4-T-bet cell line, stimulated Others Rela Santa Cruz C-20 (sc-372) EL4-GFP cell line, stimulated Others Epitope tags Sigma M2 EL4-Gata3 GFP cell line, stimulated Others Epitope tags Sigma M2 EL4-T-bet mPlum cell line, stimulated Histone H3K4me3 Abcam ab8580 In vitro differentiated Th1 cells, T-bet-/- Input control Input control Abcam ab46540 In vitro differentiated Th1 cells, T-bet-/- Histone H3K4me3 Abcam ab8580 In vitro differentiated Th1 cells, wild-type Input control Input control Abcam ab46540 In vitro differentiated Th1 cells, wild-type Input control Input control none lateral telencephalon Others Nr3c1 GR (sc-1004) from SantaCruz AtT-20 corticotroph cells treated with GR (Dex) Others Nr3c1 GR (sc-1004) from SantaCruz AtT-20 corticotroph cells treated with GR (Dex+LIF) Others Stat1 p-STAT3 (sc-7993) and STAT3 (sc-482x) from SantaCruz AtT-20 corticotroph cells treated with Stat3 (Dex+LIF) Others Stat1 p-STAT3 (sc-7993) and STAT3 (sc-482x) from SantaCruz AtT-20 corticotroph cells treated with Stat3 (LIF) Input control Input control rabbit IgG (G2018, Sigma) AtT-20 corticotroph cells treated with Control IgG Histone H3K9me2 H3K9me2 Jmjd1c -/-MLL-AF9-GFP SSC Mouse bone marrow cells Histone H3K9me2 H3K9me2 Jmjd1c primary leukemia cells Mouse bone marrow cells Input control Input control None Input DNA for GFP sample Input control Input control None Input DNA for Cre sample Histone H3K27ac Anti-H3K27Ac K27ac CHiP for wild-type GFP sample Histone H3K27ac Anti-H3K27Ac K27ac CHiP for hdac3-knockout Cre sample Input control Input control none Mouse embryonic fibroblasts, input Input control Input control ChIP-Seq with no antibody in mouse M&M MEF cells transduced with Myf5 Input control Input control ChIP-Seq with no antibody in mouse M&M MEF cells transduced with MyoD Input control Input control ChIP-Seq with no antibody in mouse M&M MEF cells transduced with GFP Others Myf5 ChIP-Seq with Myf5 antibody Sc-302x (lot CO612) in mouse M&M MEF cells transduced with GFP Others Myod1 ChIP-Seq with MyoD antibody 6975 in mouse M&M MEF cells transduced with GFP Histone H4ac ChIP-Seq with H4Ac antibody 39925 in mouse M&M MEF cells transduced with Myf5 Histone H4ac ChIP-Seq with H4Ac antibody 39925 in mouse M&M MEF cells transduced with MyoD Histone H4ac ChIP-Seq with H4Ac antibody 39925 in mouse M&M MEF cells transduced with GFP Others Myf5 ChIP-Seq with Myf5 antibody Sc-302x (lot CO612) in mouse M&M MEF cells transduced with Myf5 Others Myod1 ChIP-Seq with MyoD antibody 6975 in mouse M&M MEF cells transduced with MyoD RNA polymerase RNA polymerase II Pol2-4H8 ab5408 This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target: POL24H8 G1E-ER4 RNA polymerase RNA polymerase II Pol2-4H8 ab5408 This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target: POL24H8 G1E Others Gata2 GATA2_(SC-9008) sc-9008 The GATA family of transcription factors share a conserved zinc finger DNA-binding domain and are capable of binding the WGATAR consensus sequence. GATA1 is erythroid-specific and is essential for normal erythropeisis. By comparison, GATA2 is expressed at high levels in hematopoeitic progenitors, including early erythroid cells, but is strong repressed during erythroblast differentiaion. Rabbit polyclonal antibody raised against amino acids 120-235 of GATA-2 of human origin. Antibody Target: GATA2 G1E-ER4 Others Gata2 GATA2_(SC-9008) sc-9008 The GATA family of transcription factors share a conserved zinc finger DNA-binding domain and are capable of binding the WGATAR consensus sequence. GATA1 is erythroid-specific and is essential for normal erythropeisis. By comparison, GATA2 is expressed at high levels in hematopoeitic progenitors, including early erythroid cells, but is strong repressed during erythroblast differentiaion. Rabbit polyclonal antibody raised against amino acids 120-235 of GATA-2 of human origin. Antibody Target: GATA2 G1E Others Gata1 GATA1_(SC-265) sc-265 GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. rat monoclonal antibody raised against mouse recombinant GATA1; recommended for detection of GATA1 of mouse, rat and human origin. Antibody Target: GATA1 Megakaryo Others Pax5 PAX5_(N-15) ab12000 The PAX5 gene is a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA binding motif, known as the paired box. The PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. The PAX5 gene encodes the B cell lineage specific activator protein (BSAP) that is expressed at early, but not late stages of B cell differentiation. rabbit polyclonal antibody; epitope is a synthetic peptide: MDLEKNYPTPRTSRT, corresponding to amino acids 1-15 of Human PAX5, cross-reacts with human and mouse PAX5. Antibody Target: PAX5 CH12 Others Tal1 TAL1_(SC-12984) sc-12984 TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis. goat polyclonal antibody; epitope mapping at the C-terminus of TAL1 of human origin, recommended for detection of TAL1 of mouse, rat and human origin. Antibody Target: TAL1 Erythrobl Others Gata1 GATA1_(SC-265) sc-265 GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. rat monoclonal antibody raised against mouse recombinant GATA1; recommended for detection of GATA1 of mouse, rat and human origin. Antibody Target: GATA1 G1E Others Tal1 TAL1_(SC-12984) sc-12984 TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis. goat polyclonal antibody; epitope mapping at the C-terminus of TAL1 of human origin, recommended for detection of TAL1 of mouse, rat and human origin. Antibody Target: TAL1 G1E Others Tal1 TAL1_(SC-12984) sc-12984 TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis. goat polyclonal antibody; epitope mapping at the C-terminus of TAL1 of human origin, recommended for detection of TAL1 of mouse, rat and human origin. Antibody Target: TAL1 MEL RNA polymerase RNA polymerase II Pol2-4H8 ab5408 This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes Mouse monoclonal to RNA polymerase II CTD repeat YSPTSPS antibody (4H8) - ChIP Grade. Antibody Target: POL24H8 MEL Others Tal1 TAL1_(SC-12984) sc-12984 TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis. goat polyclonal antibody; epitope mapping at the C-terminus of TAL1 of human origin, recommended for detection of TAL1 of mouse, rat and human origin. Antibody Target: TAL1 G1E-ER4 Others Gata1 GATA1_(SC-265) sc-265 GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. rat monoclonal antibody raised against mouse recombinant GATA1; recommended for detection of GATA1 of mouse, rat and human origin. Antibody Target: GATA1 Erythrobl Others Ctcf CTCF 07-729 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. rabbit polyclonal. Antibody Target: CTCF G1E-ER4 Others Ctcf CTCF 07-729 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. rabbit polyclonal. Antibody Target: CTCF G1E Others Ctcf CTCF 07-729 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. rabbit polyclonal. Antibody Target: CTCF CH12 Input control Input control rabbit immunoglobulin G (IgG) Fetal liver Others Hnrnpu anti-hnRNP U(Abcam) Fetal liver Input control Input control None Input_mESCs Histone H1t anti-H1T (rabbit polyclonal antibody, prepared in-house) H1T_mESCs_ChIP Histone H3K4me1 H3K4me1 (1:1 mixture of ab8895, abcam and 07-436, EMD Millipore) Splenic B cell Input control Input control n/a B6 Input DNA Histone H2A.XS139ph Upstate. Anti-phospho-Histone H2A.X (Ser139) Antibody, clone JBW301 B6 Anti-gH2AX_ChIP-seq Input control Input control n/a Cg Input DNA Input control Input control n/a 1Rb_M Input DNA RNA polymerase RNA polymerase II Pol2 MMS-126R RNA Polymerase II mouse monoclonal, clone 8WG16. Antibody Target: POL2 MEF RNA polymerase RNA polymerase II Pol2 MMS-126R RNA Polymerase II mouse monoclonal, clone 8WG16. Antibody Target: POL2 BoneMarrow Others Ctcf CTCF 07-729 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. rabbit polyclonal. Antibody Target: CTCF Cerebellum RNA polymerase RNA polymerase II Pol2 MMS-126R RNA Polymerase II mouse monoclonal, clone 8WG16. Antibody Target: POL2 Kidney Others Ctcf CTCF 07-729 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. rabbit polyclonal. Antibody Target: CTCF BoneMarrow Others Ctcf CTCF 07-729 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. rabbit polyclonal. Antibody Target: CTCF Heart Others Ep300 p300 sc-585 EP300(c-20) Rabbit Polyclonal. Antibody Target: P300 ES-Bruce4 RNA polymerase RNA polymerase II Pol2 MMS-126R RNA Polymerase II mouse monoclonal, clone 8WG16. Antibody Target: POL2 ES-Bruce4 Others Ctcf CTCF 07-729 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. rabbit polyclonal. Antibody Target: CTCF ES-Bruce4 Others Ep300 p300 sc-585 EP300(c-20) Rabbit Polyclonal. Antibody Target: P300 Heart RNA polymerase RNA polymerase II Pol2 MMS-126R RNA Polymerase II mouse monoclonal, clone 8WG16. Antibody Target: POL2 Spleen Others Ctcf CTCF 07-729 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. rabbit polyclonal. Antibody Target: CTCF Spleen Others Ctcf CTCF 07-729 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. rabbit polyclonal. Antibody Target: CTCF MEF RNA polymerase RNA polymerase II Pol2 MMS-126R RNA Polymerase II mouse monoclonal, clone 8WG16. Antibody Target: POL2 Thymus Others Ctcf CTCF 07-729 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. rabbit polyclonal. Antibody Target: CTCF Limb RNA polymerase RNA polymerase II Pol2 MMS-126R RNA Polymerase II mouse monoclonal, clone 8WG16. Antibody Target: POL2 Liver Others Ctcf CTCF 07-729 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. rabbit polyclonal. Antibody Target: CTCF OlfactBulb RNA polymerase RNA polymerase II Pol2 MMS-126R RNA Polymerase II mouse monoclonal, clone 8WG16. Antibody Target: POL2 OlfactBulb Others Ctcf CTCF 07-729 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. rabbit polyclonal. Antibody Target: CTCF Thymus Others Ctcf CTCF 07-729 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. rabbit polyclonal. Antibody Target: CTCF Kidney Others Ctcf CTCF 07-729 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. rabbit polyclonal. Antibody Target: CTCF WholeBrain RNA polymerase RNA polymerase II Pol2 MMS-126R RNA Polymerase II mouse monoclonal, clone 8WG16. Antibody Target: POL2 Cortex Others Ctcf CTCF 07-729 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. rabbit polyclonal. Antibody Target: CTCF Cortex Others Ctcf CTCF 07-729 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. rabbit polyclonal. Antibody Target: CTCF BMDM RNA polymerase RNA polymerase II Pol2 MMS-126R RNA Polymerase II mouse monoclonal, clone 8WG16. Antibody Target: POL2 Cerebellum RNA polymerase RNA polymerase II Pol2 MMS-126R RNA Polymerase II mouse monoclonal, clone 8WG16. Antibody Target: POL2 Lung RNA polymerase RNA polymerase II Pol2 MMS-126R RNA Polymerase II mouse monoclonal, clone 8WG16. Antibody Target: POL2 Heart Others Ctcf CTCF 07-729 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. rabbit polyclonal. Antibody Target: CTCF Lung RNA polymerase RNA polymerase II Pol2 MMS-126R RNA Polymerase II mouse monoclonal, clone 8WG16. Antibody Target: POL2 BMDM Others Ctcf CTCF 07-729 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. rabbit polyclonal. Antibody Target: CTCF Liver Others Ctcf CTCF 07-729 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. rabbit polyclonal. Antibody Target: CTCF Testis RNA polymerase RNA polymerase II Pol2 MMS-126R RNA Polymerase II mouse monoclonal, clone 8WG16. Antibody Target: POL2 SmIntestine Others Ctcf CTCF 07-729 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. rabbit polyclonal. Antibody Target: CTCF SmIntestine RNA polymerase RNA polymerase II Pol2 MMS-126R RNA Polymerase II mouse monoclonal, clone 8WG16. Antibody Target: POL2 Limb RNA polymerase RNA polymerase II Pol2 MMS-126R RNA Polymerase II mouse monoclonal, clone 8WG16. Antibody Target: POL2 WholeBrain RNA polymerase RNA polymerase II Pol2 MMS-126R RNA Polymerase II mouse monoclonal, clone 8WG16. Antibody Target: POL2 Testis Others Atf4 ATF4 (Santa Cruz; C-20) Mouse embryonic fibroblasts Others Cebpg CEBPG C-terminal antiserum (our lab) Mouse embryonic fibroblasts Others GFP GFP (Santa Cruz; FL) Mouse embryonic fibroblasts Histone H3K4me2 H3K4me2_(ab32356) ab32356 Histone H3 (di methyl K4). Marks promoters and enhancers. Rabbit polyclonal. Antibody Target: H3K4me2 C2C12 Histone H3K79me3 H3K79me3_(ab2621) ab2621 Associated with the gene body of actively transcribed genes Rabbit polyclonal. Antibody Target: H3K79me3 C2C12 Others Rcor2 Rcor2 embryonic brain Input control Input control none embryonic brain Input control Input control rabbit IgG Sigma I5006 embryoid bodies Others Gata1 rabbit anti-Gata1, Abcam ab11963, lot I0303 embryoid bodies Input control Input control none, DNA input control Whole Intestine Others Jun cJUN Polyclonal Rabbit antibody (Santa Cruz sc-44) Whole Intestine Input control Input control none trophoblast stem cells Input control Input control Purified IgG1 k isotype control (BD Biosciences, Cat. No. 554121, Lot #70274) trophoblast stem cells Others Tead4 TEAD4 (Abcam, Cat. No. ab58310, Lot #GR33778-1) trophoblast stem cells Histone H3K4me2 H3K4me2 Mesenchymal cell Input control Input control None BCR-ABL1 transformed p19 null preB-ALL Histone H3K27me3 H3K27me3 (ab6002, abcam) BCR-ABL1 transformed p19 null preB-ALL Histone H3K27ac H3K27ac (ab4729, abcam) BCR-ABL1 transformed p19 null preB-ALL Others Phf6 PHF6 (A301-451A, Bethyl) BCR-ABL1 transformed p19 null preB-ALL Others Ctcf CTCF 07-729 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. rabbit polyclonal. Antibody Target: CTCF C2C12 Others E2f4 E2F4 sc-866 mapping at the C-terminus of E2F4 of human origin rabbit polyclonal. Antibody Target: E2F4 C2C12 Others Fosl1 FOSL1_(sc-605) sc-605 The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) Rabbit polyclonal antibody raised against the N-terminus of FOSL1 of rat origin. Antibody Target: FOSL1 C2C12 Others Tcf12 TCF12 sc-357 The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. HEB (A-20) Rabbit polyclonal IgG, 200 ?g/ml. Epitope mapping within the C-terminus of HEB of human origin. Antibody Target: TCF12 C2C12 Others Tcf3 TCF3_(SC-349) sc-349 Heterodimers between TCF3 and tissue-specific basic helix-loop-helix (bHLH) proteins play major roles in determining tissue-specific cell fate during embryogenesis, like muscle or early B-cell differentiation. Dimers bind DNA on E-box motifs: 5'-CANNTG-3'. Binds to the kappa-E2 site in the kappa immunoglobulin gene enhancer. E2A.E12(V-18) is an affinity purified rabbit polyclonal antibody raised against a peptide mapping at the C-terminus of E2A.E12 of human origin. Recommended for detection of E12 and E47 of m, r and h origin by WB, IP, IF, IHC(P), ELISA and indirect FCM using PE (sc-3739)- or FITC (sc-2012)-conjugated goat anti-rabbit IgG. Antibody Target: TCF3 C2C12 RNA polymerase RNA polymerase II Pol2 MMS-126R RNA Polymerase II mouse monoclonal, clone 8WG16. Antibody Target: POL2 C2C12 Others Rest NRSF (Made by Protein Expression Center: peccaltech.edu) Neuron-restrictive silencer transcription factor Mouse monoclonal. Antibody Target: NRSF C2C12 Others Srf SRF sc-335 Serum response transcription factor Rabbit polyclonal. Antibody Target: SRF C2C12 RNA polymerase RNA polymerase II Pol2(phosphoS2) ab5095 RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. Rabbit polyclonal against peptide conjugated to KLH derived from within residues 1600 - 1700 of S. cerevisiae RNA polymerase II CTD repeat YSPTSPS, phosphorylated at S2. Antibody Target: POL2S2 C2C12 Input control Input control IgG E14 mouse embryonic stem cells Others Ncoa3 NcoA3 E14 mouse embryonic stem cells Input control Input control Santa Cruz SC-2025 Resting T cells, conconavalin A (conA) activation for 14hrs Unclassified Unclassified Clontech, 632460 Resting T cells, conconavalin A (conA) activation for 14hrs Input control Input control Santa Cruz SC-2025 Resting T cells, conconavalin A (conA) activation for 4hrs Unclassified Unclassified Clontech, 632460 Resting T cells, conconavalin A (conA) activation for 4hrs Others Sox2 Mouse SOX2 CCE-Rx cells Input control Input control Mouse IgG CCE-Rx cells Others Myc c-Myc sc-764 transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease rabbit polyclonal to amino acids 1-262 of c-Myc human origin. Antibody Target: c-Myc MEL Others Nelfe NELFe sc-32912 NELFe (RDBP) is a part of the negative elongation factor complex which binds to RNAPII to suppress elongation. NELFe (RDBP). Antibody Target: NELFe MEL RNA polymerase RNA polymerase II Pol2(phosphoS2) ab5095 RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. Rabbit polyclonal against peptide conjugated to KLH derived from within residues 1600 - 1700 of S. cerevisiae RNA polymerase II CTD repeat YSPTSPS, phosphorylated at S2. Antibody Target: POL2S2 CH12 Others Smc3 SMC3_(ab9263) ab9263 Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. Rabbit polyclonal raised against synthetic peptide representing a portion within the last 100 amino acids of the human Structural Maintenance of Chromosomes-3 conjugated to KLH. Antibody Target: SMC3 CH12 Others Chd2 CHD2_(AB68301) ab68301 CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. Rabbit polyclonal to CHD2 Synthetic peptide derived from within residues 1250 - 1350 of Human CHD2. Antibody Target: CHD2 MEL Others Mxi1 Mxi1_(AF4185) AF4185 Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CACGATG-3', antagonizes MYC transcriptional activity by competing for MAX Goat IgG. Raised against E. coli-derived rhMxi1. Antibody Target: Mxi1 MEL RNA polymerase RNA polymerase II Pol2(phosphoS2) ab5095 RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. Rabbit polyclonal against peptide conjugated to KLH derived from within residues 1600 - 1700 of S. cerevisiae RNA polymerase II CTD repeat YSPTSPS, phosphorylated at S2. Antibody Target: POL2S2 MEL Others Chd2 CHD2_(AB68301) ab68301 CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. Rabbit polyclonal to CHD2 Synthetic peptide derived from within residues 1250 - 1350 of Human CHD2. Antibody Target: CHD2 CH12 Others Mxi1 Mxi1_(AF4185) AF4185 Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CACGATG-3', antagonizes MYC transcriptional activity by competing for MAX Goat IgG. Raised against E. coli-derived rhMxi1. Antibody Target: Mxi1 CH12 Others Nelfe NELFe sc-32912 NELFe (RDBP) is a part of the negative elongation factor complex which binds to RNAPII to suppress elongation. NELFe (RDBP). Antibody Target: NELFe CH12 Others Smc3 SMC3_(ab9263) ab9263 Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. Rabbit polyclonal raised against synthetic peptide representing a portion within the last 100 amino acids of the human Structural Maintenance of Chromosomes-3 conjugated to KLH. Antibody Target: SMC3 MEL Others Bhlhe40 BHLHE40_(NB100-1800) NB100-1800 This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. Rabbit polyclonal, maps to a region between residues 350 and the C-terminus (residue 412). Antibody Target: BHLHE40 CH12 Others Ep300 p300 sc-585 EP300(c-20) Rabbit Polyclonal. Antibody Target: P300 MEL Others Ep300 p300_(SC-584) sc-584 Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein Rabbit polyclonal IgG, epitope mapping at the N-terminus of p300 of human origin. Antibody Target: P300 CH12 Others Max Max sc-197 The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). Rabbit polyclonal IgG, epitope mapping at the C-terminus of Max of human origin. Antibody Target: Max MEL Others Jund JunD sc-74 The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) rabbit polyclonal IgG. Antibody Target: JunD MEL Others E2f4 E2F4 sc-866 mapping at the C-terminus of E2F4 of human origin rabbit polyclonal. Antibody Target: E2F4 MEL Others Tbp TBP ab62126 General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. Mouse monoclonal. Immunogen is synthetic peptide conjugated to KLH derived from within residues 1 - 100 of HumanTATA binding protein TBP. Antibody Target: TBP MEL Others E2f4 E2F4 sc-866 mapping at the C-terminus of E2F4 of human origin rabbit polyclonal. Antibody Target: E2F4 CH12 Others Rad21 Rad21 ab992 Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 Rabbit polyclonal. Antibody Target: RAD21 CH12 Others Usf2 USF2 ab60931 Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). Mouse monoclonal. Immunogen corresponds to amino acids 1-101 of Human USF2. Antibody Target: USF2 CH12 Others Ctcf CTCF_(SC-15914) sc-15914 Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. Goat polyclonal, epitope mapping near the C-terminus of CTCF of human origin. Antibody Target: CTCF CH12 Others Max Max sc-197 The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). Rabbit polyclonal IgG, epitope mapping at the C-terminus of Max of human origin. Antibody Target: Max CH12 Others Myc c-Myc sc-764 transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease rabbit polyclonal to amino acids 1-262 of c-Myc human origin. Antibody Target: c-Myc CH12 Others Myb c-Myb_(SC-7874) sc-7874 Transcriptional activator; DNA-binding protein that specifically recognize the sequence 5'-YAACGTG-3'. Plays an important role in the control of proliferation and differentiation of hematopoietic progenitor cells. Rabbit polyclonal IgG, Epitope corresponding to amino acids 500-640 mapping at the C-terminus of c-Myb of human origin. Antibody Target: c-Myb MEL Others Jund JunD sc-74 The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) rabbit polyclonal IgG. Antibody Target: JunD CH12 Others Jun c-Jun sc-1694 Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. Rabbit polyclonal to amino acids 1-79 mapping at the N-terminus of c-Jun p39 of human origin. Antibody Target: c-Jun CH12 Others Tbp TBP ab62126 General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. Mouse monoclonal. Immunogen is synthetic peptide conjugated to KLH derived from within residues 1 - 100 of HumanTATA binding protein TBP. Antibody Target: TBP CH12 Others Mafk MafK_(ab50322) ab50322 NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. Rabbit polyclonal. Raised against synthetic peptide: TTNPKPNKALKVKKEA conjugated to KLH by a C-terminal Cysteine residue linker, corresponding to amino acids 2-17 of Human MAFK. Antibody Target: MafK CH12 Others Ep300 p300_(SC-584) sc-584 Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein Rabbit polyclonal IgG, epitope mapping at the N-terminus of p300 of human origin. Antibody Target: P300 MEL RNA polymerase RNA polymerase II Pol2 MMS-126R RNA Polymerase II mouse monoclonal, clone 8WG16. Antibody Target: POL2 CH12 Others GFP anti-GFP goat polyclonal C2C12_GFP, GFP ChIP Others GFP anti-GFP goat polyclonal C2C12_NICDGFP, GFP ChIP Others Rbpj anti-RBP-J 1F1 rat monoclonal C2C12_GFP, RBP-J 1F1 ChIP Others Rbpj anti-RBP-J 1F1 rat monoclonal C2C12_NICDGFP, RBP-J 1F1 ChIP Others Ep300 anti-p300 rabbit polyclonal C2C12, DAPT 24h, p300 ChIP Others Ep300 anti-p300 rabbit polyclonal C2C12, Delta 24h, p300 ChIP Others Ep300 anti-p300 rabbit polyclonal C2C12, DAPT 6h, p300 ChIP Others Ep300 anti-p300 rabbit polyclonal C2C12, Delta 6h, p300 ChIP Others Rbpj anti-RBP-J rabbit polyclonal C2C12, DAPT 6h, RBP-J ChIP Others Rbpj anti-RBP-J rabbit polyclonal C2C12, Delta 6h, RBP-J ChIP Input control Input control none C2C12, Delta 6h, ChIP input Input control Input control none Mouse embryonic day 11.5 (e11.5) neural tube, control Others Epitope tags anti-FLAG Sigma- F1804 1mg/ml -Monoclonal ANTI-FLAG M2 antibody produced in mouse. Lot #: 088K6018 Mouse embryonic day 11.5 (e11.5) neural tube, FLAG-ChIP Input control Input control none Mouse embryonic day 11.5 (e11.5) limb, control Others Epitope tags anti-FLAG Sigma- F1804 1mg/ml -Monoclonal ANTI-FLAG M2 antibody produced in mouse. Lot #: 088K6018 Mouse embryonic day 11.5 (e11.5) limb, FLAG-ChIP Input control Input control none Mouse embryonic day 11.5 (e11.5) forebrain, control Others Epitope tags anti-FLAG Sigma- F1804 1mg/ml -Monoclonal ANTI-FLAG M2 antibody produced in mouse. Lot #: 088K6018 Mouse embryonic day 11.5 (e11.5) forebrain, FLAG-ChIP Others Epitope tags anti-FLAG Sigma- F1804 1mg/ml -Monoclonal ANTI-FLAG M2 antibody produced in mouse. Lot #: 088K6018 Mouse embryonic day 11.5 (e11.5) face, FLAG-ChIP Others Tet2 MEL-FLAG-Tet2 cells Histone H3K4me1 H3K4me1 abcam 8895 neural progenitor cells Input control Input control None Differentiated trophoblast stem cells Histone H2AS40GlcNAc S40Gc specific antibody 20B2 (mouse monoclonal antibody, made in-house) Differentiated trophoblast stem cells Histone H2AS40GlcNAc S40Gc specific antibody 20B2 (mouse monoclonal antibody, made in-house) Trophoblast stem cells Input control Input control none neural progenitor cells Others Pcgf2 Pcgf2 sc-10744x Santa Cruz neural progenitor cells Others Rnf2 Ring1b D22F2 Cell Signaling neural progenitor cells Others Ezh2 Ezh2 Diagenode pAB-039-050 neural progenitor cells Others Suz12 Suz12 Abcam ab12073 neural progenitor cells Others Pcgf2 Pcgf2 sc-10744x Santa Cruz mouse embryonic stem cells Others Rnf2 Ring1b D22F2 Cell Signaling mouse embryonic stem cells Others Ezh2 Ezh2 Diagenode pAB-039-050 mouse embryonic stem cells Others Suz12 Suz12 Abcam ab12073 mouse embryonic stem cells Others Smarca4 BRG1-FLAG retina_BRG1_P0 Input control Input control Rabbit IgG (Cat. 2729, Cell Signaling) Dendritic cells Unclassified Unclassified D10.G4.1 Th2 cell line Histone H3K9me3 H3K9me3 (Diagenode, pAb-056-050) B cell enriched splenocytes from KAP1 KO mouse Histone H3K9me3 H3K9me3 (Diagenode, pAb-056-050) B cell enriched splenocytes Others Trim28 RBCC (Schultz et al. Genes Dev. 2001) B cell enriched splenocytes from KAP1 KO mouse Others Trim28 RBCC (Schultz et al. Genes Dev. 2001) B cell enriched splenocytes Input control Input control none (input) Sensitive line Input control Input control none (input) Resistant line Others Yy1 YY1 (Santa Cruz) C2C12 myoblasts Others Ets1 Santa Cruz (sc-350x) P5424 thymic cell line Others E2f1 E2F1 c20 ( santa cruz sc193) primary culture of hepatocytes Input control Input control none (input) primary culture of hepatocytes Histone H3K4me3 H3K4me3 EpiSC/MM401-H3K4me3-ChIP-seq Histone H3K4me1 H3K4me1 EpiSC/MM401-H3K4me1-ChIP-seq Others Kmt2a MLL1 EpiSC/MM401-MLL1-ChIP-seq Input control Input control input EpiSC/MM401-input Others Kmt2a MLL1 EpiSC-MLL1-ChIP-Seq Input control Input control input EpiSC-input Others Arntl anti-BMAL1 (Abcam; #ab3350-200; lot 805009) Liver Others Clock anti-CLK (Novus Biological; #NB100-126; lot B1) Liver Input control Input control NA mouse embryonic kidney Histone H3K27me3 H3K27me3 antibody (Abcam, ab6002) Cited1 expressing cells from mouse embryonic kidney Histone H3K27ac H3K27ac antibody (Abcam, ab4729) mouse embryonic kidney Others Six2 Six2 antibody (Proteintech,11562-1-AP) mouse embryonic kidney Input control Input control control_E13.5_cortex_input Input control Input control dcKO_E13.5_cortex_input Input control Input control control_P1_cortex_input Input control Input control dcKO_P1_cortex_input Others Men1 Menin (Bethyl, catalog# A300-105A, lot# A300-105A-1) Five-day cultured Th2 cells generated from primary splenic CD4_T cells were treated with trichostatin A (TSA) Others Ezh2 Ezh2 (Diagenode, catalog# pAb-039-050, lot# 001) Five-day cultured Th2 cells generated from primary splenic CD4_T cells were treated with trichostatin A (TSA) Input control Input control none Five-day cultured Th2 cells generated from primary splenic CD4_T cells were treated with trichostatin A (TSA) Others Ezh2 Ezh2 (Diagenode, catalog# pAb-039-050, lot# 001) Five-day cultured Th2 cells generated from primary splenic CD4_T cells Others Bmi1 Bmi1 (Santa Cruz, catalog# sc-10745, lot# K1008) B6N-22 ES cells RNA polymerase RNA polymerase II RNA polymerase II (Abcam, catalog# ab5408, lot# 646081) B6N-22 ES cells Input control Input control Mouse IgG1 Isotype Control Ab (Southern Biotech, catalog# 0102-01, lot# JC044-V877) B6N-22 ES cells RNA polymerase RNA polymerase II RNA polymerase II (Abcam, catalog# ab5408, lot# 646081) Primary CD4_T cells isolated from 6-8 week old mice (C57BL/6) Others Ezh2 Ezh2 (Diagenode, catalog# pAb-039-050, lot# 001) Primary B220_B cells isolated from 6-8 week old mice (C57BL/6) RNA polymerase RNA polymerase II RNA polymerase II (Abcam, catalog# ab5408, lot# 646081) Primary B220_B cells isolated from 6-8 week old mice (C57BL/6) Others Men1 Menin (Bethyl, catalog# A300-105A, lot# A300-105A-1) Two-week cultured Th2 cells generated from primary splenic CD4_T cells Others Bmi1 Bmi1 (Santa Cruz, catalog# sc-10745, lot# K1008) Two-week cultured Th2 cells generated from primary splenic CD4_T cells Input control Input control Mouse IgG1 Isotype Control Ab (Southern Biotech, catalog# 0102-01, lot# JC044-V877) Two-week cultured Th2 cells generated from primary splenic CD4_T cells Input control Input control none Two-week cultured Th2 cells generated from primary splenic CD4_T cells Others Bmi1 Bmi1 (Santa Cruz, catalog# sc-10745, lot# K1008) Five-day cultured Th2 cells generated from primary splenic CD4_T cells Input control Input control Mouse IgG1 Isotype Control Ab (Southern Biotech, catalog# 0102-01, lot# JC044-V877) Five-day cultured Th2 cells generated from primary splenic CD4_T cells Others Men1 Menin (Bethyl, catalog# A300-105A, lot# A300-105A-1) Five-day cultured Th1 cells generated from primary splenic CD4_T cells Others Bmi1 Bmi1 (Santa Cruz, catalog# sc-10745, lot# K1008) Five-day cultured Th1 cells generated from primary splenic CD4_T cells Input control Input control Mouse IgG1 Isotype Control Ab (Southern Biotech, catalog# 0102-01, lot# JC044-V877) Five-day cultured Th1 cells generated from primary splenic CD4_T cells Input control Input control none Five-day cultured Th1 cells generated from primary splenic CD4_T cells Others Bmi1 Bmi1 (Santa Cruz, catalog# sc-10745, lot# K1008) Primary CD4_T cells isolated from 6-8 week old mice (C57BL/6) Others Men1 Menin (Bethyl, catalog# A300-105A, lot# A300-105A-1) Primary B220_B cells isolated from 6-8 week old mice (C57BL/6) Others Bmi1 Bmi1 (Santa Cruz, catalog# sc-10745, lot# K1008) Primary B220_B cells isolated from 6-8 week old mice (C57BL/6) Input control Input control none (input) input for all P5 samples Input control Input control none (input) input for all P25 samples Input control Input control none (input) input for all P14 samples Histone H3K27me3 H3K27me3 (Millipore, 17-622) H3K27me3_Heto_P25 Histone H3K27me3 H3K27me3 (Millipore, 07-449) H3K27me3_CKO_luc_P25 Histone H3K27ac H3K27ac (Abcam, ab4729) H3K27ac_Heto_P25 Histone H3K27ac H3K27ac (Active Motif, 39133) H3K27ac_CKO_luc_P25 Others Smc3 Smc3 (Abcam; ab9263) primary T cells Others Smc1a Smc1 (Bethyl; A300-055A) primary T cells Others Nipbl Nipbl (Bethyl; A301-779A) primary T cells Others Kdm6b JMJD3 neural stem cells Others Smad3 Smad3 neural stem cells Others Epitope tags Wild type 3t3 pulled down with V5 antibody V5- Abcam (ab15828) In-vitro cell culture of NIH_3T3 cell Others Nkx3-2 V5 tagged Bapx1 over expressed in NIH_3T3 cells V5- Abcam (ab15828) In-vitro cell culture of NIH_3T3 cell Input control Input control IgG Embryonic day 12.5 vertebral column pulled down with IgG Others Sox9 Sox9 R&D system (AF3075) Embryonic day 12.5 vertebral column Others Epitope tags S-pepetide in wild type embryo S-Pepetide - Bethyl laboratories (A-190-134A) Embryonic day 12.5 vertebral column of wild type mice Others Nkx3-2 S-peptide tagged Bapx1 S-Pepetide - Bethyl laboratories (A-190-134A) Embryonic day 12.5 vertebral column Others Epitope tags FLAG (Sigma, F3165) Flag_ChIPSeq Others Cbx8 M2 Flag-agarose beads Bone marrow cells_flagCbx8_flagChIP Others Cbx7 M2 Flag-agarose beads Bone marrow cells_flagCbx7_flagChIP Others Epitope tags M2 Flag-agarose beads Bone marrow cells_empty vector_flagChIP Histone H3K4me3 H3K4me3 Bone Marrow_H3K4me3 Unclassified Unclassified O-GlcNAc Bone Marrow_OGlcNAc Others Tet2 Tet2 Bone Marrow_Tet2 Input control Input control None asynchrnous G1E-ER4+E2 cells Others Gata1 GATA1 (Santacruz,clone N6, sc-265) asynchrnous G1E-ER4+E2 cells Input control Input control None mitotic G1E-ER4+E2 cells Others Gata1 GATA1 (Santacruz,clone N6, sc-265) mitotic G1E-ER4+E2 cells Others Smarca4 Brg1 Lab Generated (Crabtree) J1 Chromatin IP against Brg1 Histone H3K4me3 H3K4me3 Abcam AB8550 Chromatin IP against H3K4me3 Histone H3K9ac H3K9Ac,K14Ac Upstate 06-599 Chromatin IP against H3K9,K14Ac Others Stag1 SA1 Bethyl A300-157A Chromatin IP against SA1 Others Stag2 SA2 Bethyl A300-158A Chromatin IP against SA2 Others Gata2 Gata2 (Santa Cruz, cat# sc9008x, lot# I0109) Lhx2, TGFb, 2h, Gata2 ChIP Others Ctnnb1 B-catenin Sensitive line Histone H3K27ac H3K27ac Sensitive line Others Brd4 BRD4 Sensitive line Histone H3K27ac H3K27ac Resistant line Others Brd4 BRD4 Resistant line Input control Input control Input (none) ESC shControl WITH LIF Input control Input control none (input) ESC shPhf5a WITH LIF Input control Input control none (input) ESC shControl WITH LIF RNA polymerase RNA polymerase II Ser-5-Phosphorylated RNA polymerase II: Abcam, ab5136 ESC shPhf5a WITH LIF RNA polymerase RNA polymerase II Ser-5-Phosphorylated RNA polymerase II: Abcam, ab5135 ESC shPhf5a WITH LIF RNA polymerase RNA polymerase II Ser-5-Phosphorylated RNA polymerase II: Abcam, ab5134 ESC shPhf5a WITH LIF RNA polymerase RNA polymerase II Ser-5-Phosphorylated RNA polymerase II: Abcam, ab5133 ESC shControl WITH LIF RNA polymerase RNA polymerase II Ser-5-Phosphorylated RNA polymerase II: Abcam, ab5132 ESC shControl WITH LIF RNA polymerase RNA polymerase II Ser-5-Phosphorylated RNA polymerase II: Abcam, ab5131 ESC shControl WITH LIF Input control Input control Input 3T3-L1 preadipocytes RNA polymerase RNA polymerase II PolII 3T3-L1 adipocytes Others Setdb1 SETDB1 3T3-L1 adipocytes Others 5-mC m5CpG 3T3-L1 adipocytes Histone H3K9me3 H3K9me3 3T3-L1 adipocytes Histone H3K4me3 H3K4me3 3T3-L1 adipocytes Others 5-mC m5CpG 3T3-L1 preadipocytes Input control Input control Input 10T1/2 MSCs Others Setdb1 SETDB1 10T1/2 MSCs Others 5-mC m5CpG 10T1/2 MSCs Histone H3K9me3 H3K9me3 10T1/2 MSCs Histone H3K27me3 H3K27me3 10T1/2 MSCs Histone H3K4me3 H3K4me3 10T1/2 MSCs Input control Input control Input TT2 ESCs Others Setdb1 SETDB1 TT2 ESCs Others 5-mC m5CpG TT2 ESCs Histone H3K9me3 H3K9me3 TT2 ESCs Histone H3K27me3 H3K27me3 TT2 ESCs Histone H3K4me3 H3K4me3 TT2 ESCs Others Nono Nono, Abcam, ab70335 Mouse embryonic stem cells Others Zfp42 Anti-V5 Agarose Affinity Gel antibody produced in mouse purified immunoglobulin, clone V5-10 V5-tagged REX1_ESCs Unclassified Unclassified WT_ESCs Others Pou5f1 anti-Flag antibody ZHBTc4 F-Oct4_alpha-Oct4-SWGA Input control Input control anti-Flag antibody ZHBTc4 F-Oct4_input_IgG_control Input control Input control none (input) p1 mouse rib chondrocytes Others Jun Jun(Abcam Cat#ab31419) p1 mouse rib chondrocytes Others Nr1d1 Rev-erb(alpha) Homogenized mouse liver, Rev-erb(alpha) KO, 5pm/ZT10, Rev-erb(alpha) ChIP Others Nr1d2 Rev-erb(beta) Homogenized mouse liver, WT, 5am/ZT22, Rev-erb(beta) ChIP Others Nr1d2 Rev-erb(beta) Homogenized mouse liver, WT, 5pm/ZT10, Rev-erb(beta) ChIP Histone H3K4me2 H3K4me2 HPC H3K4me2 ChIPseq Histone H3K4me2 H3K4me2 MEF H3K4me2 ChIPseq Histone H3K4me2 H3K4me2 ESC H3K4me2 ChIPseq Histone H3K4me3 H3K4me3 HPC H3K4me3 ChIPseq Histone H3K4me3 H3K4me3 MEF H3K4me3 ChIPseq Histone H3K4me3 H3K4me3 ESC H3K4me3 ChIPseq Histone H3K27me3 H3K27me3 HPC H3K27me3 ChIPseq Histone H3K27me3 H3K27me3 MEF H3K27me3 ChIPseq Histone H3K27me3 H3K27me3 ESC H3K27me3 ChIPseq Input control Input control MEF input DNA Input control Input control ESC input DNA Input control Input control none Hearts Others Sox9 SOX9 (Millipore, catalog# AB5535, lot# LV 1478872) Limb buds Others Sox9 SOX9 (Millipore, catalog# AB5535, lot# LV 1478872) Atrioventicular canals (AVC) of the heart Histone H3K4me1 H3K4me1 (Abcam) Islets Input control Input control None CD4 T cells Histone H3K9ac H3K9Ac CD4 T cells Histone H3K27ac H3K27Ac CD4 T cells Histone H3K27me3 H3K27Me3 CD4 T cells Histone H3K4me3 H3K4Me3 CD4 T cells Input control Input control Input Plasmacytoid dendritic cell (pDC) Input control Input control Input Classical dendritic cell (cDC) Input control Input control Input Common dendritic cell progenitor (CDP) Input control Input control Input Multipotent progenitor (MPP) Others Ctcf CTCF (Millipore; 07-729 DAM1772428) Neural progenitor cells Others Smc1a Smc1 (Bethyl; A300-055A) Neural progenitor cells Histone H4ac anti-H4Ac (anti-acetyl-histone H4) Unstimulated macrophages, Foxo3 knockout, H4Ac ChIP Histone H4ac anti-H4Ac (anti-acetyl-histone H4) Unstimulated macrophages, wildtype, H4Ac ChIP Others Foxo3 anti-Foxo3a (FKHRL1 (H-144)) Unstimulated macrophages, wildtype, Foxo3a ChIP Histone H3K36me2 H3K36me2 MLL-AF9/NrasG12D murine cell line Input control Input control none embryonic fibroblasts, input Input control Input control none (input) In vitro activated CD8+ Treg Histone H3K27me3 H3K27me3 (Millipore, 07-449) In vitro activated CD8+ Treg Histone H3K27ac H3K27ac (Abcam, ab4729) In vitro activated CD8+ Treg Others Ikzf2 Helios (Santa Cruz, G-20, sc-9866) In vitro activated CD8+ Treg Histone H3K27me3 H3K27me3 (Millipore, 07-449) In vitro activated CD4+ Treg Histone H3K27ac H3K27ac (Abcam, ab4729) In vitro activated CD4+ Treg Others Ikzf2 Helios (Santa Cruz, G-20, sc-9866) In vitro activated CD4+ Treg Histone H3K9me3 H3K9me3 mESC E14 under Activin A differentiation, day 6 Histone H3K4me3 H3K4me3 mESC E14 under Activin A differentiation, day 6 Histone H3K4me2 H3K4me2 mESC E14 under Activin A differentiation, day 6 Histone H3K4me1 H3K4me1 mESC E14 under Activin A differentiation, day 6 Histone H3K36me3 H3K36me3 mESC E14 under Activin A differentiation, day 6 Histone H3K27me3 H3K27me3 mESC E14 under Activin A differentiation, day 6 Histone H3K27ac H3K27ac mESC E14 under Activin A differentiation, day 6 Histone H2A.Z H2AZ mESC E14 under Activin A differentiation, day 6 Histone H3K9me3 H3K9me3 mESC E14 under Activin A differentiation, day 4 Histone H3K4me3 H3K4me3 mESC E14 under Activin A differentiation, day 4 Histone H3K4me2 H3K4me2 mESC E14 under Activin A differentiation, day 4 Histone H3K4me1 H3K4me1 mESC E14 under Activin A differentiation, day 4 Histone H3K36me3 H3K36me3 mESC E14 under Activin A differentiation, day 4 Histone H3K27me3 H3K27me3 mESC E14 under Activin A differentiation, day 4 Histone H3K27ac H3K27ac mESC E14 under Activin A differentiation, day 4 Histone H2A.Z H2AZ mESC E14 under Activin A differentiation, day 4 Histone H3K4me3 H3K4me3 mouse embryonic stem cells (E14) Histone H3K4me2 H3K4me2 mouse embryonic stem cells (E14) Histone H3K4me1 H3K4me1 mouse embryonic stem cells (E14) Histone H3K36me3 H3K36me3 mouse embryonic stem cells (E14) Histone H3K27ac H3K27ac mouse embryonic stem cells (E14) Histone H2A.Z H2AZ mouse embryonic stem cells (E14) Input control Input control IgG mouse embryonic stem cells (E14) Others Taf1 TAF1 mouse embryonic stem cells (E14) Input control Input control input Primary mouse OCP cells (Anet al. 2014 J Biol Chem 289: 24366-24373) Input control Input control none melan-a cells Input control Input control none (input) Mouse Embryonic Fibroblast(MEF)_wildtype_gluscose_starvation_input Input control Input control none (input) Mouse Embryonic Fibroblast(MEF)_wildtype_rich_nutrients_input Histone H3R17me2 H3R17me2 Mouse Embryonic Fibroblast(MEF)_wildtype_gluscose_starvation_ChIP Histone H3R17me2 H3R17me2 Mouse Embryonic Fibroblast(MEF)_wildtype_rich_nutrients_ChIP Input control Input control SCOS#2 Dox ON 72h_input Unclassified Unclassified SCOS#2 Dox ON 72h_ChIP Input control Input control none BV2 microglia cells Input control Input control none Mouse embryonic stem cell Histone H3K27ac H3K27ac( Abcam ab4729, lot 509313) Mouse embryonic stem cell Histone H2BK20ac H2BK20ac ( Abcam ab52988, lot 527003) Mouse embryonic stem cell Histone H2BK20ac H2BK20ac ( Abcam ab52988, lot 527003) E11.5 Mouse forebrain RNA polymerase RNA polymerase II PolII ( Abcam ab5131, lot 536530) E11.5 Mouse forebrain Histone H3K27me3 H3K27me3 ( Millipore 07-449, lot DAM1588246 ) E11.5 Mouse forebrain Histone H3K27ac H3K27ac( Abcam ab4729, lot 509313) E11.5 Mouse forebrain Histone H3K4me1 H3K4me1(Abcam:ab8895, lot 718019) E11.5 Mouse forebrain Histone H3K4me2 H3K4me2 (Abcam ab32356, lot 780430)) E11.5 Mouse forebrain RNA polymerase RNA polymerase II K7me2 19B4 ES cells RNA polymerase RNA polymerase II K7me1 3D3 ES cells Input control Input control None Neural progenitor cells Input control Input control IgG (Santa Cruz, SC-2027) Neural progenitor cells Input control Input control Control IgG (Millipore 12-370) Mouse embryonic stem cells Others Dnmt3b Dnmt3b (ab122932) Mouse embryonic stem cells Others Nkx3-1 anti-Nkx3.1 (Santa Cruz Biotechnology, sc-15022) Nkx3-1_KO_ChIP-Seq Others Chd4 anti-CHD4 (70469, Abcam) thymus Others Mta2 anti-Mta2 (ab8106, Abcam) thymus Histone H3K4me3 anti-H3K4me3 (ab8580, Abcam) thymus Input control Input control none ILC87 cell line derived from a thymic T cell tumor Histone H3K4me3 H3K4me3; abcam; lot# GR37544-1; catalog# ab8580 splenic B cells Histone H3K4me2 H3K4me2; millipore; lot# DAM1724042; catalog# 07-030 splenic B cells Input control Input control NA splenic B cells Others Ebf1 Ebf1 (custom-made against murine Ebf1b) splenic B cells Histone H3K27ac anti-H3K27ac embryonic hindlimb bud Input control Input control none embryonic hindlimb bud Histone H3K27ac anti-H3K27ac embryonic forelimb bud Input control Input control none embryonic forelimb bud Input control Input control IgG sc-2027, lot number C0411 3T3-L1 differentiated TNF Others Rela p65 abcam 7970, lot number GR51446-1 3T3-L1 differentiated TNF Unclassified Unclassified G1ME cells Others Rara anti-RAR murine embryonic stem cells grown as embryoid bodies for 4 days and treated 24 hours with 5 micromolar all trans retinoic acid Others Rara anti-RAR murine embryonic stem cells grown as embryoid bodies for 4 days and treated 2 hours with 5 micromolar all trans retinoic acid Input control Input control none Mammary RNA polymerase RNA polymerase II RNA Pol II (Abcam, Ab5408) Mammary Others Sox2 goat polyclonal Anti-Sox2 (AF2018, R&D); lot#: KOY0213101 OKSM reprogramming intermediates from Mouse Embryonic Fibroblasts Histone H3K4me3 Anti-H3K4me3 Millipore (#07-473) Anti-H3K4me3 Spo11-/-_testis_ChIP-Seq Histone H3K4me3 Anti-H3K4me3 Millipore (#07-473) Anti-H3K4me3 Prdm9-/-_liver_ChIP-Seq Histone H3K4me3 Anti-H3K4me3 Millipore (#07-473) Anti-H3K4me3 Prdm9-/-_testis_ChIP-Seq Histone H3K4me3 Anti-H3K4me3 Millipore (#07-473) Anti-H3K4me3 9R_testis_ChIP-Seq Histone H3K4me3 Anti-H3K4me3 Millipore (#07-473) Anti-H3K4me3 13R_testis_ChIP-Seq Input control Input control none Rbp2 f/f ES cells Histone H3K4me3 Anti-trimethyl-Histone H3 (Lys4) Rbp2 KO ES cells Histone H3K4me3 Anti-trimethyl-Histone H3 (Lys4) Rbp2 f/f ES cells Others Ppara PPARalpha C57BL/6 LXRdKO mouse liver Others Ppara PPARalpha C57BL/6 wild type mouse liver Input control Input control none, input DNA ES-cell derived erythroid progenitors Input control Input control none Cardiac progenitor cells, input Histone H3K9me3 H3K9me3 abcam (ab8898); lot# GR165657-6 OKSM reprogramming intermediates from Mouse Embryonic Fibroblasts Histone H3K9me3 H3K9me3 abcam (ab8898); lot# GR165657-5 OKSM reprogramming intermediates from Mouse Embryonic Fibroblasts Histone H3K9me3 H3K9me3 abcam (ab8898); lot# GR165657-4 OKSM reprogramming intermediates from Mouse Embryonic Fibroblasts Histone H3K9me3 H3K9me3 abcam (ab8898); lot# GR165657-3 OKSM reprogramming intermediates from Mouse Embryonic Fibroblasts Histone H3K9me3 H3K9me3 abcam (ab8898); lot# GR165657-2 OKSM reprogramming intermediates from Mouse Embryonic Fibroblasts Histone H3K9me3 H3K9me3 abcam (ab8898); lot# GR165657-1 OKSM reprogramming intermediates from Mouse Embryonic Fibroblasts Input control Input control mm9ES_Vezf1 ko_Input RNA polymerase RNA polymerase II Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody mm9ES_Vezf1_ko_RNA Polymerase 2 ChIP-Seq Input control Input control mm9ES_wt_Input DNA RNA polymerase RNA polymerase II Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody mm9ES_wt_RNA Polymerase 2 ChIP-Seq Histone H3K4me3 H3K4me3 Pro-B_H3K4me3 ChIP-seq Histone H3R2me2K4me3 H3R2me2sK4me3 Pro-B_H3R2me2sK4me3 ChIP-seq Histone H3R2me2 H3R2me2s Pro-B_H3R2me2s ChIP-seq Input control Input control Input for ChIP107.H3K4me3_siNS and ChIP108.H3_siNS Input control Input control Input for ChIP104.H3K4me3_siSki8 and ChIP105.H3_siSki8 Histone H3 H3 ChIP-seq, siSki8 Histone H3K4me3 H3K4me3 ChIP-seq, siSki8 Input control Input control Input forChIP102.H3K36me3_siNS Input control Input control Input for ChIP100.H3K36me3_siSki8 Histone H3K36me3 H3K36me3 ChIP-seq, siSki8 Input control Input control Input for ChIP094.PolIICTD_siNS RNA polymerase RNA polymerase II PolIICTD ChIP-seq, siNS Input control Input control Input for ChIP091.PolIICTD_siSki8 RNA polymerase RNA polymerase II PolIICTD ChIP-seq, siSki8 Input control Input control Input for ChIP087.H3K4me3_siNS and ChIP088.H3_siNS Input control Input control Input for ChIP084.H3K4me3_siPaf1 and ChIP085.H3_siPaf1 Histone H3 H3 ChIP-seq, siPaf1 Histone H3K4me3 H3K4me3 ChIP-seq, siPaf1 Input control Input control Input for ChIP082.H3K36me3_siNS Input control Input control Input for ChIP080.H3K36me3_siPaf1 Histone H3K36me3 H3K36me3 ChIP-seq, siPaf1 Input control Input control Input for PolIICTD_siNS RNA polymerase RNA polymerase II PolII ChIP-seq, siNS Input control Input control Input for PolIICTD_siPaf1 RNA polymerase RNA polymerase II PolII ChIP-seq, siPaf1 Input control Input control Input for ChIP-seq Ski8MT Others Wdr61 ChIP-seq Ski8MT Input control Input control Input for ChIP-seq Ski8MB Others Wdr61 ChIP-seq Ski8MB Input control Input control Input for ChIP-seq Rtf1MT Others Rtf1 ChIP-seq Rtf1MT Input control Input control Input for ChIP-seq Rtf1MB Others Rtf1 ChIP-seq Rtf1MB Input control Input control Input for ChIP-seq Paf1MT Others Paf1 ChIP-seq Paf1MT Input control Input control Input for ChIP-seq Paf1MB Others Paf1 ChIP-seq Paf1MB Input control Input control Input for ChIP-seq Leo1MT Others Leo1 ChIP-seq Leo1MT Input control Input control Input for ChIP-seq Leo1MB Others Leo1 ChIP-seq Leo1MB Input control Input control Input for ChIP-seq Ctr9MT Others Ctr9 ChIP-seq Ctr9MT Input control Input control Input for ChIP-seq Ctr9MB Others Ctr9 ChIP-seq Ctr9MB Input control Input control Input for ChIP-seq Cdc73MT Others Cdc73 ChIP-seq Cdc73MT Input control Input control Input for ChIP-seq Cdc73MB Others Cdc73 ChIP-seq Cdc73MB Others Glis3 Antibody: ANTI-FLAG M2 Affinity Gel A2220 (Sigma-Aldrich) pancreatic alpha cells aTC1-9 expressing 3xFlag-Glis3-mcherry Input control Input control none (input) pancreatic alpha cells aTC1-9 expressing 3xFlag-Glis3-mcherry Others Tcf4 ChIP/ antibody against Tcf4 Transgenic Hepatocytes Others Tcf4 Tcf4 (mouse monoclonal, clone 6H5-3) 05-511 Transgenic Hepatocytes Others Ctnnb1 beta-catenin (mouse monoclonal, clone 14) 610154 Transgenic Hepatocytes Others Spi1 Pu1 SantaCruz Sc-352X, lot B0314 Bcell+Cebpa6h Histone H3K27me3 H3K27me3 EMD Millipore 07-449, lot 1959680 Bcell+Cebpa6h Others Spi1 Pu1 SantaCruz Sc-352X, lot B0314 Bcell Histone H3K27me3 H3K27me3 EMD Millipore 07-449, lot 1959680 Bcell Others Spi1 Pu1 SantaCruz Sc-352X, lot B0314 Bcell+Cebpa6h+wash6d Histone H3K27me3 H3K27me3 EMD Millipore 07-449, lot 1959680 Bcell+Cebpa6h+wash6d Histone H3K4me3 H3K4me3 Bcell Histone H3K4me1 H3K4me1 EMB Millipore 04-790, clone AW30 Bcell Input control Input control none (input) Bcell+wash6d Histone H3K4me2 H3K4me2 EMB Millipore 04-790, clone AW30 Bcell+wash6d Input control Input control none (input) Bcell+Cebpa6h Histone H3K4me2 H3K4me2 EMB Millipore 04-790, clone AW30 Bcell+Cebpa6h Input control Input control none (input) Bcell+Cebpa6h+wash6d Histone H3K4me3 H3K4me3 EMB Millipore 05-1339, clone CMA304 Bcell+Cebpa6h+wash6d Histone H3K4me2 H3K4me2 EMB Millipore 04-790, clone AW30 Bcell+Cebpa6h+wash6d Histone H3K4me1 H3K4me1 Diagenode C15410037, lot A1657D Bcell+Cebpa6h+wash6d Others Epitope tags FLAG M2 Sigma F1804 mouse V6.5 ES Cells RNA polymerase RNA polymerase II PolII (Santa Cruz, N-20, sc-899X, lot#C0813) MEF_WT Others Nkx2-5 Nkx2-5 (N-19) WT_Nkx2-5_ChIP Others Gata4 Gata4 (C-20) WT_Gata4_ChIP Others Tbx3 Tbx3 (A-20) Myh6-MCM_control_Tbx3_ChIP Others Tbx3 Tbx3 (A-20) Myh6-MCM;CAG-CAT-TBX3_Tbx3_ChIP Others Rfx3 RFX3 mouse pancreatic beta cell line MIN6 Others Rfx1 RFX1 mouse pancreatic beta cell line MIN6 Histone H3K4me1 rabbit H3K4me1 antibody (Abcam, ab8895) Low fat diet Histone H3K4me1 rabbit H3K4me1 antibody (Abcam, ab8895) High fat diet Input control Input control IgG in vivo-generated T follicular helper (Tfh) cells from Bcl6-RFP reporter mice Others Bcl6 Bcl6 in vivo-generated non-T follicular helper (nonTfh) cells from Bcl6-RFP reporter mice Others Bcl6 Bcl6 in vivo-generated T follicular helper (Tfh) cells from Bcl6-RFP reporter mice Input control Input control IgG E14_IgG_ChIPSeq Histone macroH2A2 MacroH2A1 (Buschbeck et al, 2009, NSMB) E14_MacroH2A_ChIPSeq Others Hsf1 HSF1 Liver Histone H3K27me3 H3K27me3 leukemic spleen cells, secondary, Ezh2-null, H3K27me3 ChIP Histone H3K27me3 H3K27me3 leukemic spleen cells, secondary, WT, H3K27me3 ChIP Histone H3K27me3 H3K27me3 leukemic spleen cells, primary, Ezh2-null, H3K27me3 ChIP Histone H3K27me3 H3K27me3 leukemic spleen cells, primary, WT, H3K27me3 ChIP Input control Input control IgG control MEF_STAT5-KO-empty-GH-IgG Others Stat5a anti-STAT5 MEF_STAT5-KO-empty-GH-IP Input control Input control IgG control MEF_STAT5-KO-GH-IgG Others Stat5a anti-STAT5 MEF_STAT5-KO-GH-IP Input control Input control IgG control MEF_STAT5-OE-GH-IgG Input control Input control IgG control MEF_STAT5-OE-IgG Input control Input control IgG control MEF_STAT5-WT-GH-IgG Others Stat5a anti-STAT5 MEF_STAT5-WT-GH-IP Histone H2A.Z H2A.Z E14 embryonic stem cells Others 5-hmC 5-hmC E14 embryonic stem cells Histone H3K27ac H3K27ac E14 embryonic stem cells Input control Input control none (input) T-ALL sonicated input Others Notch1 Notch1 T-ALL Notch1 Others Sox4 anti-Sox4 mouse pancreatic cancer cell line Others Med1 anti-Med1 mouse pancreatic cancer cell line Unclassified Unclassified mouse pancreatic cancer cell line Others Klf5 anti-Klf5 mouse pancreatic cancer cell line Input control Input control none Mouse uterus Others Pgr PR Mouse uterus epithelium Histone H4ac acetyl-H4 antibody P19_NeuroD2_acetylH4_ChIP-seq Histone H4ac acetyl-H4 antibody P19_control_acetylH4_ChIP-seq Others Neurod2 two NEUROD2 antibodies raised in rabbits by our lab (1240J, 1168J) MM_NeuroD2_ChIP-seq Others Myod1 two MyoD antibody raised in rabbits by our lab (6196 and 6975) and previously described (Tapscott et al., 1988) MM_MyoD_ChIP-seq Others Myod1 two MyoD antibody raised in rabbits by our lab (6196 and 6975) and previously described (Tapscott et al., 1988) P19_MyoD_ChIP-seq Others Neurod2 two NEUROD2 antibodies raised in rabbits by our lab (1240J, 1168J) P19_NeuroD2_ChIP-seq Input control Input control preimmune serum P19_preimmune serum_ChIP-seq Others Rnf2 Ring1b (Home made) Villi Input control Input control none (input) Villi Histone H2AK119Ub Ubiquityl-Histone H2A (Lys119) (D27C4) (Cell signaling, catalog# 8240S, lot# 2) Villi Histone H2A.X customize H2AX antibody Alkbh1 KO ESC Histone H3K27ac K27Ac (Abcam, ab4729) Alkbh1 KO ESC Histone H3K4me1 K4Me1 (Abcam, ab8895) Alkbh1 KO ESC Input control Input control wildtype TT2 ESC Histone H3K9me3 K9Me3 (Abcam, ab8898) wildtype TT2 ESC Histone H3K4me1 K4Me1 (Abcam, ab8895) wildtype TT2 ESC Histone H2A.X customize H2AX antibody wildtype TT2 ESC Histone H3K27ac K27Ac (Abcam, ab4729) wildtype TT2 ESC Histone H3K9me3 K9Me3 (Abcam, ab8898) Alkbh1 KO ESC Input control Input control ESCs_input Histone H3K27ac H3K27Ac (ActivMotif, 39133, 16612005) Embryonic stem cell Histone H3K27me3 H3K27Me3 (Diagenode, pAb-069-050, A1821D) Embryonic stem cell Histone H3K4me3 H3K4Me3 (Millipore, 04-745, 2326991) Embryonic stem cell Histone H3 H3 antibody (Abcam, Ab1791, GR20203823-1) MII oocyte Histone H3K4me3 custom-made H3K4Me3 antibody (Abmart) Cortex Histone H3K4me3 custom-made H3K4Me3 antibody (Abmart) E6.5 epiblast Histone H3K4me3 custom-made H3K4Me3 antibody (Abmart) GV oocyte Unclassified Unclassified DNMT triple knockout mouse embryonic stem cell Unclassified Unclassified gift from Morimoto lab (MM) MEFs_HSF1KO_60minHS Others Hsf1 Cell Signaling (CS) #4356 MEFs_HSF1KO_60minHS Unclassified Unclassified gift from Morimoto lab (MM) MEFs_HSF1KO_12minHS Others Hsf1 Cell Signaling (CS) #4356 MEFs_HSF1KO_12minHS Unclassified Unclassified gift from Morimoto lab (MM) MEFs_HSF1KO_NHS Others Hsf1 Cell Signaling (CS) #4356 MEFs_HSF1KO_NHS Unclassified Unclassified MEFs_WT_60minHS Input control Input control non-specific IgG MEFs_WT_60minHS Unclassified Unclassified gift from Morimoto lab (MM) MEFs_WT_60minHS Others Hsf1 Cell Signaling (CS) #4356 MEFs_WT_60minHS Unclassified Unclassified MEFs_WT_12minHS Input control Input control non-specific IgG MEFs_WT_12minHS Unclassified Unclassified gift from Morimoto lab (MM) MEFs_WT_12minHS Others Hsf1 Cell Signaling (CS) #4356 MEFs_WT_12minHS Unclassified Unclassified MEFs_WT_NHS Input control Input control non-specific IgG MEFs_WT_NHS Unclassified Unclassified gift from Morimoto lab (MM) MEFs_WT_NHS Others Hsf1 Cell Signaling (CS) #4356 MEFs_WT_NHS Input control Input control Control mouse villus cells Histone H3K27me3 H3K27me3 antibody (07-449, Millipore) Control mouse intestinal stem cells Histone H3K27me3 H3K27me3 antibody (07-449, Millipore) Control mouse villus cells Histone H3K9ac H3K9ac Ab (07-352 Millipore) H3K9ac PB Histone H3K9ac H3K9ac Ab (07-352 Millipore) H3K9ac Act B cell Histone H3K4me3 H3K4me3 Art.Nr: pAb-003-050 Lot.Nr: A5051-001P H3K4me3 PB Histone H3K4me3 H3K4me3 Art.Nr: pAb-003-050 Lot.Nr: A5051-001P H3K4me3 Act B cell Histone H3K4me2 H3K4me2 Art.Nr: 07-030 Lot.Nr: DAM1724042 H3K4me2 PB Histone H3K4me2 H3K4me2 Art.Nr: 07-030 Lot.Nr: DAM1724042 H3K4me2 Act B cell Histone H3K27me3 H3K27me3 cell signaling H3K27me3 PB Histone H3K27me3 H3K27me3 Ab TJ crude serum H3K27me3 PB Histone H3K27me3 H3K27me3 Ab TJ crude serum H3K27me3 Act B cell Others Irf4 Irf4 Ab, SantaCruz SC6059X, lot: E0608 ChIP-seq IRF4 Pre-PB Others Irf4 Irf4 Ab, SantaCruz SC6059X, lot: E0608 ChIP-seq IRF4 PB Others Irf4 Irf4 Ab, SantaCruz SC6059X, lot: E0608 ChIP-seq IRF4 Act B cell Others Spi1 Streptavidin Bio-ChIP-seq PU.1 PB Others Prdm14 PRDM14 (Homemade) KH2 mESCs Others Pou5f1 POU5F1 (Santa Cruz, catalog# sc-5279) KH2 mESCs Input control Input control none KH2 mESCs Others Cbfa2t2 CBFA2T2 (Bethyl, catalog# A303-593A) KH2 mESCs Input control Input control input KH2 mES Others Ell custom ELL, see Lin et al. 2010 (Mol. Cell) KH2 mES Input control Input control None Mouse thymus Histone H3K27ac Active motif, 39133 Mouse thymus RNA polymerase RNA polymerase II Canvance, MMS-126R Mouse thymus Histone H3K4me3 Millipore, 05-745 Mouse thymus Histone H3K4me1 Abcam, ab8895 Mouse thymus Unclassified Unclassified Kim et al., 2007 Mouse thymus Input control Input control None Mouse testis Histone H3K27ac Active motif, 39133 Mouse testis RNA polymerase RNA polymerase II Canvance, MMS-126R Mouse testis Histone H3K4me3 Millipore, 05-745 Mouse testis Histone H3K4me1 Abcam, ab8895 Mouse testis Unclassified Unclassified Kim et al., 2007 Mouse testis Input control Input control None Mouse placenta Histone H3K27ac Active motif, 39133 Mouse placenta RNA polymerase RNA polymerase II Canvance, MMS-126R Mouse placenta Histone H3K4me3 Millipore, 05-745 Mouse placenta Histone H3K4me1 Abcam, ab8895 Mouse placenta Unclassified Unclassified Kim et al., 2007 Mouse placenta Input control Input control None Mouse olfactory bulb Histone H3K27ac Active motif, 39133 Mouse olfactory bulb RNA polymerase RNA polymerase II Canvance, MMS-126R Mouse olfactory bulb Histone H3K4me3 Millipore, 05-745 Mouse olfactory bulb Histone H3K4me1 Abcam, ab8895 Mouse olfactory bulb Unclassified Unclassified Kim et al., 2007 Mouse olfactory bulb Input control Input control None Mouse intestine Histone H3K27ac Active motif, 39133 Mouse intestine RNA polymerase RNA polymerase II Canvance, MMS-126R Mouse intestine Histone H3K4me3 Millipore, 05-745 Mouse intestine Histone H3K4me1 Abcam, ab8895 Mouse intestine Unclassified Unclassified Kim et al., 2007 Mouse intestine Input control Input control None Mouse E14.5 liver Histone H3K27ac Active motif, 39133 Mouse E14.5 liver RNA polymerase RNA polymerase II Canvance, MMS-126R Mouse E14.5 liver Histone H3K4me3 Millipore, 05-745 Mouse E14.5 liver Histone H3K4me1 Abcam, ab8895 Mouse E14.5 liver Unclassified Unclassified Kim et al., 2007 Mouse E14.5 liver Input control Input control None Mouse E14.5 limb Histone H3K27ac Active motif, 39133 Mouse E14.5 limb RNA polymerase RNA polymerase II Canvance, MMS-126R Mouse E14.5 limb Histone H3K4me3 Millipore, 05-745 Mouse E14.5 limb Histone H3K4me1 Abcam, ab8895 Mouse E14.5 limb Unclassified Unclassified Kim et al., 2007 Mouse E14.5 limb Input control Input control None Mouse E14.5 heart Histone H3K27ac Active motif, 39133 Mouse E14.5 heart RNA polymerase RNA polymerase II Canvance, MMS-126R Mouse E14.5 heart Histone H3K4me3 Millipore, 05-745 Mouse E14.5 heart Histone H3K4me1 Abcam, ab8895 Mouse E14.5 heart Unclassified Unclassified Kim et al., 2007 Mouse E14.5 heart Input control Input control None Mouse E14.5 brain Histone H3K27ac Active motif, 39133 Mouse E14.5 brain RNA polymerase RNA polymerase II Canvance, MMS-126R Mouse E14.5 brain Histone H3K4me3 Millipore, 05-745 Mouse E14.5 brain Histone H3K4me1 Abcam, ab8895 Mouse E14.5 brain Unclassified Unclassified Kim et al., 2007 Mouse E14.5 brain Histone H3K27ac Active motif, 39133 Mouse spleen Histone H3K27ac Active motif, 39133 Bruce4 embryonic stem cells Histone H3K27ac Active motif, 39133 Mouse embryonic fibroblast Histone H3K27ac Active motif, 39133 Mouse lung Histone H3K27ac Active motif, 39133 Mouse liver Histone H3K27ac Active motif, 39133 Mouse kidney Histone H3K27ac Active motif, 39133 Mouse heart Histone H3K27ac Active motif, 39133 Mouse cortex Histone H3K27ac Active motif, 39133 Mouse cerebellum Histone H3K27ac Active motif, 39133 Mouse bone marrow Input control Input control N/A Mixture of various non-specific antibodies B cells Others Aicda AID Santa Cruz rabbit polyclonal anti-AID antibody (Catalog No. sc-25620) Activated B cells Others Bcl6 BCL6 wild-type primary bone marrow-derived macrophages Unclassified Unclassified newborn lens Unclassified Unclassified pancreas/brain Input control Input control none Mouse villus cell input DNA Histone H3K4me2 Millipore 07-030, lots DAM1570816 and DAM1724043 H3K4me2 ChIP-Seq in Cdx2-Hnf4a D KO mouse villus cells Histone H3K4me2 Millipore 07-030, lots DAM1570816 and DAM1724042 H3K4me2 ChIP-Seq in Cdx2-Hnf4a D KO mouse villus cells Histone H3K4me2 Millipore 07-030, lots DAM1570816 and DAM1724042 H3K4me2 ChIP-Seq in Hnf4a KO mouse villus cells Histone H3K4me2 Millipore 07-030, lots DAM1570816 and DAM1724042 H3K4me2 ChIP-Seq in Cdx2 KO mouse villus cells Histone H3K4me2 Millipore 07-030, lots DAM1570816 and DAM1724042 H3K4me2 ChIP-Seq in WT mouse villus cells Others Hnf4a HNF4 c-19 (Santa Cruz 6556, lot c1810) Hnf4a ChIP-Seq in Cdx2 KO mouse villus cells Others Hnf4a HNF4 c-19 (Santa Cruz 6556, lot c1810) Hnf4a ChIP-Seq in WT mouse villus cells Others Cdx2 Bethyl BL3194, lotA300-691A-1 CDX2 ChIP-Seq in Hnf4a KO mouse villus cells Unclassified Unclassified ARID1A-KO_colon Unclassified Unclassified wild type_colon Histone H3K27ac H3K27ac (Cell Signaling Technology, D5E4, 8173) ARID1A-KO_colon Histone H3K4me3 H3K4me3 (Millipore, 07-473) wild type_colon Histone H3K27ac H3K27ac (Cell Signaling Technology, D5E4, 8173) wild type_colon Histone H3K4me3 H3K4me3 (Millipore, 07-473) MEF_Smarca4-KO Histone H3K4me3 H3K4me3 (Millipore, 07-473) MEF_Smarcb1-KO Histone H3K4me3 H3K4me3 (Millipore, 07-473) MEF_WT Others Smarca4 SMARCA4/BRG1 (Abcam, EPNCIR111A, ab110641) MEF_Smarcb1-KO Others Smarcc1 SMARCC1/BAF155 (Santa Cruz, R-8, sc-9746) MEF_Smarcb1-KO Others Smarca4 SMARCA4/BRG1 (Abcam, EPNCIR111A, ab110641) MEF_WT Others Smarcc1 SMARCC1/BAF155 (Santa Cruz, R-8, sc-9746) MEF_WT Histone H3K4me1 H3K4me1 HOXA9-MEIS1 LSCs Input control Input control none HOXA9-MEIS1 LSCs Histone H3K27me3 H3K27me3 RH-RAS LSCs Histone H3K4me3 H3K4me3 RH-RAS LSCs Histone H3K4me1 H3K4me1 RH-RAS LSCs Others Epitope tags myc tag, 9e10 RH-RAS LSCs Input control Input control none RH-RAS LSCs Unclassified Unclassified B220+ LMP2a B cells Histone H3K4me3 H3K4me3 B220+ LMP2a B cells Histone H3K4me1 H3K4me1 B220+ LMP2a B cells Histone H3K27ac H3K27ac B220+ LMP2a B cells Unclassified Unclassified B220+ GFP B cells Histone H3K4me3 H3K4me3 B220+ GFP B cells Histone H3K4me1 H3K4me1 B220+ GFP B cells Histone H3K27ac H3K27ac B220+ GFP B cells Input control Input control none A-20 Undifferentiated ES cells Input control Input control Control none Undifferentiated ES cells Histone H3K36me3 H3K36me3 13C9 Undifferentiated ES cells Histone H2Aub H2Aub1 E6C5 (Upstate) Undifferentiated ES cells RNA polymerase RNA polymerase II RNAPII S2P H5 (MMS-129R, Covance) Undifferentiated ES cells RNA polymerase RNA polymerase II RNAPII 8WG16 8WG16 (MMS-126R, Covance) Undifferentiated ES cells RNA polymerase RNA polymerase II RNAPII S7P 4E12 Undifferentiated ES cells Histone H3K79me3 H3K79me3 MEFs cells knockout MED23 Histone H3K79me3 H3K79me3 MEFs cells wildtype Histone H3K4me3 H3K4me3 MEFs cells knockout MED23 Histone H3K4me3 H3K4me3 MEFs cells wildtype Histone H3K4me2 H3K4me2 (Abcam, Ab7766) cardiomyocytes Input control Input control none cardiomyocytes Input control Input control none (input) Whole cortex dissected from embryonic day 15.5 (E15.5) embryos Others Tbr1 Rabbit anti TBR1 (Abcam) antibody Whole cortex dissected from embryonic day 15.5 (E15.5) embryos Histone H2A.Z mouse ES cells, shMLL4, H2A.Z ChIP Histone H2A.Z mouse ES cells, shluc control, H2A.Z ChIP Histone H2A.Zac mouse ES cells, WT, acetylated H2A.Z ChIP Histone H2A.Z mouse ES cells, WT, H2A.Z ChIP Others Foxo1 ab39670 Haftl pre-B cells Others Pax5 sc-1974 Haftl pre-B cells Histone H3K27me3 H3K27me3 PDGF K27M EPZ me3 Histone H3K27me3 H3K27me3 PDGF K27M DMSO me3 Histone H3K27me3 H3K27me3 PDGF H3 3 EPZ me3 Histone H3K4me3 ChIP H3K4me3 Diagenode, C15410003 Bcell+Cebpa18h+OSKM2d Histone H3K4me3 ChIP H3K4me3 Diagenode, C15410003 Bcell+Cebpa18h+OSKM1d Histone H3K4me3 ChIP H3K4me3 Diagenode, C15410003 Bcell+Cebpa18h Histone H3K4me3 ChIP H3K4me3 Diagenode, C15410003 Bcell Input control Input control none (input) Bcell+Cebpa18h+OSKM2d Input control Input control none (input) Bcell+Cebpa18h+OSKM1d Input control Input control none (input) Bcell+Cebpa18h Histone H3K27me3 H3K27me3 (Millipore, 07-449) Neural progenitors t72 + SAG Histone H3K27me3 H3K27me3 (Millipore, 07-449) Neural progenitors t0 Input control Input control n/a Cerebellum Others Gli2 Gli2 (R&D Systems, AF3635) Cerebellum Input control Input control n/a Limb bud Others Gli2 Gli2 (R&D Systems, AF3635) Trunk Others Gli2 Gli2 (R&D Systems, AF3635) Limb bud Others Gli2 Gli2 (R&D Systems, AF3635) Head Others Gata3 anti-GATA3 (L50-823) type 2 T helper cells (Th2s) Others Gata3 anti-GATA3 (L50-823) type 2 Innate lympoid cells (ILC2s) Others Gata3 anti-GATA3 (L50-823) type 3 Innate lympoid cells (ILC3s) Input control Input control anti-mouse IgG type 3 Innate lympoid cells (ILC3s) Others Brd4 BRD4 (A301-985A; Bethyl) MLL-AF9/NrasG12D murine cell line Unclassified Unclassified Primary splenic cells Others Nr5a2 LRH-1 Lrh1 ChIP Input control Input control none input RNA polymerase RNA polymerase II Pol_II (Millipore, 17-672) Forelimb Histone H3K27me3 H3K27me3 (Millipore, 07-449) Forelimb Histone H3K4me3 H3K4me3 (Abcam, ab1342) Forelimb Input control Input control none, Input Forelimb Unclassified Unclassified embryonic stem cell Others Cbx1 HP1b (D2F2), NEB #8676 embryonic stem cell Others Kmt2a anti-MLL1 MLL-AF9 transfromed blasts Others Rcor1 CoREST AB32631 Embryonic stem cells Input control Input control IgG IgG_ChIP Others Egr2 anti-EGR2 (Krox-20) VA14tg_NKT_EGR2_ChIP Others Egr2 anti-EGR2 (Krox-20) anti-TCRb injected_thymocytes_EGR2_ChIP Input control Input control none none 3T3-L1 cells (ATCC #CL-173) Input control Input control None Input DNA for H3K36me3 ChIP Histone H3K36me3 anti-H3K36me3 H3K36me3 ChIP Input control Input control None input DNA for H3K4me3 ChIP Histone H3K4me3 anti-H3K4me3 H3K4me3 ChIP Others Ctcfl V5 ES_CTCFL_V5_NODOX Others Ctcfl V5 ES_CTCFL_V5_DOX Others Ctcf CTCF ES_CTCF Unclassified Unclassified (in vitro pulldown, w/ Ni-NTA beads) purified DNA Input control Input control purified DNA Histone H3K27ac H3K27ac (AbCam, ab4729) Tip5-knockdown E14 cells Others Jarid2 Jarid2 (AbCam, ab48137) Tip5-knockdown E14 cells Histone H3K27me3 H3K27me3 (Millipore, 07-449) Tip5-knockdown E14 cells Others Suz12 Suz12 (Millipore, 17-661) Tip5-knockdown E14 cells Others Baz2a Tip5 (Diagenode, CS-090-100) wild-type E14 cells Histone H3K27me3 H3K27me3 (Millipore, 07-449) wild-type E14 cells Histone H3K27ac H3K27ac (AbCam, ab4729) wild-type E14 cells Others Jarid2 Jarid2 (AbCam, ab48137) wild-type E14 cells Others Suz12 Suz12 (Millipore, 17-661) wild-type E14 cells Input control Input control none MMTV-Myc cells Others GFP GFP (A-6455, life technologies) Daxx fl/fl Embryonic stem cell_tamoxifen-treated to induce Daxx -/- Others GFP GFP (A-6455, life technologies) Daxx fl/fl Embryonic stem cell_DMSO-treated Others GFP GFP (A-6455, life technologies) Daxx -/- Embryonic stem cell Others GFP GFP (A-6455, life technologies) Daxx fl/- Embryonic stem cell Others Gfi1 Gfi Gfi1-KO CD4 Thn cell Others Gfi1 Gfi Gfi1-WT CD4 Thn cell Input control Input control none INK4A/ARF -/- mNPC 2 Input Input control Input control none INK4A/ARF -/- mNPC 1 Input Others Bmi1 anti-BMI1 INK4A/ARF -/- Astrocytes BMI1 Others Bmi1 anti-BMI1 INK4A/ARF -/- mGIC BMI1 Others Bmi1 anti-BMI1 INK4A/ARF -/- mNPC 2 BMI1 Others Bmi1 anti-BMI1 INK4A/ARF -/- mNPC 1 BMI1 Input control Input control none liver input Others Nr1d2 REV-ERB beta liver_REV-ERB beta_ChIP Others Nr1d1 REV-ERB alpha liver_REV-ERB alpha_ChIP Input control Input control none EB cells cultured with a hematopietic cytokine cocktail for 20 days Others Hoxb4 anti-HoxB4 EB cells cultured with a hematopietic cytokine cocktail for 20 days Input control Input control none EB cells cultured with a hematopietic cytokine cocktail for 10 days Others Hoxb4 anti-HoxB4 EB cells cultured with a hematopietic cytokine cocktail for 10 days Input control Input control none day 6 embryoid body cels Input control Input control Goat IgG (Santa Cruz: sc2028) NS5 Neural Stem Cell Others Smad4 Goat Smad4 antibody (R&D Systems: AF2097) NS5 Neural Stem Cell Others Olig2 Rabbit Anti-Olig2 (Milipore: AB9610) NS5 Neural Stem Cell Others Npas3 Rabbit Anti-Npas3 (Sigma: HPA002892) NS5 Neural Stem Cell Others Hoxb4 anti-HoxB4 day 6 embryoid body cells Others Trim28 rabbit anti-KAP-1 Affinity Purified, 1mg/ml, A300-274A,BETHYL E14 Others Sumo2 Anti-Sumo2+3 (abcam), Cat #:ab3742, Lot:GR54180-2 E14 Others Cebpa C/EBPa, sc-61, Santa Cruz AAV_Cebpa_rep2 Others Cebpa C/EBPa, sc-61, Santa Cruz AAV_Cebpa_rep1 Others Cebpa C/EBPa, sc-61, Santa Cruz AAV_Null_rep2 Others Cebpa C/EBPa, sc-61, Santa Cruz AAV_Null_rep1 Others Cebpa C/EBPa, sc-61, Santa Cruz Trib1_LSKO_rep2 Others Cebpa C/EBPa, sc-61, Santa Cruz Trib1_LSKO_rep1 Others Cebpa C/EBPa, sc-61, Santa Cruz Trib1_WT_rep2 Others Cebpa C/EBPa, sc-61, Santa Cruz Trib1_WT_rep1 Histone H3K4me3 anti-H3K4me3 (Millipore, catalog# 07-473, lot# 2500603) Short-term Hematopoietic stem cells Unclassified Unclassified Rabbit IgG mouse ES cell (TKO) Others Daxx DAXX antibody (SC-7152) mouse ES cell (TKO) Others Atrx ATRX antibody (SC-15408) mouse ES cell (TKO) Unclassified Unclassified Rabbit IgG mouse ES cell (J1) Others Daxx DAXX antibody (SC-7152) mouse ES cell (J1) Others Atrx ATRX antibody (SC-15408) mouse ES cell (J1) Input control Input control none Mouse Round spermatids Others Ctcfl custom rabbit polyclonal BORIS (characterized in PMID:20231363) Mouse Round spermatids Others Ctcf custom mouse monoclonal CTCF (characterized in PMID:15731119) Mouse Round spermatids Histone H3K9ac H3K9ac (Abcam, #ab10812) drug resistance Lewis lung carcinoma isograft Histone H3K36me3 H3K36me3 (Abcam, #ab9050) drug resistance Lewis lung carcinoma isograft Histone H3K27me3 H3K27me3 (Abcam, #ab6002) drug resistance Lewis lung carcinoma isograft Histone H3K4me3 H3K4me3 (Abcam, #ab8580) drug resistance Lewis lung carcinoma isograft Histone H3K9ac H3K9ac (Abcam, #ab10812) drug sensitive Lewis lung carcinoma isograft Histone H3K36me3 H3K36me3 (Abcam, #ab9050) drug sensitive Lewis lung carcinoma isograft Histone H3K27me3 H3K27me3 (Abcam, #ab6002) drug sensitive Lewis lung carcinoma isograft Histone H3K4me3 H3K4me3 (Abcam, #ab8580) drug sensitive Lewis lung carcinoma isograft Others Irf8 anti-IRF8 (Santa Cruz, C-19) GC B cells Others Stat5a STAT5 multipotent myeloid progenitor cell line_no_treatment Others Stat5a STAT5 multipotent myeloid progenitor cell line_TPO Histone H3K27ac H3K27ac (39133, Active Motif) TAF4-/- EB8 Histone H3K27ac H3K27ac (39133, Active Motif) wt EB8 Histone H3K27ac H3K27ac (39133, Active Motif) TAF4-/- Escells Histone H3K27ac H3K27ac (39133, Active Motif) wt ES cells Histone H3K4me3 anti-H3K4Me3 (04-745, Millipore) TAF4-/- EB8 Histone H3K4me3 anti-H3K4Me3 (04-745, Millipore) wt EB8 Histone H3K4me3 anti-H3K4Me3 (04-745, Millipore) TAF4-/- Escells Histone H3K4me3 anti-H3K4Me3 (04-745, Millipore) wt ES cells Others Tbp TBP (ab28175, Abcam) TAF4-/- EB8 Others Tbp TBP (ab28175, Abcam) wt EB8 Others Tbp TBP (ab28175, Abcam) TAF4-/- Escells Others Tbp TBP (ab28175, Abcam) wt ES cells RNA polymerase RNA polymerase II Pol II (sc-9001x, Santa Cruz) TAF4-/- EB8 RNA polymerase RNA polymerase II Pol II (sc-9001x, Santa Cruz) wt EB8 RNA polymerase RNA polymerase II Pol II (sc-9001x, Santa Cruz) TAF4-/- Escells RNA polymerase RNA polymerase II Pol II (sc-9001x, Santa Cruz) wt ES cells Others Gtf2b TFIIB (sc225x, Santa Cruz) TAF4-/- EB8 Others Gtf2b TFIIB (sc225x, Santa Cruz) wt EB8 Others Gtf2b TFIIB (sc225x, Santa Cruz) TAF4-/- Escells Others Gtf2b TFIIB (sc225x, Santa Cruz) wt ES cells Input control Input control WT input ChIP-seq Input control Input control NT input ChIP-seq Histone H3K9me3 H3K9me3 NT H3K9me3 ChIP-seq Input control Input control NT Kdm4b input ChIP-seq Input control Input control CC input ChIP-seq Histone H3K9me3 H3K9me3 CC H3K9me3 ChIP-seq Input control Input control input mouse embryonic stem cells Others Epitope tags anti-Flag (F3165, Sigma) mouse embryonic stem cells Others Epitope tags anti-HA (H3663, Sigma) mouse embryonic stem cells Others Tcf3 anti-Tcf3 Santa Cruz Biotechnology/sc-8635X mouse embryonic stem cells Others Smad2 anti-Smad2/3 Cell Signaling Technology/8685 mouse embryonic stem cells Others Tcf3 anti-Tcf3 Santa Cruz Biotechnology/sc-8635X mouse embroid bodies Others Nr4a1 anti-NR4A1 antibody, clone H1648 (Perseus Proteomics, catalog# PP-H1648-00, lot# A-1) Regulatory T (Treg) cells Others Shox2 ChIP-Sequencing on Shox2-HA E12.5 heart (contain proximal part of pulmonary vein and R/LSVC, part of ventricle was dissected away) Others Rxra in-house polyclonal Ab against RXRa mRXRa(1) Others Rxra in-house polyclonal Ab against RXRa mRXRa 100xfold-diluted LinDA Others Rxra in-house polyclonal Ab against RXRa and RAR mRXRa RARg reChIP LinDA Unclassified Unclassified na Whole Thymus Others Tbx21 T-bet primary CD4+ T cells from spleen and lymph nodes Others Ctcf CTCF anti-CTCF Mouse Mature B cells, Spleen, in vitro LPS/IL-4 activated Others Irf8 Irf8 antibody Santa Cruz sc-6058 Bone Marrow Unclassified Unclassified Bone Marrow Others Gfi1 Gfi1 antibody http://www.ncbi.nlm.nih.gov/pubmed/24141388 Bone Marrow Input control Input control embryonic stem cells_input Unclassified Unclassified embryonic stem cells_ChIP Input control Input control none TSC Histone H2A.X anti-H2A.X (Xiaolab_Maked) MEF cells Histone H2A.X anti-H2A.X (Xiaolab_Maked) ES cell Unclassified Unclassified - genomic DNA, Mnase Histone H3K27me3 Mouse anti-H3K27me3 (Active Motif:39535) genomic DNA, Mnase Histone H3K4me3 Rabbit anti-H3K4me3 (Cell Signaling: #9751) genomic DNA, Mnase RNA polymerase RNA polymerase II Mouse anti-RNA Polymerase II, CTD clone 8WG16 (Millipore: 05-952) genomic DNA, Cross link Input control Input control NA Mutant-newborn-mouse-liver(GLP 3A homozygous) Histone H3K9me2 H3K9me2, mAbcam 1220 Mutant-newborn-mouse-liver(GLP 3A homozygous) Input control Input control NA WT-newborn-mouse-liver Histone H3K9me2 H3K9me2, mAbcam 1220 WT-newborn-mouse-liver Others Pou3f2 Brn-2 Antibody (C-20); goat polyclonal ES-derived NS5 cells_control Input control Input control rabbit polyclonals ES-derived NS5 cells_control Others Sox2 Sox-2 Antibody (Y-17); goat polyclonal ES-derived NS5 cells_control Others Pou3f2 Brn-2 Antibody (C-20); goat polyclonal ES-derived NS5 cells_ChIP Others Sox2 Sox-2 Antibody (Y-17); goat polyclonal ES-derived NS5 cells_ChIP Unclassified Unclassified Embryonic Cortical NeuN+ Cells (E16.5) Input control Input control none input DNA_+Tam Histone H3K27me3 H3K27me3 (Millipore: 07-449) H3K27me3_ChIPSeq+Tam Histone H3K27me3 H3K27me3 (Millipore: 07-449) H3K27me3_ChIPSeq_noTam Input control Input control none H3K9me3_ChIPSeq_noTam Others Pou3f1 Pou3f1 antibody (Santa Cruz, sc-11661, Lot# C2012) Embryonic stem cell Input control Input control none (input) Embryonic stem cell Input control Input control IgG myeloid progenitor cell line Others Tal1 Tal1 myeloid progenitor cell line Others Runx1 Runx1 myeloid progenitor cell line Others Spi1 Spi-1 myeloid progenitor cell line Others Meis1 Meis1 myeloid progenitor cell line Others Lyl1 Lyl1 myeloid progenitor cell line Others Gfi1b Gfi-1b myeloid progenitor cell line Others Gata2 Gata-2 myeloid progenitor cell line Others Fli1 Fli1 myeloid progenitor cell line Others Erg Erg myeloid progenitor cell line Histone H3K27ac H3K27Ac myeloid progenitor cell line Histone H3K27ac anti-H3K27ac (abcam cat# 4729-100) H3K27ac_stim_3T3 Unclassified Unclassified IgG_thymocyte_Runx1KO_ChIPseq Others Rnf2 Ring1b_thymocyte_Runx1KO_ChIPseq Others Cbfb CBFb_thymocyte_Runx1KO_ChIPseq Others Runx1 Runx1_thymocyte_Runx1KO_ChIPseq Input control Input control IgG_thymocyte_control_ChIPseq Others Rnf2 Ring1b_thymocyte_control_ChIPseq Others Cbfb CBFb_thymocyte_control_ChIPseq Others Runx1 Runx1_thymocyte_control_ChIPseq Others Rnf2 Ring1b_alt_ab_ChIPseq Unclassified Unclassified Runx1_for_Ring1b_alt_ab_ChIPseq Unclassified Unclassified IgG_uninduced_ChIPseq Others Rnf2 Ring1b_uninduced_ChIPseq Others Cbfb CBFb_uninduced_ChIPseq Others Runx1 Runx1_uninduced_ChIPseq Unclassified Unclassified IgG_induced_ChIPseq Others Rnf2 Ring1b_induced_ChIPseq Others Cbfb CBFb_induced_ChIPseq Others Runx1 Runx1_induced_ChIPseq Others Kat5 anti-Tip60 mESCs Input control Input control none (input) SmoM2 medulloblastoma_primary tumor Others Smarca4 Brg1/Brm (J1) (Khavari et al., 1993). SmoM2 medulloblastoma_primary tumor Input control Input control input Input Macrophage Pool Histone H3K9ac H3K9Ac (Upstate Biotechnologies, 06-942) HDAC3KO IL4 H3K9Ac Histone H3K9ac H3K9Ac (Upstate Biotechnologies, 06-942) HDAC3KO No Treat H3K9Ac Histone H3K9ac H3K9Ac (Upstate Biotechnologies, 06-942) Control IL4 H3K9Ac Histone H3K9ac H3K9Ac (Upstate Biotechnologies, 06-942) Control No Treat H3K9Ac Others Hdac3 HDAC3 (Abcam, ab7030) IL4 HDAC3 Others Hdac3 HDAC3 (Abcam, ab7030) BSA HDAC3 Input control Input control None (input) Terminally Differentiated Podocyte Input control Input control none fS248A-Tg mESC, input Input control Input control none fSOX2-Tg mESC, input Input control Input control none whole uterus Others Nr5a1 SF1 whole uterus Others Rag1 RAG1 Abelson Input control Input control none Tumor Others Ascl1 mouse anti-ASCL1 antibody (BD Biosciences, cat# 556604) Tumor Others Cdk9 His tag Cdk9(amino acids 204-372) KH2 Others Sox6 anti-Sox6 Sox6 ChIP-seq Others Sox6 rabbit IgG Sox6 ChIP-seq IgG Control Others Sox5 anti-HA Sox5 ChIP-seq Others Sox5 rabbit IgG Sox5 ChIP-seq negative control Unclassified Unclassified Extraembryonic endoderm stem cell line2 Others Gata6 anti-Gata6 (R&D, catalog number AF1700) Extraembryonic endoderm stem cell line2 Unclassified Unclassified Extraembryonic endoderm stem cell line1 Others Gata6 anti-Gata6 (R&D, catalog number AF1700) Extraembryonic endoderm stem cell line1 Unclassified Unclassified Mouse embryonic stem cell line2 Others Epitope tags anti-FLAG (Sigma, catalog number F1804) Mouse embryonic stem cell line2 Unclassified Unclassified Mouse embryonic stem cell line1 Others Epitope tags anti-FLAG (Sigma, catalog number F1804) Mouse embryonic stem cell line1 Input control Input control Ebf1+/- ProB, no treatment, input Input control Input control Pax5+/- ProB, no treatment, input Input control Input control Ebf1+/- Pax5+/- ProB, no treatment, input Input control Input control WT ProB, no treatment, input Others Ebf1 Ebf1+/- ProB, no treatment, Ebf1 ChIP Others Ebf1 Pax5+/- ProB, no treatment, Ebf1 ChIP Others Ebf1 Ebf1+/- Pax5+/- ProB, no treatment, Ebf1 ChIP Others Ebf1 WT ProB, no treatment, Ebf1 ChIP Histone H3K4me3 Antibody pAB-030-050 Diagenode 100 eyes from E10.5 mouse embryos Histone H3K4me1 Antibody CS-037-100, Diagenode 100 eyes from E10.5 mouse embryos Input control Input control None proxmial half site of small intestine Input control Input control none Naive CD4 T cells Others Pou5f1 Pou5F1 Santa Cruz sc8628 Mesoderm Others Elk4 Elk4 Santa Cruz sc13030 Mesoderm Others Cebpb Cebpb Santa Cruz sc150 Mesoderm Others Tal1 Tal1 Santa Cruz sc12984 Macrophages Others Spi1 Spi1 Santa Cruz sc352 Macrophages Others Runx1 Runx1 AbCam ab23980 Macrophages Others Lmo2 Lmo2 R&D systems AF2726 Macrophages Others Fli1 Fli1 Santa Cruz sc356 Macrophages Others Cebpb Cebpb Santa Cruz sc150 Macrophages Others Tal1 Tal1 Santa Cruz sc12984 Hematopoietic Progenitors Others Spi1 Spi1 Santa Cruz sc352 Hematopoietic Progenitors Others Runx1 Runx1 AbCam ab23980 Hematopoietic Progenitors Others Lmo2 Lmo2 R&D systems AF2726 Hematopoietic Progenitors Others Gfi1b Gfi1b Santa Cruz sc8559 Hematopoietic Progenitors Others Gfi1 Gfi1 AbCam ab21061 Hematopoietic Progenitors Others Gata2 Gata2 Santa Cruz sc267 Hematopoietic Progenitors Others Gata1 Gata1 AbCam ab11963 Hematopoietic Progenitors Others Fli1 Fli1 Santa Cruz sc356 Hematopoietic Progenitors Others Cebpb Cebpb Santa Cruz sc150 Hematopoietic Progenitors Others Tal1 Tal1 Santa Cruz sc12984 Hemogenic Endothelium Others Meis1 Meis1 Santa Cruz sc10599 Hemogenic Endothelium Others Lmo2 Lmo2 R&D systems AF2726 Hemogenic Endothelium Others Fli1 Fli1 Santa Cruz sc356 Hemogenic Endothelium Others Cebpb Cebpb Santa Cruz sc150 Hemogenic Endothelium Others Tal1 Tal1 Santa Cruz sc12984 Hemangioblast Others Lmo2 Lmo2 R&D systems AF2726 Hemangioblast Others Gata2 Gata2 Santa Cruz sc267 Hemangioblast Others Cebpb Cebpb Santa Cruz sc150 Hemangioblast Histone H3K27ac H3K27Ac, 39685, Active Motif Pancreatic Beta Cells Unclassified Unclassified E17.5 Nsal chondrocytes Others Sox9 Sox9 E17.5 Nsal chondrocytes Unclassified Unclassified rabbit IgG p1 mouse rib chondrocytes RNA polymerase RNA polymerase II RNA_Pol_II p1 mouse rib chondrocytes Others Ep300 p300 p1 mouse rib chondrocytes Histone H3K27ac H3K27ac p1 mouse rib chondrocytes Histone H3K26me3 H3K26me3 p1 mouse rib chondrocytes Histone H3K27me3 H3K27Me3 p1 mouse rib chondrocytes Histone H3K4me3 H3K4Me3 p1 mouse rib chondrocytes Histone H3K4me2 H3K4me2 p1 mouse rib chondrocytes Others Sox9 Sox9 p1 mouse rib chondrocytes Unclassified Unclassified Macrophages Unclassified Unclassified Hematopoietic Progenitors Unclassified Unclassified Hemogenic Endothelium Unclassified Unclassified Hemangioblast Unclassified Unclassified Mesoderm Histone H3K4me3 H3K4me3 Millipore 04-745 Macrophages Histone H3K27me3 H3K27me3 Abcam ab6002 Macrophages Histone H3K27ac H3K27ac Abcam ab4729 Macrophages Histone H3K9ac H3K9ac Abcam ab4441 & Millipore ABE18 Macrophages Histone H3K4me3 H3K4me3 Millipore 04-745 Hemogenic Endothelium Histone H3K27me3 H3K27me3 Abcam ab6002 Hemogenic Endothelium Histone H3K27ac H3K27ac Abcam ab4729 Hemogenic Endothelium Histone H3K27me3 H3K27me3 Abcam ab6002 Hemangioblast Histone H3K27ac H3K27ac Abcam ab4729 Hemangioblast Histone H3K9ac H3K9ac Abcam ab4441 & Millipore ABE18 Hemangioblast Histone H3K27me3 H3K27me3 Abcam ab6002 Mesoderm Histone H3K27ac H3K27ac Abcam ab4729 Mesoderm Histone H3K9ac H3K9ac Abcam ab4441 & Millipore ABE18 Mesoderm Histone H3K36me3 H3K36me3 C2C12 myotube Histone H3K27ac H3K27ac C2C12 myotube Histone H3K27me3 H3K27me3 C2C12 myotube Histone H3K4me1 H3K4me1 C2C12 myotube Histone H3K4me2 H3K4me2 C2C12 myotube Histone H3K4me3 H3K4me3 C2C12 myotube Histone H3K36me3 H3K36me3 C2C12 myoblast Histone H3K27ac H3K27ac C2C12 myoblast Histone H3K27me3 H3K27me3 C2C12 myoblast Histone H3K4me1 H3K4me1 C2C12 myoblast Histone H3K4me2 H3K4me2 C2C12 myoblast Histone H3K4me3 H3K4me3 C2C12 myoblast Unclassified Unclassified Sinoatrial node (SAN) cells Others Isl1 ISL1 Sinoatrial node (SAN) cells Input control Input control none RA-treated P19.6 cells, input Input control Input control none Untreated P19.6 cells, input Histone H3K27ac anti-H3K27ac RA-treated P19.6 cells, H3K27ac ChIP Histone H3K27ac anti-H3K27ac Untreated P19.6 cells, H3K27ac ChIP Others Satb2 SATB2 antibody cortex Input control Input control none cortex Input control Input control none (Input DNA) K14CreER SmoM2 cells Others Sox9 Sox9 (Millipore, AB5535) K14CreER SmoM2 cells Others Smarca5 anti-SNF2h (Abcam ab3749) Mouse embryonic fibroblasts, SNF2h ChIP Others Baz1b anti-WSTF (Abcam ab50850) Mouse embryonic fibroblasts, WSTF ChIP Others Actb anti-beta-actin, clone AC74 (Sigma Aldrich) Mouse embryonic fibroblasts, beta-actin ChIP Others Sox3 Sox3 (T. Edlund) C2C12 muscle progenitor cells Input control Input control IgG (Millipore) Neurons Others Meis1 anti-MEIS1 RA-treated P19.6 cells, MEIS1 ChIP Input control Input control no MEF cells Others Smad1 Smad1 Santa Cruz SC-7965 Smad1 ChIP-Seq in mouse G1ER treated with BMP Others Gata1 Gata1 Santa Cruz SC-265 Gata1 ChIP-Seq in mouse G1ER treated with BIO Input control Input control None None WCE Input ChIP-Seq in mouse G1ER treated with BIO Others Smad1 Smad1 Santa Cruz SC-7965 Smad1 ChIP-Seq in mouse G1E treated with BMP Others Gata2 Gata2 Santa Cruz SC-9008 Gata2 ChIP-Seq in mouse G1E treated with BMP Input control Input control None None WCE Input ChIP-Seq in mouse G1E treated with BMP Histone Pan lysine crotonylation pan anti-lysine crotonylation antibody Round spermatids Histone Pan lysine acetylation pan anti-lysine acetylation antibody Round spermatids Input control Input control None Round spermatids Histone Pan lysine crotonylation pan anti-lysine crotonylation antibody Spermatocyte Histone Pan lysine acetylation pan anti-lysine acetylation antibody Spermatocyte Input control Input control None Spermatocyte Others Ep300 anti-acetyl-CBP/p300 (rabbit polyclonal) MouseP2Heart_acCBP-p300 Histone H3K36me3 H3K36me3 Terminally differentiated Neurons (TN) derived from mouse embryonic stem cells Histone H3K36me3 H3K36me3 Terminally differentiated Neurons (TN) derived from mouse embryonic stem cells Others Aicda AID Rabbit polyclonal described in Chaudhuri et al., Nature (2003) ActivatedBCell_AIDmm RNA polymerase RNA polymerase II PolII ab5131 mouse Ik knockout DP thymocytes RNA polymerase RNA polymerase II PolII ab5131 mouse wt DP thymocytes Histone H3K36me3 H3K36me3 ab9050 mouse wt DP thymocytes Histone H3K9ac H3K9ac2 06-599 mouse wt DP thymocytes Histone H3K27me3 H3K27me3 07-449 mouse wt DP thymocytes Histone H3K4me3 H3K4me3 ab8580 and 07-473 mouse wt DP thymocytes Others Chd4 homemade Mi2beta (Chd4) mouse wt DP thymocytes Others Ikzf1 homemade Ikaros (Ikzf1) mouse wt DP thymocytes Input control Input control none mouse wt DP thymocytes Others Chd4 homemade Mi2beta (Chd4) mouse Ik knockout DP thymocytes Others Ikzf3 homemade Aiolos mouse Ik knockout DP thymocytes Others Biotin streptavidin beads MLL-AF9 transformed blasts Histone H4ac anti-H4ac (upstate cat# 06-866) H4ac_stim_3T3 Histone H4ac anti-H4ac (upstate cat# 06-866) H4ac_unstim_3T3 Histone H4ac anti-H4ac (upstate cat# 06-866) H4ac_stim_DC Histone H4ac anti-H4ac (upstate cat# 06-866) H4ac_unstim_DC Histone H3K27ac anti-H3K27ac (abcam cat# 4729-100) H3K27ac_unstim_3T3 Histone H3K27ac anti-H3K27ac (abcam cat# 4729-100) H3K27ac_stim_DC Histone H3K27ac anti-H3K27ac (abcam cat# 4729-100) H3K27ac_unstim_DC Histone H3K4me1 anti-H3K4me1 (clone CMA302) H3K4me1_stim_3T3 Histone H3K4me1 anti-H3K4me1 (clone CMA302) H3K4me1_unstim_3T3 Histone H3K4me1 anti-H3K4me1 (clone CMA302) H3K4me1_stim_DC Histone H3K4me1 anti-H3K4me1 (clone CMA302) H3K4me1_unstim_DC Others Kdm4a anti-JmjD2-family (clone 34) JmjD2_34_stim_DC Others Kdm4d anti-JmjD2d (clone 1-7) JmjD2d_stim_DC Histone H3K9me3 anti-H3K9me3 (clone 2F3) H3K9me3_stim_3T3 Histone H3K9me3 anti-H3K9me3 (clone 2F3) H3K9me3_unstim_3T3 Histone H3K9me3 anti-H3K9me3 (clone 2F3) H3K9me3_stim_DC Histone H3K9me3 anti-H3K9me3 (clone 2F3) H3K9me3_unstim_DC Input control Input control none Pool of all samples Input Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal CH12 Histone H3K14ac Mouse monoclonal, H3K14ac_7G8 Embryonic stem cells Histone H3K14ac Mouse monoclonal, H3K14ac_13HH3_1A5.A1 Embryonic stem cells Histone H3K9ac Rabbit polyclonal, H3K9a AB4441 Embryonic stem cells Others Jun cJun cJun-ChIP_1uM Dex_LPS Others Jun cJun cJun-ChIP_LPS Others Rela p65 NF-kB/p65-ChIP_1uM Dex_LPS Others Nr3c1 Glucocorticoid Receptor GR-ChIP_1uM Dex_LPS Others Nr3c1 Glucocorticoid Receptor GR-ChIP_1uM Dex Histone H3K4me3 anti-H3K4me3 (Millipore 17-614) T-helper 2 cells Histone H3K4me1 anti-H3K4me1 (Abcam Ab8895-100) T-helper 2 cells Others Tcf7l1 TCF7L1 (M-20) 3T3-L1 cells Histone H3K4me1 H3K4me1 Neural progenitor cells RNA polymerase RNA polymerase II PolII Brg1 KD-RNA Polymerase II ChIP RNA polymerase RNA polymerase II PolII Mbd3 KD-RNA Polymerase II ChIP RNA polymerase RNA polymerase II PolII EGFP KD-RNA Polymerase II ChIP Others Mbd3 Mbd3 Brg1 KD-Mbd3 ChIP Others Mbd3 Mbd3 Tet1 KD-Mbd3 ChIP Unclassified Unclassified FBio-Ctrl_ChIPseq Others Yy1 FBio-Yy1_ChIPseq Input control Input control none Anterior trunk cells Histone H3K4me3 H3K4me3 Anterior trunk cells Histone H3K27me3 H3K27me3 Anterior trunk cells Histone H3K4me3 H3K4me3 Forebrain cells Histone H3K27me3 H3K27me3 Forebrain cells Input control Input control IgG (isotypic control antibody) Abcam; Cat. no.: ab46540 NSCs & pOLs Others Ezh2 Anti Ezh2 Diagenode (http://www.diagenode.com/en/index.php); Cat. no.: CS-039-100; Lot no.: 001 Pre-myelinating oligodendrocytes (pOLs) Others Ezh2 Anti Ezh2 Diagenode (http://www.diagenode.com/en/index.php); Cat. no.: CS-039-100; Lot no.: 001 Neural stem cells (NSCs) Others Gfi1 Gfi1 MLL-ENL immortalized bone marrow progenitor cells Histone H3K27me3 anti-H3K27me3 07-449 Megakaryocyte Progenitor Cell Line (G1ME) Histone H3K4me3 anti-H3K4me3 07-473 Megakaryocyte Progenitor Cell Line (G1ME) Others Ets1 anti-ETS1 sc-350 Megakaryocyte Progenitor Cell Line (G1ME) Others Epitope tags anti-HA sc-7392 Megakaryocyte Progenitor Cell Line (G1ME) Others Gata2 anti-GATA2 sc-9008 Megakaryocyte Progenitor Cell Line (G1ME) Others Tcf7 TCF7 goat polyclonal antibody TCF1(H18) SC8589 EML cells Others Isl1 anti-Isl1/2 (gift from Dr. T. Jessell) induced motor neurons (Day4 iNIL differentiation) Others Epitope tags anti-V5 (Abcam, ab15828, Lot: 103968) induced motor neurons (Day4 iNIL differentiation) Input control Input control None Input chromatin from IL-10 treated (4 hours) macrophages Input control Input control None Input chromatin from untreated macrophages Others Stat3 anti-STAT3 (Santa Cruz sc-482) ChIP in IL-10 treated (4 hours) macrophages against STAT3 Others Stat3 anti-STAT3 (Santa Cruz sc-482) ChIP in untreated macrophages against STAT3 RNA polymerase RNA polymerase II anti-PolII Embryonic stem cells, PolII ChIP Input control Input control mock IgG Embryonic stem cells, TBP/PolII mock Others Tbp anti-TBP ab62126 Embryonic stem cells, TBP ChIP Input control Input control mock IgG Embryonic stem cells, TAF1 mock Others Raf1 anti-RAF1 Embryonic stem cells, TAF1 ChIP Input control Input control mock IgG Embryonic stem cells, TAF3 mock Others Taf3 anti-TAF3 Embryonic stem cells, TAF3 ChIP Input control Input control None ThyDP Input control Input control None ThyDN3 Input control Input control None FLDN2b Input control Input control None FLDN2a Input control Input control None FLDN1 Others Gata3 GATA3 (Santa cruz sc-268) ThyDP Others Gata3 GATA3 (Santa cruz sc-268) FLDN2b Others Gata3 GATA3 (Santa cruz sc-268) FLDN1 Others Spi1 PU.1 (Santa cruz sc-352) ThyDP Others Spi1 PU.1 (Santa cruz sc-352) FLDN2b Others Spi1 PU.1 (Santa cruz sc-352) FLDN2a Others Spi1 PU.1 (Santa cruz sc-352) FLDN1 Histone H3K27me3 H3K27me3 (Millipore 07-449) FLDN2a Histone H3K4me2 H3K4me2 (Millipore 07-030) FLDN2a Histone H3K9K14ac H3K(9,14)Ac (Millipore 06-599) FLDN2a Others Trim28 KAP1 (RBCC) KAP1 ChIP in E14 ES cells Others Epitope tags HA HA ChIP in ES cells expressing HAZFP57 Others Epitope tags HA HA ChIP in ES cells Input control Input control none embryonal carcinoma cells Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal Spleen Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal Spleen Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal MEF Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal MEF Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal Cerebellum Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal Cortex Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal Heart Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal BoneMarrow Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal Kidney Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal Cortex Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal BoneMarrow Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal Cerebellum Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal Heart Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal Kidney Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal Liver Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal Liver Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal Lung Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal Lung Histone H3K4me1 H3K4me1 ab8895 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. rabbit polyclonal ES-Bruce4 Histone H3K4me3 H3K4me3 07-473 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. rabbit polyclonal ES-Bruce4 Histone H3K4me3 Anti- Histone H3 trimethyl Lys4 (Active Motif, Catolog # 39159) ChIP_H3K4me3_MLL4_KO_LPS_4h Histone H3K4me3 Anti- Histone H3 trimethyl Lys4 (Active Motif, Catolog # 39159) ChIP_H3K4me3_MLL4_KO_Untreated Histone H3K4me3 Anti- Histone H3 trimethyl Lys4 (Active Motif, Catolog # 39159) ChIP_H3K4me3_MLL4_HET_LPS_4h Histone H3K4me3 Anti- Histone H3 trimethyl Lys4 (Active Motif, Catolog # 39159) ChIP_H3K4me3_MLL4_HET_Untreated Others Ncaph2 CAPH2 Bethyl A302-276A Embryonic stem cells Others Ncaph2 CAPH2 Bethyl A300-275A Embryonic stem cells Input control Input control none Uninduced Id2-HPC cells, input Histone H3K4me3 H3K4me3 Id2-HPC cells induced under myeloid conditions, H3K4me3 ChIP Histone H3K4me3 H3K4me3 Id2-HPC cells induced under B-cell conditions, Cd19+, 120h, H3K4me3 ChIP Histone H3K4me3 H3K4me3 Uninduced Id2-HPC cells, 0h, H3K4me3 ChIP Others Epitope tags anti-Flag (Sigma, F1804-200UG) Chromatin IP against Flag Others Olig2 Olig2 (Millipore, ab9610) Chromatin IP against Olig2 Histone H3K36me3 H3K36me3 Mature CD8+ T cells Histone H3K4me3 H3K4me3 Mature CD8+ T cells Input control Input control none Mature CD8+ T cells Histone H3K36me3 H3K36me3 Mature CD4+ T cells Histone H3K4me3 H3K4me3 Mature CD4+ T cells Input control Input control none Mature CD4+ T cells Input control Input control none Rag2-/- thymocytes, input Histone H3K4me1 anti-H3K4me1 Rag2-/- thymocytes, anti-CD3e Ab injection, H3K4me1 ChIP Histone H3K4me1 anti-H3K4me1 Rag2-/- thymocytes, H3K4me1 ChIP Others Tcf3 anti-E2A Rag2-/- thymocytes, anti-CD3e Ab injection, E2A ChIP Others Tcf3 anti-E2A Rag2-/- thymocytes, E2A ChIP Histone H3K27me3 H3K27me3 (Millipore 07-449 lot DAM1641103) Pancreatic islets Others Mafa MafA (Abcam ab17976 lot 950583) Pancreatic islets_MafA Others Neurod1 NeuroD1 (Santa Cruz sc-1084 X lot H1709) Pancreatic islets_NeuroD1 Histone H3K9me3 H3K9me3 (Abcam ab8898 lot AP248039) Liver_H3K9me3 Unclassified Unclassified Lin et al. 2010 (Mol. Cell.) KH2 RNA polymerase RNA polymerase II anti-PolII(N20) (SantaCruz #sc-899) ES_PolII_ChIPseq Histone H3K4me1 anti-monomethyl-H3K4 (Abcam #ab8895) ES_H3K4me2_ChIPseq Histone H3K4me1 anti-monomethyl-H3K4 (Abcam #ab8895) ES_H3K4me1_ChIPseq Histone H3K27me3 anti-H3K27me3 (Upstate 07-449) ES_H3K27me3_ChIPseq Input control Input control N/A Ter119+ cells Histone H3K4me3 H3K4me3 ab8580 G1E cells Histone H3K4me3 H3K4me3 07-473 G1E cells Input control Input control N/A G1E cells Input control Input control none E12.5 heart apex. 120 hearts Others Ezh2 Ezh2 E12.5 heart apex. 120 hearts Histone H3K27me3 H3K27me3 E12.5 heart apex. 120 hearts Others Gata3 anti-Gata3 (558686, BD bioscience) T-helper 2 cells Histone H2A.Z H2A.Z Chromatin IP against H2A.Z Histone H2A.Bbd1 H2A.Lap1-2 Chromatin IP against H2A.Lap1 (technical replicate) Histone H2A.Bbd1 H2A.Lap1 Chromatin IP against H2A.Lap1 Input control Input control none G4A2: input Others Rbpj Rabbit anti RBPJ G4A2: RBPJ Chromatin IP Others Notch1 Rabbit anti Notch1 G4A2: Notch1 Chromatin IP Input control Input control none T6E: Input Others Rbpj Rabbit anti RBPJ T6E: RBPJ Chromatin IP Others Notch1 Rabbit anti Notch1 T6E: Notch1 Chromatin IP Others GFP Goat anti-GFP (kindly provided by Kevin P White, University of Chicago) adult whole heart Input control Input control IgG Runx1(Venus/+) ES cell line, IgG control Others Runx1 anti-Runx1 ab23980-100 FACS-sorted day 6 differentiated ES cells, Runx1+/VE-cadherin-/CD41+, Runx1 ChIP Others Runx1 anti-Runx1 ab23980-100 FACS-sorted day 6 differentiated ES cells, Runx1+/VE-cadherin+/CD41-, Runx1 ChIP Others Runx1 anti-Runx1 ab23980-100 FACS-sorted day 6 differentiated ES cells, Runx1+/VE-cadherin+/CD41+, Runx1 ChIP Histone H3K9me3 H3K9me3 (Active Motif, #39161, lot #170) Embyonic Stem Cell Others Ercc3 sc-293x Primary T-cells Others Gtf2f1 sc-235x Primary T-cells Others Gtf2e2 sc-238x Primary T-cells Others Gtf2b sc-225x Primary T-cells Others Gtf2a2 sc-25365x Primary T-cells Others Taf1 sc-17134x Primary T-cells Others Ets1 sc-350x Primary T-cells RNA polymerase RNA polymerase II sc-899x Primary T-cells Others Crebbp ab2832 Primary T-cells Histone H3K4me3 anti-histone 3 lysine 4 trimethylation (anti-H3K4me3) (Abcam) Lsh-/- H3K4me3 sequence Histone H3K4me3 anti-histone 3 lysine 4 trimethylation (anti-H3K4me3) (Abcam) Lsh+/+ H3K4me3 sequence Input control Input control none (Input) None Bruce4 embryonic stem cells RNA polymerase RNA polymerase II Pol2 Canvance, MMS-126R Bruce4 embryonic stem cells Others Ep300 P300 Santa Cruz, sc585 Bruce4 embryonic stem cells Histone H3K4me3 H3K4me3 Millipore, 05-745 Bruce4 embryonic stem cells Histone H3K4me1 H3K4me1 Abcam, ab8895 Bruce4 embryonic stem cells Others Ctcf CTCF Kim et al., 2007 Bruce4 embryonic stem cells Input control Input control none (Input) None Mouse embryonic fibroblast RNA polymerase RNA polymerase II Pol2 Canvance, MMS-126R Mouse embryonic fibroblast Histone H3K4me3 H3K4me3 Millipore, 05-745 Mouse embryonic fibroblast Histone H3K4me1 H3K4me1 Abcam, ab8895 Mouse embryonic fibroblast Others Ctcf CTCF Kim et al., 2007 Mouse embryonic fibroblast RNA polymerase RNA polymerase II Pol2 Canvance, MMS-126R Mouse spleen Others Ctcf CTCF Kim et al., 2007 Mouse spleen Input control Input control none (Input) None Mouse lung RNA polymerase RNA polymerase II Pol2 Canvance, MMS-126R Mouse lung Others Ep300 P300 Santa Cruz, sc585 Mouse lung Histone H3K4me3 H3K4me3 Millipore, 05-745 Mouse lung Histone H3K4me1 H3K4me1 Abcam, ab8895 Mouse lung Others Ctcf CTCF Kim et al., 2007 Mouse lung Input control Input control none (Input) None Mouse liver RNA polymerase RNA polymerase II Pol2 Canvance, MMS-126R Mouse liver Others Ep300 P300 Santa Cruz, sc585 Mouse liver Histone H3K4me3 H3K4me3 Millipore, 05-745 Mouse liver Histone H3K4me1 H3K4me1 Abcam, ab8895 Mouse liver Others Ctcf CTCF Kim et al., 2007 Mouse liver Input control Input control none (Input) None Mouse kidney RNA polymerase RNA polymerase II Pol2 Canvance, MMS-126R Mouse kidney Others Ep300 P300 Santa Cruz, sc585 Mouse kidney Histone H3K4me3 H3K4me3 Millipore, 05-745 Mouse kidney Histone H3K4me1 H3K4me1 Abcam, ab8895 Mouse kidney Others Ctcf CTCF Kim et al., 2007 Mouse kidney Input control Input control none (Input) None Mouse heart RNA polymerase RNA polymerase II Pol2 Canvance, MMS-126R Mouse heart Others Ep300 P300 Santa Cruz, sc585 Mouse heart Histone H3K4me3 H3K4me3 Millipore, 05-745 Mouse heart Histone H3K4me1 H3K4me1 Abcam, ab8895 Mouse heart Others Ctcf CTCF Kim et al., 2007 Mouse heart Input control Input control none (Input) None Mouse cerebellum RNA polymerase RNA polymerase II Pol2 Canvance, MMS-126R Mouse cerebellum Histone H3K4me3 H3K4me3 Millipore, 05-745 Mouse cerebellum Histone H3K4me1 H3K4me1 Abcam, ab8895 Mouse cerebellum Others Ctcf CTCF Kim et al., 2007 Mouse cerebellum Input control Input control none (Input) None Mouse bone marrow RNA polymerase RNA polymerase II Pol2 Canvance, MMS-126R Mouse bone marrow Histone H3K4me3 H3K4me3 Millipore, 05-745 Mouse bone marrow Histone H3K4me1 H3K4me1 Abcam, ab8895 Mouse bone marrow Others Ctcf CTCF Kim et al., 2007 Mouse bone marrow Input control Input control none (Input) None Mouse cortex RNA polymerase RNA polymerase II Pol2 Canvance, MMS-126R Mouse cortex Histone H3K4me3 H3K4me3 Millipore, 05-745 Mouse cortex Histone H3K4me1 H3K4me1 Abcam, ab8895 Mouse cortex Others Ctcf CTCF Kim et al., 2007 Mouse cortex Histone H4K12ac anti-H4K12Ac 07-595 C2C12 myotubes differentiated for 96h Histone H4K12ac anti-H4K12Ac 07-595 Growing C2C12 myoblasts Histone H3K18ac anti-H3K18Ac ab1191 C2C12 myotubes differentiated for 96h Histone H3K18ac anti-H3K18Ac ab1191 Growing C2C12 myoblasts Histone H3K9ac anti-H3K9Ac ab4441 C2C12 myotubes differentiated for 96h Histone H3K9ac anti-H3K9Ac ab4441 Growing C2C12 myoblasts Histone H3K36me3 anti-H3K36me3 ab9050 C2C12 myotubes differentiated for 96h Histone H3K36me3 anti-H3K36me3 ab9050 Growing C2C12 myoblasts Histone H3K27me3 anti-H3K27me3 ab6002 C2C12 myotubes differentiated for 96h Histone H3K27me3 anti-H3K27me3 ab6002 Growing C2C12 myoblasts Histone H3K4me3 anti-H3K4me3 ab8580 C2C12 myotubes differentiated for 96h Histone H3K4me3 anti-H3K4me3 ab8580 Growing C2C12 myoblasts Histone H3K4me2 anti-H3K4me2 ab32356 C2C12 myotubes differentiated for 96h Histone H3K4me2 anti-H3K4me2 ab32356 Growing C2C12 myoblasts Histone H3K4me1 anti-H3K4me1 ab8895 C2C12 myotubes differentiated for 96h Histone H3K4me1 anti-H3K4me1 ab8895 Growing C2C12 myoblasts RNA polymerase RNA polymerase II anti-RnaPol2 8WG16 C2C12 myotubes differentiated for 96h RNA polymerase RNA polymerase II anti-RnaPol2 8WG16 Growing C2C12 myoblasts Histone H3K79me2 H3K79me2 murine L-GMP Histone H3K79me2 H3K79me2 murine GMP Histone H3K79me2 H3K79me2 murine HSC Histone H3K36me3 H3K36me3 murine L-GMP Histone H3K36me3 H3K36me3 murine GMP Histone H3K36me3 H3K36me3 murine HSC Histone H3K27me3 H3K27me3 murine L-GMP Histone H3K27me3 H3K27me3 murine GMP Histone H3K27me3 H3K27me3 murine HSC Histone H3K4me3 H3K4me3 murine L-GMP Histone H3K4me3 H3K4me3 murine GMP Histone H3K4me3 H3K4me3 murine HSC Others Ep300 p300 Control liver Others Ep300 p300 Mutant liver Others Crebbp CBP Control liver Others Crebbp CBP Mutant liver Others Cbx5 HP1 Mutant liver Others Cbx5 HP1 Control liver Others Sox2 Sox2 produced in-house 2TS22C ES cells, +Tet, Day 2 Others Sox2 Sox2 produced in-house ZHBTc4 ES cells, +Tet, Day 4 Others Sox2 Sox2 produced in-house ZHBTc4 ES cells, +Tet, Day 3 Others Sox2 Sox2 produced in-house ZHBTc4 ES cells, +Tet, Day 2 Others Sox2 Sox2 produced in-house ZHBTc4 ES cells, +Tet, Day 1 Others Sox2 Sox2 produced in-house ZHBTc4 ES cells, untreated Others 5-hmC rabbit anti-5hmC antibody 39769 ES cells, Tet1 shRNA2863, hMeDIP Input control Input control none ES cells, Tet1 shRNA2863, input Others 5-hmC rabbit anti-5hmC antibody 39769 ES cells, Luc shRNA, hMeDIP Input control Input control none ES cells, Luc shRNA, input Others 5-hmC rabbit anti-5hmC antibody 39769 ES cells, hMeDIP Others Tet1 rabbit polyclonal antibody against mouse Tet1 (made in-house) ES cells, Tet1 ChIP Others Tet1 ES cells, Tet1 CXXC mutant2 Others Tet1 ES cells, Tet1 CXXC mutant1 Others Tet1 ES cells, Tet1 CXXC Input control Input control none Kdm5a f/f ES cells Others Kdm5a 1416 (Benevolenskaya et al.,Mol Cell 18, 623-635) Kdm5a KO ES cells Histone H3K4me3 anti-H3K4me3 07-473 Embryonic stem cells Others Dpy30 anti-Dpy-30 Embryonic stem cells Histone H3K4me2 H3K4me2 Terminally differentiated Neurons (TN) Input control Input control none Embryonic Stem Cells (ESCs) Histone H3K4me2 H3K4me2 Embryonic Stem Cells (ESCs) Input control Input control n/a Preadipocyte cell line Others Rxra RXR Preadipocyte cell line Others Stat5a Stat5a Preadipocyte cell line Others Nr3c1 GR Preadipocyte cell line Histone H3K27me3 anti-H3K27me3 (07-499; Millipore) Th1 cells H3K27me3 ChIP-seq Histone H3K27me3 anti-H3K27me3 (07-499; Millipore) Dendritic cells H3K27me3 ChIP-seq Others Rest REST Upstate 07-574 Embyonic stem cells Input control Input control none 266.6 Pancreatic Cells Others Ptf1a Ptf1a (Beta Cell Biology Consortium) 266.6 Pancreatic Cells Others Rad21 Rad21 Rad21 ChIP DNA from Pro-B cells Others Ctcf CTCF Ctcf ChIP DNA from Mature B cells Others Ctcf CTCF Ctcf ChIP DNA from Pro-B cell Rag2-/- cells Others Ctcf CTCF Ctcf ChIP DNA from DP T wt cells Others Stat5b STAT5B Th1 cell Others Stat5a STAT5A Th1 cell Others Stat4 STAT4 Th1 cell Input control Input control IgG Th1 cell Others Ncor1 anti-NCoR Bcl6 knockout primary bone marrow-derived macrophages Others Ncor2 anti-SMRT Bcl6 knockout primary bone marrow-derived macrophages Others Ncor1 anti-NCoR wild-type primary bone marrow-derived macrophages Others Ncor2 anti-SMRT wild-type primary bone marrow-derived macrophages Input control Input control None Negative control- input DNA, no immunoprecipitation Others Smarca4 BRG (J1 antibody described in Genes Dev. 1996 Sep 1;10(17):2117-30, PubMed ID: 8804307) Chromatin IP against BRG1, stimulated Th17 Others Smarca4 BRG (J1 antibody described in Genes Dev. 1996 Sep 1;10(17):2117-30, PubMed ID: 8804307) Chromatin IP against BRG1, stimulated Th2 Others Smarca4 BRG (J1 antibody described in Genes Dev. 1996 Sep 1;10(17):2117-30, PubMed ID: 8804307) Chromatin IP against BRG1, stimulated Th1 Others Smarca4 BRG (J1 antibody described in Genes Dev. 1996 Sep 1;10(17):2117-30, PubMed ID: 8804307) Chromatin IP against BRG1, resting Th2 Others Smarca4 BRG (J1 antibody described in Genes Dev. 1996 Sep 1;10(17):2117-30, PubMed ID: 8804307) Chromatin IP against BRG1, resting Th1 Others Smarca4 BRG (J1 antibody described in Genes Dev. 1996 Sep 1;10(17):2117-30, PubMed ID: 8804307) Chromatin IP against BRG1, uNaive Others Ets1 Ets1 (santa cruz, cat#sc111X, Lot#G1905) T-helper 2 cells Others Fli1 Fli1 (santa cruz, cat#sc356X, Lot#L0407) T-helper 2 cells Others Epitope tags anti-Flag F3165 C2C12 cells expressing Flag-Msx1, Flag ChIP Others Epitope tags anti-Flag F3165 C2C12 cells infected with empty vector, Flag ChIP Histone H4K20me3 H4K20me3 AB9053 Embryonic stem cells, H4K20me3 ChIP Others Atf7ip MCAF1 A300-169A Embryonic stem cells, MCAF1 ChIP Others Rest REST 07-579 Embryonic stem cells, REST ChIP Others Rnf2 Ring1b Embryonic stem cells, Ring1b ChIP RNA polymerase RNA polymerase II RNA Pol II (Rpb1 N-terminus) SC-899 Embryonic stem cells, control knockdown, total RNA pol2 ChIP RNA polymerase RNA polymerase II RNA Pol II (Rpb1 N-terminus) SC-899 Embryonic stem cells, NelfE knockdown, total RNA pol2 ChIP RNA polymerase RNA polymerase II RNA Pol II (Rpb1 N-terminus) SC-899 Embryonic stem cells, Spt5 knockdown, total RNA pol2 ChIP RNA polymerase RNA polymerase II RNA Pol II (Rpb1 N-terminus) SC-899 Embryonic stem cells, Spt4 knockdown, total RNA pol2 ChIP Histone H3K9me3 H3K9me3 AB8898 Mouse embryonic fibroblasts with Dox-inducible Klf4, Sox2 and Oct4 (KSO), H3K9me3 ChIP Histone H3K4me3 H3K4me3 AB8580 Mouse embryonic fibroblasts, H3K4me3 ChIP Histone H3K9me3 H3K9me3 AB8898 Mouse embryonic fibroblasts, H3K9me3 ChIP Histone H3K27me3 H3K27me3 AB6002 Mouse embryonic fibroblasts, H3K27me3 ChIP Input control Input control none Liver cells Others Stat5a mixture of STAT5a (PA-ST5A: R&D) and STAT5b (PA-ST5B: R&D) antibodies, 2 ul each per IP primary CD4+ T cells from spleen and lymph nodes Others Stat3 5 ug of STAT3 (14-6727: eBioScience) per IP primary CD4+ T cells from spleen and lymph nodes Others Epitope tags anti-FLAG antibody (Sigma) SYTSSX2_FLAG_ChIP Input control Input control IgG antibody (Abcam) Control_IgG_ChIP Others Rad21 Rad21 (Millipore #ab992) Rad21 ChIP Others Ctcf CTCF (Millipore 07-729) CTCF ChIP Input control Input control IgG Bone marrow hematopoietic progenitor cells enriched by depletion of Lin+ cells Others Gata2 anti-Gata2 Bone marrow hematopoietic progenitor cells enriched by depletion of Lin+ cells Others Tal1 anti-Scl/Tal1 Bone marrow hematopoietic progenitor cells enriched by depletion of Lin+ cells Others Ldb1 anti-Ldb1 Bone marrow hematopoietic progenitor cells enriched by depletion of Lin+ cells Input control Input control none Uninduced MEFs Histone H3K36me3 H3K36me3 Uninduced MEFs Histone H3K4me3 H3K4me3 Uninduced MEFs Histone H3K4me1 H3K4me1 Uninduced MEFs Histone H3K27me3 H3K27me3 Uninduced MEFs Histone H3K4me2 H3K4me2 Uninduced MEFs Input control Input control NA Mouse Embryonic Stem Cells RNA polymerase RNA polymerase II Pol2-S2P (Abcam H5 clone ab24758) Day2+8hrs post-RA exposure Histone H3K4me3 anti-H3K4me3 (07-473; Millipore) Th1 cells H3K4me3 ChIP-seq Histone H3K4me3 anti-H3K4me3 (07-473; Millipore) Dendritic cells H3K4me3 ChIP-seq Others Pparg PPARgamma sc-7196X Mouse 3T3-L1 Adipocyte Culture RNA polymerase RNA polymerase II anti-RNA Pol II Terminally differentiated Neurons (TN) Histone H3K4me2 anti-H3K4me2 Terminally differentiated Neurons (TN) RNA polymerase RNA polymerase II anti-RNA Pol II Neuronal Progenitor (NP) Cells Histone H3K4me2 anti-H3K4me2 Neuronal Progenitor (NP) Cells Input control Input control none (input) Embryonic Stem Cells (ESCs) RNA polymerase RNA polymerase II anti-RNA Pol II Embryonic Stem Cells (ESCs) Histone H3K4me2 anti-H3K4me2 Embryonic Stem Cells (ESCs) Input control Input control Goat IgG isotype control ESC Others Yy1 YY1 sc-1703 Neural Progenitor Cells Others Yy1 YY1 sc-1703 Embryonic Stem Cells Histone H3K4me1 Rabbit polyclonal to Histone H3K4me1, Abcam, Catalog ab8895 (lot 721955) mouse ES cells Unclassified Unclassified mouse ES cells Histone H3K36me3 H3K36Me3 mammary epithelial cells Histone H3K36me3 H3K36Me3 mammary gland Histone H3K36me3 H3K36Me3 liver Others Crebbp rabbit polyclonal Cbp antibody BM-HPC cell line Input control Input control rabbit IgG BM-HPC cell line Histone H3K4me2 H3K4me2 mammary epithelial cells Histone H3K4me2 H3K4Me2 liver Unclassified Unclassified myoblasts Others Pax3 myoblasts with TAP tagged Pax3 Others Pax7 myoblasts with TAP tagged Pax7 Input control Input control IgG ctrl embryonic stem cells Others Sin3a Sin3A from Santa Cruz embryonic stem cells Others Sin3a Sin3A from Abcam embryonic stem cells Histone H3K4me3 H3K4me3 DC Input control Input control control (empty vector) control C3H10T1/2 fibroblasts with empty vector, forced to undergo myogenic differentiation by expression of MyoD Input control Input control control (empty vector) control myotubes with empty vector, 48h in differentiating medium Input control Input control control (empty vector) control myocytes with empty vector, 10h in differentiating medium Input control Input control control (empty vector) control cycling myoblasts with empty vector Others Myod1 MyoD ChIP C3H10T1/2 fibroblasts with TAP tagged MyoD, forced to undergo myogenic differentiation by expression of MyoD Others Myod1 MyoD ChIP myotubes with TAP tagged MyoD, 48h in differentiating medium Others Myod1 MyoD ChIP myocytes with TAP tagged MyoD, 10h in differentiating medium Others Myod1 MyoD ChIP cycling myoblasts with TAP tagged MyoD Others Myf5 Myf5 ChIP cycling myoblasts with TAP tagged Myf5 Histone H3K4me3 H3K4me3 (ab8580, Abcam, MA) CD4+ T cells Histone H3ac pan-H3Ac (Millipore, 06-599) CD4+ T cells Others Stat3 phospho-Stat3 (14-6727, ebiosciences, CA) CD4+ T cells Input control Input control none (input) Mouse villus Others Cdx2 CDX2 Mouse villus Others Rnf2 Ring1B Embryonic stem cells Histone H3K27me3 anti-H3K27me3 tissue Spleen FFPE sections of leukemic blasts-injected mice, H3K27me3 ChIP Input control Input control none tissue Spleen FFPE sections of leukemic blasts-injected mice, input Histone H3K27me3 anti-H3K27me3 cells Cells isolated from the spleen of leukemic blasts-injected mice, H3K27me3 ChIP Input control Input control none cells Cells isolated from the spleen of leukemic blasts-injected mice, input Histone H3K4me3 anti-H3K4me3 tissue Spleen FFPE sections of leukemic blasts-injected mice, H3K4me3 ChIP Histone H3K4me3 anti-H3K4me3 cells Cells isolated from the spleen of leukemic blasts-injected mice, H3K4me3 ChIP RNA polymerase RNA polymerase II RNA Pol II (8WG16) Covance MMS-126R Mouse Embryonic Fibroblasts with Dox-inducible Klf4, Sox2 and Oct4 (KSO) Histone H3K27me3 H3K27me3 Abcam AB6002 Mouse Embryonic Fibroblasts with Dox-inducible Klf4, Sox2 and Oct4 (KSO) Others E2f4 E2F4 Santa Cruz SC-1082 Mouse Embryonic Fibroblasts with Dox-inducible Klf4, Sox2 and Oct4 (KSO) Input control Input control input DNA liver Histone H3K4me3 H3K4me3 07-473 liver Input control Input control input DNA adult testis Histone H3K4me3 H3K4me3 07-473 adult testis Input control Input control input DNA and IgG pups testis Input control Input control input DNA and IgG adult testis Histone H3K4me1 H3K4me1 Abcam AB8895 iPS cells Histone H3 H3 Abcam AB1791 mouse embryonic fibroblasts Histone H3K4me1 H3K4me1 Abcam AB8895 mouse embryonic fibroblasts Input control Input control none proB cells Histone H3K4me3 H3K4me3 Abcam AB8580 proB cells Histone H3 H3 Abcam AB1791 proB cells Histone H3K27ac H3K27ac Abcam AB4729 proB cells Histone H3K4me1 H3K4me1 Abcam AB8895 proB cells Input control Input control none Whole Liver Histone H3K4me3 H3K4me3 Abcam AB8580 Whole Liver Histone H3 H3 Abcam AB1791 Whole Liver Histone H3K27ac H3K27ac Abcam AB4729 Whole Liver Histone H3K4me1 H3K4me1 Abcam AB8895 Whole Liver Histone H3K27ac H3K27ac Abcam AB4729 Neural progenitors Others Rfx1 Rfx1 Santa Cruz s.c. 10562X Neural progenitors Histone H3K4me3 H3K4me3 Abcam AB8580 Embyonic stem cells Histone H3 H3 Abcam AB1791 Embyonic stem cells RNA polymerase RNA polymerase II PolII Abcam (4H8) ab5408 ActivatedBCell_PolII Others Aicda AID Rabbit polyclonal described in Chaudhuri et al., Nature (2003) ActivatedBCell_AID Input control Input control none mouse embryonic fibroblast Others Nelfb anti-Nelf-b (purified polyclonal) mouse embryonic fibroblast Input control Input control Goat IgG isotype control 005-000-003 EB Input control Input control Goat IgG isotype control 005-000-003 ESC Others GFP goat-anti-eGFP, raised against His-tagged full-length eGFP and affinity-purified with GST-tagged full-length eGFP EB Others Tbp TBP (Santa Cruz sc-204, LOT H0508) RAW264.7 cells Input control Input control IgG Adult(P56)_Cerebellum Input control Input control IgG PostNatal-Day15_Cerebellum Input control Input control IgG PostNatal-Day5_Cerebellum Input control Input control IgG PostNatal-Day0_Cerebellum Histone H3K27me3 anti-H3K27me3 Adult(P56)_Cerebellum Histone H3K27me3 anti-H3K27me3 PostNatal-Day15_Cerebellum Histone H3K27me3 anti-H3K27me3 PostNatal-Day5_Cerebellum Histone H3K27me3 anti-H3K27me3 PostNatal-Day0_Cerebellum Histone H3K4me3 anti-H3K4me3 Adult(P56)_Cerebellum Histone H3K4me3 anti-H3K4me3 PostNatal-Day15_Cerebellum Histone H3K4me3 anti-H3K4me3 PostNatal-Day5_Cerebellum Histone H3K4me3 anti-H3K4me3 PostNatal-Day0_Cerebellum RNA polymerase RNA polymerase II anti-RNAP-II Adult(P56)_Cerebellum RNA polymerase RNA polymerase II anti-RNAP-II PostNatal-Day15_Cerebellum RNA polymerase RNA polymerase II anti-RNAP-II PostNatal-Day5_Cerebellum RNA polymerase RNA polymerase II anti-RNAP-II PostNatal-Day0_Cerebellum Others Myod1 MyoD F-3165 Embryonic stem cells Histone H3 anti-H3 AB1791 myotubes Histone H3 anti-H3 AB1791 pro-B cell Input control Input control polyclonal rabbit IgG Th2 cells, IgG Histone H3Kac anti-H3KAc Th2 cells, H3KAc Input control Input control None MDER cells Histone H3K9me3 H3K9me3 AB8898 MDER cells Histone H3K4me3 H3K4me3 AB8580 MDER cells Histone H3K27me3 H3K27me3 AB6002 MDER cells Input control Input control rabbit IgG negative control mouse B cells Others Ash2l ASH2 mouse B cells Others Wdr5 WDR5-FL F3165 ES cell Others Wdr5 Wdr5 A302-429A ES cell Others Rbbp5 Rbbp5 not applicable ES cell Others Pou5f1 Oct4 sc8628 ES cell Histone H3K4me3 H3K4me3 17-614 ES cell Input control Input control Rabbit IgG, Millipore, 12-371 IgG.s_5 Histone H3K4me3 Histone H3 (tri methyl K4) AB8580 H3K4me3.rep2.s_4 Histone H3K4me3 Histone H3 (tri methyl K4) AB8580 H3K4me3.rep1.s_3 Histone H3K4me1 Histone H3 (mono methyl K4) AB8895 H3K4me1.rep2.s_2 Histone H3K4me1 Histone H3 (mono methyl K4) AB8895 H3K4me1.rep1.s_1 Input control Input control none Atoh1.control Others Epitope tags ANTI-FLAG BioM2 F9291 Atoh1.rep2 Others Epitope tags ANTI-FLAG BioM2 F9291 Atoh1.rep1 Input control Input control none C2C12 myoblasts Input control Input control None None Embyonic stem cells Others Med12 Med12 Bethyl A300-774A Mouse embryonic fibroblasts Others Smc1a Smc1 Bethyl A300-055A-1 Embyonic stem cells Others Smc1a Smc1 Bethyl A300-055A Embyonic stem cells Unclassified Unclassified Mouse embryonic day 11.5 (e11.5) heart Others Ep300 p300 mouse ES cells Others Chd7 CHD7 mouse ES cells Others Ep300 P300 antibody (Santa Cruz, catalog# sc-585x, lot# c0509) HL-1 cells Histone H3K4me3 H3K4me3 07-474 Embryonic stem cells Input control Input control None Mouse embryonic fibroblasts Others Atrx ATRX H300 (Santa Cruz Biotechnology, batch G0105) Mouse Embryonic Stem Cells Input control Input control none Lymphoid cell Others Tcf3 E2A.E12(V-18) (sc-349) A12 (E2A-/- T cell) Others Ctcf CTCF (07-729), DAM1421463 RAG1-/- pro-B cell Others Foxo1 FKHR (H-128) (sc-11350) RAG1-/- pro-B cell Others Ebf1 EBF (H00001879-M01), 08344-1C2 RAG1-/- pro-B cell Histone H3K4me1 H3K4me1 (ab8895) EBF-/- pre-pro-B cell Input control Input control Normal Rabbit Serum<Upstate#12-370> primary CD4+ T cells from spleen and lymph nodes Input control Input control N/A Murine erythroleukemia (MEL) cells stably transfected with Gata-1 fused to ER Others Epitope tags anti-V5 (Abcam, ab15828) Day5 motor neurons RNA polymerase RNA polymerase II RNA Pol II (Ser7 phospho CTD) Embyonic stem cells Input control Input control -- 6hr_Input Input control Input control -- 240hr_Input Input control Input control -- 24hr_Input Input control Input control -- 0hr_Input Others Nr3c1 GR (Santa Cruz Biotechnologies, sc-1004; and Affinity BioReagents, PA1-511A) Chromatin IP against GR Others Stat3 Phospho-STAT3(Ser727) 9134 in vitro polarized Th17 T cells Input control Input control none, input Input RNA polymerase RNA polymerase II Pol II (8WG16) sc-56767 PMWT_227 Others Rxra RXRa (D-20) sc-553 RMWT_227 Others Rxra RXRa (D-20) sc-553 RMWT_315 RNA polymerase RNA polymerase II Pol II (8WG16) sc-56767 PMWT_315 RNA polymerase RNA polymerase II Pol II (8WG16) sc-56767 PFWT_235 Others Rxra RXRa (D-20) sc-553 RFWT_235 Others Rxra RXRa (D-20) sc-553 RFWT_234 RNA polymerase RNA polymerase II Pol II (8WG16) sc-56767 PFWT_234 Others Rxra RXRa (D-20) sc-553 RMKO_314 RNA polymerase RNA polymerase II Pol II (8WG16) sc-56767 PMKO_314 RNA polymerase RNA polymerase II Pol II (8WG16) sc-56767 PMKO_225 Others Rxra RXRa (D-20) sc-553 RMKO_225 Others Rxra RXRa (D-20) sc-553 RFKO_233 RNA polymerase RNA polymerase II Pol II (8WG16) sc-56767 PFKO_233 Others Rxra RXRa (D-20) sc-553 RFKO_232 RNA polymerase RNA polymerase II Pol II (8WG16) sc-56767 PFKO_232 Others Biotin Streptavidin (NanoLink Streptavidin Magnetic Microspheres (Vendor: SoluLink, cat# M1002-010, lot# LM041609)) BirA RAW264.7 cells Others Nr1h2 Biotin-tagged LXRb bound to NanoLink Streptavidin Magnetic Microspheres (Vendor: SoluLink, cat# M1002-010, lot# LM041609) BirA/BLRP-LXRb RAW264.7 cells Histone H3K4me1 H3K4me1 (Vendor: Abcam, cat# ab8895, lot# 721955) PU.1-/- myloid cell Histone H3K4me1 H3K4me1 (Vendor: Abcam, cat# ab8895, lot# 721955) resting splenic B cells Histone H3K4me1 H3K4me1 (Vendor: Abcam, cat# ab8895, lot# 721955) thioglycollate-elicited peritoneal macrophages RNA polymerase RNA polymerase II anti-RNA Polymerase II (ab817; Abcam) ES cells Histone H3K4me3 anti-H3K4me3 (ab8580; Abcam) ES cells Others Pparg PPARG (81B1) Call Signaling Technologies, Cat# 2443, Lot# 5/29/2007 3T3-L1 Others Pparg PPARG (H-100) SCBT, Cat# SC-7196X, Lot# A0380 3T3-L1 Input control Input control None None 3T3-L1, Whole Cell Extract (input control) Histone H3K4me2 H3K4me2 Embyonic stem cells Others Kdm1a LSD1 Embyonic stem cells Input control Input control IgG Embyonic stem cells Histone H3K9ac H3K9Ace 3T3-L1 Histone H3K9ac H3K9Ace primary macrophage Others Cebpb C/EBPbeta primary macrophage Others Spi1 PU.1 primary macrophage Others Pparg PPARgamma 3T3-L1 Others Pparg PPARgamma primary macrophage Input control Input control none cerebellum Input control Input control none differentiated 3T3-L1 cells Input control Input control none liver hepatocytes Others Sirt1 Sirt1 cerebellum Others E2f4 E2F4 differentiated 3T3-L1 cells Others Cebpa C/EBPalpha differentiated 3T3-L1 cells Others Ep300 p300 differentiated 3T3-L1 cells Others E2f4 E2F4 liver hepatocytes Others Foxa1 FOXA1 liver hepatocytes Others Foxa2 FOXA2 liver hepatocytes Others Cebpa C/EBPalpha liver hepatocytes Others Ep300 p300 liver hepatocytes Histone H3K4me3 anti-H3K4me3 Chromatin IP against H3K4me3 Input control Input control none pre B-cells, input Others Ebf1 anti-EBF1b pre B-cells, ChIP Input control Input control none Day3, seq Input control Input control none Day2 pre-RA, seq Others Rara RAR sc-773 Day2+8hrs post-RA exposure, ChIP-seq Others Rara RAR sc-773 Day2 pre-RA, ChIP-seq Histone H3ac H3ac mouse cardiomyocytes (HL1-cells) Others Srf Srf mouse cardiomyocytes (HL1-cells) Input control Input control IgG Retina, wt, IgG ChIP Others Gata3 anti-Gata3 (558686, BD bioscience) Natural Killer T cells Others Gata3 anti-Gata3 (558686, BD bioscience) Nave regulatory T cells Others Gata3 anti-Gata3 (558686, BD bioscience) Inducible regulatory T cells Others Gata3 anti-Gata3 (558686, BD bioscience) T-helper 17 cells Others Gata3 anti-Gata3 (558686, BD bioscience) Unstimulated T-helper 2 cells Others Gata3 anti-Gata3 (558686, BD bioscience) T-helper 1 cells Others Gata3 anti-Gata3 (558686, BD bioscience) Nave CD4 cells Others Gata3 anti-Gata3 (558686, BD bioscience) Double negative cells Input control Input control none Primary bone marrow-derived macrophages (BMDM) from Fvb mice, untreated, input RNA polymerase RNA polymerase II RNA polymerase II CTD repeat YSPTSPS (phospho S5) Abcam (ab5131) Primary bone marrow-derived macrophages (BMDM) from Fvb mice, 2hrs LPS, ChIP RNA polymerase RNA polymerase II RNA polymerase II CTD repeat YSPTSPS (phospho S5) Abcam (ab5131) Primary bone marrow-derived macrophages (BMDM) from Fvb mice, untreated, ChIP Unclassified Unclassified Whole Brain Others Kdm2a KDM2A Embryonic stem cells Histone H3K4me3 H3K4me3 (AB8580 Abcam) Whole Brain Others Cxxc1 CFP1 (Sc-25391 Santa Cruz) Whole Brain RNA polymerase RNA polymerase II RNA Polymerase II (Unmodified - AB817 - Abcam) Whole Brain Input control Input control no antibody mouse embryonic fibroblasts (MEF) Others Ctr9 Ctr9 V6.5 mES cells Others Supt5 Spt5 V6.5 mES cells Others Nelfa NelfA V6.5 mES cells RNA polymerase RNA polymerase II RNA Pol II (Ser2 phospho CTD) V6.5 mES cells RNA polymerase RNA polymerase II RNA Pol II (Ser5 phospho CTD) V6.5 mES cells Input control Input control anti-HA (12CA5) control. No HA epitope in untagged ES cells Embryonic stem cells Histone H3K27me3 H3K27me3 (Upstate/Millipore #07-449) Embryonic stem cells RNA polymerase RNA polymerase II anti-RNAPII_Ser5p (CTD4H8) Neural progenitor cells Histone H3K4me1 anti-H3K4me1 Neural progenitor cells RNA polymerase RNA polymerase II anti-RNAPII_Ser5p (CTD4H8) Embryonic stem cells Histone H3K4me1 anti-H3K4me1 Embryonic stem cells RNA polymerase RNA polymerase II Pol_II primary bone marrow-derived macrophages Input control Input control n/a (input_DNA) primary bone marrow-derived macrophages Input control Input control IgG primary bone marrow-derived macrophages Others Mtf2 PCL2 (MTF2) Undifferentiated mouse embryonic stem cells Input control Input control none Embryonic stem cells (total chromatin) Others Kdm5a Jarid1a Embryonic stem cells (chromatin IP fraction) Others Suz12 Suz12 Embryonic stem cells (chromatin IP fraction) Others Ezh2 Ezh2 Embryonic stem cells (chromatin IP fraction) Others Jarid2 Jarid2 Embryonic stem cells (chromatin IP fraction) Others Jarid2 Jarid2 Embryonic Stem cells Others Mtf2 MTF2 Embryonic Stem cells Unclassified Unclassified GIgG B cells Unclassified Unclassified GIgG murine CD4+ T Input control Input control IgG B cells Others Gata1 GATA-1 MEL86 erythroid cell line expressing metabolically biotinylated GATA-1 (MEL Bio-GATA-1) Histone H3K9me3 anti-H3K9Me3 antibody embryonic stem cells, Eset shRNA Histone H3K9me3 anti-H3K9Me3 antibody embryonic stem cells, control shRNA Others Setdb1 rabbit polyclonal anti-Eset antibody embryonic stem cells, unperturbed Input control Input control WCE V6.5 mES cells Input control Input control None Chromatin input as control Others Gata1 GATA1 Chromatin IP against GATA1 Others Kdm6b jmjd3 mouse bone marrow-derived macrophages Others Epitope tags Flag M2 Embyonic stem cells Input control Input control Rabbit control IgG Others Smarca4 anti-Brg/Brm Clone J1 Others Sox2 Sox2 Others Pou5f1 Oct4 Others Suz12 SUZ12 Others Rnf2 RING1B Others Ezh2 EZH2 RNA polymerase RNA polymerase II RNAP2 Others Stat1 source Deckers_lab_May2015_STAT1_Y701F_IFNb Others Stat1 source Deckers_lab_May2015_STAT1_KO_IFNb Others Stat1 source Deckers_lab_May2015_STAT1_KO_untreated Others Stat1 source Deckers_lab_May2015_STAT1_Y701F_untreated Unclassified Unclassified source do607 Unclassified Unclassified source do178 Unclassified Unclassified source WL9 Unclassified Unclassified source do39 Unclassified Unclassified source WL123 Unclassified Unclassified source WL135 Unclassified Unclassified source do349 Unclassified Unclassified source do302 Unclassified Unclassified source WL132 Unclassified Unclassified source WL124 Unclassified Unclassified source WL16 Unclassified Unclassified source do71 Unclassified Unclassified source do352 Unclassified Unclassified source WL134 Unclassified Unclassified source WL122 Unclassified Unclassified source WL121 Others Kdm1a source Lsd1 rep1 Others Esrrb source Esrrb rep4 Input control Input control source Esrrb igg control rep1 Others Nr0b1 source Dax1 rep1 Input control Input control source Esrrb igg control rep2 Others Esrrb source Esrrb rep1 Others Esrrb source Esrrb rep2 Others Esrrb source Esrrb rep5 Input control Input control source Dax1/Lsd1 igg control Others Esrrb source Esrrb rep3 Unclassified Unclassified ERS724780 Others Foxa1 source Foxa1_ChIP_A Input control Input control source Input Others Foxa2 source Foxa2_ChIP_A Others Foxa1 source Foxa1_ChIP_B Others Foxa2 source Foxa2_ChIP_B Histone H3K4me3 source H3K4me3_M1_3 Histone H3K4me3 source H3K4me3_M1Salt_3 Histone H3K4me3 source H3K4me3_M1Salt_2 Histone H3K4me3 source H3K4me3_M1_2 Histone H3K4me3 source H3K4me3_M1Salt_1 Histone H3K4me3 source H3K4me3_M1_1 Histone H3K4me3 source H3K4me3_Salt_1 Histone H3K4me3 source H3K4me3_M2_2 Histone H3K4me3 source H3K4me3_control_1 Histone H3K4me3 source H3K4me3_M2Salt_2 Histone H4ac source H4ac_control_1 Histone H4ac source H4ac_M2_1 Histone H4ac source H4ac_M2_2 Histone H4ac source H4ac_control_2 Histone H4ac source H4ac_M2Salt_2 Histone H4ac source H4ac_M2Salt_1 Histone H4ac source H4ac_Salt_2 Histone H3K4me3 source H3K4me3_M2Salt_1 Histone H4ac source H4ac_Salt_1 Histone H3K4me3 source H3K4me3_M2_1 Unclassified Unclassified source mouse 22 pancreas Unclassified Unclassified source mouse 16 pancreas Input control Input control source IgG Control Others Phf13 source Spoc1 ChIP-seq Unclassified Unclassified source Sample 3 Unclassified Unclassified source Sample 1 Unclassified Unclassified source Sample 4 Unclassified Unclassified source Sample 2 RNA polymerase RNA polymerase II source Deckers_lab_Sep2014_Pol2_HKL RNA polymerase RNA polymerase II source Deckers_lab_Sep2014_Pol2_IFNb RNA polymerase RNA polymerase II source Deckers_lab_Sep2014_Pol2_HKL_IFNb RNA polymerase RNA polymerase II source Deckers_lab_Sep2014_Pol2_untreated Others Nfkb1 source Deckers_lab_Sep2014_NFkB_untreated Others Stat1 source Deckers_lab_Sep2014_STAT1_IFNb Others Stat1 source Deckers_lab_Sep2014_STAT1_untreated Others Nfkb1 source Deckers_lab_Sep2014_NFkB_HKL_IFNb Others Epitope tags source Flag_Sp2koMEFs Others Epitope tags source Flag-Sp2FL_Sp2koMEFs Others Nfyb source Nf-yb_wtMEFs Others Nfya source Nf-ya_Sp2koMEFs Others Sp3 source Sp3_Ab2_Sp3koMEFs Others Sp3 source Sp3_Ab2_MEFs Others Nfyb source Nf-yb_Sp2koMEFs Others Sp3 source Sp3_Ab1_MEFs Others Nfyc source Nf-yc_wtMEFs Others Epitope tags source Flag-Sp2ZF_Sp2koMEFs Others Sp1 source Sp1_Ab1_MEFs Others Epitope tags source Flag-Sp2NT_Sp2koMEFs Others Nfyc source Nf-yc_Sp2koMEFs Others Nfya source Nf-ya_wtMEFs Others Sp1 source Sp1_Ab2_MEFs Others Sp3 source Sp3_Ab1_Sp3koMEFs Input control Input control source IgG_1_MEFs Input control Input control source IgG_Sp2koMEFs Input control Input control source IgG_2_MEFs Unclassified Unclassified source ERS425890 Unclassified Unclassified source ERS425889 Unclassified Unclassified source ERS425888 Others Zeb1 source 3t3D0_Zeb1_1 Others Zeb1 source 3t3D2_Zeb1_1 Input control Input control source 3t3D0_Input_1 Others Zeb1 source 3t3D-2_Zeb1_2 Others Zeb1 source 3t3D0_Zeb1_2 Others Zeb1 source 3t3D4_Zeb1_1 Others Zeb1 source 3t3D-2_Zeb1_1 Others Zfp277 source 3t3D0_Zfp277OE_1 Unclassified Unclassified Chromotek GFP trap Agarose source ERS383020 Unclassified Unclassified Chromotek GFP trap Agarose source ERS383019 Unclassified Unclassified Chromotek GFP trap Agarose source ERS383018 Unclassified Unclassified Chromotek GFP trap Agarose source ERS383017 Unclassified Unclassified Chromotek GFP trap Agarose source ERS383016 Unclassified Unclassified Chromotek GFP trap Agarose source ERS383015 Unclassified Unclassified Chromotek GFP trap Agarose source ERS383014 Unclassified Unclassified Chromotek GFP trap Agarose source ERS383013 Unclassified Unclassified Chromotek GFP trap Agarose source ERS383012 Unclassified Unclassified Chromotek GFP trap Agarose source ERS383011 Others Pou5f1 source oct4_0hr_trep1 Others Pou5f1 source oct4_0hr_trep2 Others Pou5f1 source oct4_16hr Unclassified Unclassified source 11/7/12 5 Others Ascl1 source NS5_Ascl1 Unclassified Unclassified source mESCs Serum/Lif Unclassified Unclassified source mESCs 2i Unclassified Unclassified source P29_b_01 Unclassified Unclassified source E15.5_l_02 Unclassified Unclassified source E9.5_WE_01 Unclassified Unclassified source P0.5_l_01 Unclassified Unclassified source P29_l_02 Unclassified Unclassified source P4_b_02 Input control Input control source E18.5_l_input Input control Input control source E18.5_b_input Unclassified Unclassified source P22_b_01 Unclassified Unclassified source P4_l_02 Unclassified Unclassified source E15.5_b_01 Input control Input control source P0.5_b_input Input control Input control source P29_l_input Unclassified Unclassified source P0.5_b_02 Unclassified Unclassified source P29_b_02 Unclassified Unclassified source E18.5_b_02 Input control Input control source P29_b_input Input control Input control source E15.5_b_input Input control Input control source P4_l_input Unclassified Unclassified source P22_l_02 Unclassified Unclassified source P0.5_b_01 Unclassified Unclassified source P4_l_01 Unclassified Unclassified source E12.5_b_01 Unclassified Unclassified source P4_b_01 Unclassified Unclassified source P0.5_l_02 Unclassified Unclassified source P29_l_01 Unclassified Unclassified source E15.5_l_01 Input control Input control source P4_b_input Unclassified Unclassified source E18.5_l_02 Input control Input control source P0.5_l_input Unclassified Unclassified source E12.5_l_02 Unclassified Unclassified source E18.5_b_01 Unclassified Unclassified source P22_b_02 Unclassified Unclassified source E12.5_l_01 Unclassified Unclassified source E15.5_b_02 Unclassified Unclassified source E12.5_b_02 Unclassified Unclassified source E18.5_l_01 Input control Input control source P22_l_input Input control Input control source P22_b_input Input control Input control source E15.5_l_input Unclassified Unclassified source P22_l_01 Unclassified Unclassified ERS400849 Unclassified Unclassified ERS400848 Unclassified Unclassified ERS400847 Unclassified Unclassified ERS400846 Unclassified Unclassified ERS400845 Unclassified Unclassified ERS400844 Unclassified Unclassified ERS400843 Unclassified Unclassified ERS400842 Unclassified Unclassified ERS400841 Unclassified Unclassified ERS400840 Histone H3K27ac source K27Ac-0hr Histone H3K4me1 source K4Me1-12hr Histone H3K4me1 source K4Me1-0hr Histone H3K4me1 source K4Me1-8hr Input control Input control source Input-0hr Histone H3K27ac source K27Ac-12hr Histone H3K27ac source K27Ac-8hr Input control Input control source input_0hr Others Otx2 source OTX2_0hr Others Otx2 source OTX2_4hr Others Otx2 source OTX2_12hr Others Otx2 source OTX2_8hr Input control Input control source input_12hr Others Foxp2 Foxp2 source ERS254615 Others Foxp2 Foxp2 source ERS254614 Others Foxp1 Foxp1 source ERS254613 Others Bcl6 Bcl6 source ERS254612 Others Bcl6 Bcl6 source ERS254611 Others Tcf3 source Tcf3 Others Sox21 source Sox21 Others Nfic source NFI Others Olig2 source Olig2 Others Ascl1 source Ascl1 Others Sox9 source Sox9 Others Sox2 source Sox2 Others Max source Max Unclassified Unclassified source ERS022703 Unclassified Unclassified source ERS001845 Unclassified Unclassified source ERS001844 Unclassified Unclassified source ERS001843 Unclassified Unclassified source ERS001617 Unclassified Unclassified source ERS001616 Unclassified Unclassified source ERS001619 Unclassified Unclassified source ERS001618 Unclassified Unclassified source ERS002988 Unclassified Unclassified source ERS002635 Unclassified Unclassified source ERS004189 Unclassified Unclassified source ERS004187 Unclassified Unclassified source ERS340306 Unclassified Unclassified source ERS340305 Unclassified Unclassified source ERS340304 Unclassified Unclassified source ERS340303 Unclassified Unclassified source ERS340302 Others Mecp2 Chromotek GFP trap Agarose source ERS353243 Others Mecp2 Chromotek GFP trap Agarose source ERS353242 Others Mecp2 Chromotek GFP trap Agarose source ERS353241 Others Mecp2 Chromotek GFP trap Agarose source ERS353240 Unclassified Unclassified source ERS223727 Unclassified Unclassified source ERS223728 Unclassified Unclassified source ERS223732 Unclassified Unclassified source ERS223731 Unclassified Unclassified source ERS223730 Others Epitope tags flag source ERS067621 Others Epitope tags flag source ERS067620 Others Epitope tags flag source ERS067619 Others Epitope tags flag source ERS067618 Unclassified Unclassified source 0SQ40 Unclassified Unclassified source 0SQ42 Unclassified Unclassified source 0SQ41 Unclassified Unclassified source ERS223729 Unclassified Unclassified source ERS223726 Unclassified Unclassified source ERS223725 Unclassified Unclassified source ERS223724 Unclassified Unclassified source ERS223723 Unclassified Unclassified source ERS223722 Unclassified Unclassified source ERS182801 Unclassified Unclassified source ERS182802 Unclassified Unclassified source ERS182803 Unclassified Unclassified source ERS182804 Histone H3K4me3 Anti Histone H3K4me3, Abcam, ab8587 source ERS184550 Histone H3K4me3 Anti Histone H3K4me3, Abcam, ab8586 source ERS184549 Histone H3K4me3 Anti Histone H3K4me3, Abcam, ab8585 source ERS184548 Histone H3K4me3 Anti Histone H3K4me3, Abcam, ab8584 source ERS184547 Histone H3K4me3 Anti Histone H3K4me3, Abcam, ab8583 source ERS184546 Histone H3K4me3 Anti Histone H3K4me3, Abcam, ab8582 source ERS184545 Histone H3K9K14ac Anti H3K9,K14 acetyl, Millipore 06-606 source ERS184542 Histone H3K9K14ac Anti H3K9,K14 acetyl, Millipore 06-605 source ERS184541 Histone H3K9K14ac Anti H3K9,K14 acetyl, Millipore 06-604 source ERS184540 Histone H3K9K14ac Anti H3K9,K14 acetyl, Millipore 06-603 source ERS184539 Histone H3K4me3 Anti Histone H3K4me3, Abcam, ab8581 source ERS184544 Histone H3K4me3 Anti Histone H3K4me3, Abcam, ab8580 source ERS184543 Input control Input control Sonicated DNA control source ERS184552 Input control Input control Sonicated DNA control source ERS184551 Histone H3K9K14ac Anti H3K9,K14 acetyl, Millipore 06-602 source ERS184538 Histone H3K9K14ac Anti H3K9,K14 acetyl, Millipore 06-601 source ERS184537 Histone H3K9K14ac Anti H3K9,K14 acetyl, Millipore 06-600 source ERS184536 Histone H3K9K14ac Anti H3K9,K14 acetyl, Millipore 06-599 source ERS184535 Others Nanog source Nanog_Oct4++mESC Histone H3K27me3 source H3K27me3_Oct4+-mESC Others Nanog source Nanog_Oct4+-mESC Others Pou5f1 source Oct4_Oct4++mESC Others Pou5f1 source Oct4_Oct4+-mESC Histone H3K27me3 source H3K27me3_Oct4++mESC Input control Input control source Input_Oct4+-mESC Input control Input control source Input_Oct4++mESC Unclassified Unclassified source Tc0_B230_b Unclassified Unclassified source tc1_137.1_a Unclassified Unclassified source Tc0_B230_a Unclassified Unclassified source tc1_122.1_and_122.2_a Unclassified Unclassified source tc1_122.1_b Unclassified Unclassified source tc1_122.1_and_122.2_b Unclassified Unclassified source tc1_137.1_b Unclassified Unclassified source tc1_122.1_a Unclassified Unclassified source mmuOON404 Unclassified Unclassified source mmu12 Unclassified Unclassified source mmuOON405 Unclassified Unclassified ERS1792140 Unclassified Unclassified ERS1792139 Unclassified Unclassified ERS1792138 Unclassified Unclassified ERS1792137 Unclassified Unclassified ERS1792136 Unclassified Unclassified source Mouse liver 1 Unclassified Unclassified source Mouse liver 2 Others Rad21 Rad21 Others Foxa1 FoxA1 RNA polymerase RNA polymerase III Pol3 Unclassified Unclassified ERS074963 Unclassified Unclassified ERS074962 Unclassified Unclassified ERS074961 Unclassified Unclassified ERS074960 Unclassified Unclassified ERS074959 Unclassified Unclassified ERS074958 Unclassified Unclassified ERS074957 Unclassified Unclassified ERS074956 Unclassified Unclassified ERS074955 Unclassified Unclassified ERS074954 Unclassified Unclassified ERS074953 Unclassified Unclassified ERS074951 Unclassified Unclassified ERS074952 Unclassified Unclassified ERS074950 Unclassified Unclassified ERS074949 Unclassified Unclassified ERS074948 Unclassified Unclassified ERS1642952 Unclassified Unclassified ERS1642951 Unclassified Unclassified ERS1642950 Unclassified Unclassified ERS1642949 Unclassified Unclassified ERS1642948 Unclassified Unclassified ERS1642947 Unclassified Unclassified ERS1642946 Unclassified Unclassified ERS1642945 Unclassified Unclassified ERS1642944 Unclassified Unclassified ERS1642943 Unclassified Unclassified ERS1642942 Unclassified Unclassified ERS1642941 Unclassified Unclassified ERS1642940 Unclassified Unclassified ERS1642939 Unclassified Unclassified ERS1642938 Unclassified Unclassified ERS1642937 Unclassified Unclassified ERS1642936 Unclassified Unclassified ERS1642935 Unclassified Unclassified ERS1642934 Unclassified Unclassified ERS1642933 Unclassified Unclassified ERS1642932 Unclassified Unclassified ERS1642931 Unclassified Unclassified ERS1642930 Unclassified Unclassified ERS1642929 Unclassified Unclassified ERS1642928 Unclassified Unclassified ERS1642927 Unclassified Unclassified ERS1642926 Unclassified Unclassified ERS1642925 Unclassified Unclassified ERS1642924 Unclassified Unclassified ERS1642923 Unclassified Unclassified ERS1642922 Unclassified Unclassified ERS1642921 Unclassified Unclassified ERS1642920 Unclassified Unclassified ERS1642919 Unclassified Unclassified ERS1642918 Unclassified Unclassified ERS1642917 Unclassified Unclassified ERS1642916 Unclassified Unclassified ERS1642915 Unclassified Unclassified ERS1587689 Unclassified Unclassified ERS1587688 Unclassified Unclassified ERS1587687 Unclassified Unclassified ERS1587686 Unclassified Unclassified ERS1587685 Unclassified Unclassified ERS1587684 Unclassified Unclassified ERS1587683 Unclassified Unclassified ERS1587682 Unclassified Unclassified ERS1587681 Unclassified Unclassified ERS1587680 Unclassified Unclassified ERS1587679 Unclassified Unclassified ERS1587678 Others Pou5f1 source p300_proNSC Histone H3K27ac source H3K27ac_proNSC Unclassified Unclassified source NFI_quiNSC Histone H3K27ac source H3K27ac_quiNSC Others Ep300 source p300_quiNSC Input control Input control source Input_proNSC Input control Input control source Input_quiNSC Unclassified Unclassified source N10 Unclassified Unclassified source 0SQ22 Unclassified Unclassified source 0SQ20 Unclassified Unclassified source 0SQ36 Unclassified Unclassified source 0ON404 Unclassified Unclassified ERS1464739 Unclassified Unclassified ERS1464738 Unclassified Unclassified ERS1464737 Unclassified Unclassified ERS1464736 Unclassified Unclassified ERS1464735 Unclassified Unclassified ERS1464734 Unclassified Unclassified ERS1464733 Unclassified Unclassified ERS1464732 Unclassified Unclassified ERS1464731 Unclassified Unclassified ERS1464730 Unclassified Unclassified ERS1464729 Unclassified Unclassified ERS1464728 Unclassified Unclassified ERS1464727 Unclassified Unclassified ERS1464726 Unclassified Unclassified ERS1464725 Unclassified Unclassified ERS1464724 Unclassified Unclassified ERS1464723 Unclassified Unclassified ERS1464722 Unclassified Unclassified ERS1464721 Unclassified Unclassified ERS1464720 Unclassified Unclassified ERS1361310 Unclassified Unclassified ERS1361309 Unclassified Unclassified ERS1361308 Unclassified Unclassified ERS1361307 Unclassified Unclassified ERS1289935 Unclassified Unclassified ERS1289934 Unclassified Unclassified ERS1289933 Unclassified Unclassified ERS1289932 Unclassified Unclassified ERS1289931 Unclassified Unclassified ERS1289930 Unclassified Unclassified ERS1289929 Unclassified Unclassified ERS1289928 Unclassified Unclassified ERS1289927 Unclassified Unclassified ERS1289926 Unclassified Unclassified ERS1289925 Unclassified Unclassified ERS1289924 Unclassified Unclassified ERS1289923 Unclassified Unclassified ERS1289922 Unclassified Unclassified ERS1289921 Unclassified Unclassified ERS1289920 Unclassified Unclassified ERS1289919 Unclassified Unclassified ERS1289918 Unclassified Unclassified ERS1289917 Unclassified Unclassified ERS1289916 Unclassified Unclassified ERS1289915 Unclassified Unclassified ERS1289914 Unclassified Unclassified ERS1289913 Unclassified Unclassified ERS1289912 Unclassified Unclassified ERS1289911 Unclassified Unclassified ERS1289910 Unclassified Unclassified ERS1289909 Unclassified Unclassified ERS1289908 Unclassified Unclassified ERS1289907 Unclassified Unclassified ERS1289906 Unclassified Unclassified ERS1289905 Unclassified Unclassified ERS1289904 Unclassified Unclassified ERS1289903 Unclassified Unclassified ERS1289902 Unclassified Unclassified ERS1289901 Unclassified Unclassified ERS1289900 Unclassified Unclassified ERS1289899 Unclassified Unclassified ERS1289898 Unclassified Unclassified ERS1289897 Unclassified Unclassified ERS1289896 Unclassified Unclassified ERS1289895 Unclassified Unclassified ERS1289894 Unclassified Unclassified ERS1289893 Unclassified Unclassified ERS1289892 Unclassified Unclassified ERS1289891 Unclassified Unclassified ERS1289890 Unclassified Unclassified ERS1289889 Unclassified Unclassified ERS1289888 Unclassified Unclassified ERS1289887 Unclassified Unclassified ERS1289886 Unclassified Unclassified ERS1289885 Unclassified Unclassified ERS1289884 Unclassified Unclassified ERS1289883 Unclassified Unclassified ERS1289882 Unclassified Unclassified ERS1289881 Unclassified Unclassified ERS1289880 Unclassified Unclassified ERS1289879 Unclassified Unclassified ERS1289878 Unclassified Unclassified ERS1289877 Unclassified Unclassified ERS1289876 Unclassified Unclassified ERS1289875 Unclassified Unclassified ERS1289874 Unclassified Unclassified ERS1289873 Unclassified Unclassified ERS1289872 Unclassified Unclassified ERS1289871 Unclassified Unclassified ERS1289870 Unclassified Unclassified ERS1289869 Unclassified Unclassified ERS1289868 Unclassified Unclassified ERS1289867 Unclassified Unclassified ERS1289866 Unclassified Unclassified ERS1289865 Unclassified Unclassified ERS1289864 Unclassified Unclassified ERS1289863 Unclassified Unclassified ERS1288045 Unclassified Unclassified ERS1288044 Unclassified Unclassified ERS1288043 Unclassified Unclassified ERS1288042 Unclassified Unclassified ERS1288041 Unclassified Unclassified source tc152038_testes Unclassified Unclassified source tc128_3_4m11m12_spleen Unclassified Unclassified source tc141208 Unclassified Unclassified source tc141238 Unclassified Unclassified source tc152038_spleen Unclassified Unclassified source tc128_3_4m11m12_muscle Unclassified Unclassified source tc152039_liver Unclassified Unclassified source tc152038_muscle Unclassified Unclassified ERS1207589 Unclassified Unclassified ERS1207588 Unclassified Unclassified ERS1207587 Unclassified Unclassified ERS1207586 Unclassified Unclassified ERS1207585 Unclassified Unclassified ERS1207584 Unclassified Unclassified ERS1207583 Unclassified Unclassified ERS1207582 Unclassified Unclassified ERS1207581 Unclassified Unclassified ERS1207580 Others Nap1l1 source Nap1l1_pEHP Others Kat5 source Kat5_pEHP Others Kat5 source Kat5_ES Others Nap1l1 source Nap1l1_ES Unclassified Unclassified source Nucleosomes_ES Histone H2A.X source H2A.X_ES Histone H2A.Z source H2A.Z_pEHP Histone H2A.Z source H2A.Z_ES Others Foxa2 source Foxa2_EHP Others Smarca4 source Smarca4_EHP Histone H2A.Z source H2A.Z_EHP Others Smarca4 source Smarca4_ES Others Foxa2 source Foxa2_pEHP Others Smarca4 source Smarca4_pEHP Others Kat5 source Kat5_EHP Others Nap1l1 source Nap1l1_EHP Histone H3K4me3 source mouse_testis_H3K4me3_1 Input control Input control source mouse_testis_input_1 RNA polymerase RNA polymerase I source mouse_liver_pol1_1 RNA polymerase RNA polymerase III source mouse_testis_pol3_3 Input control Input control source mouse_liver_input_3 RNA polymerase RNA polymerase III source mouse_liver_pol3_2 Histone H3K36me3 source mouse_testis_H3K36me3_2 RNA polymerase RNA polymerase II source mouse_testis_pol2_1 RNA polymerase RNA polymerase I source mouse_liver_pol1_2 Input control Input control source mouse_liver_input_1 RNA polymerase RNA polymerase III source mouse_testis_pol3_2 RNA polymerase RNA polymerase III source mouse_testis_pol3_4 Histone H3K27me3 source mouse_liver_H3K27me3_1 RNA polymerase RNA polymerase III source mouse_liver_pol3_1 Histone H3K36me3 source mouse_testis_H3K36me3_4 Histone H3K27me3 source mouse_testis_H3K27me3_1 Input control Input control source mouse_testis_MybL1_input_1 Histone H3K36me3 source mouse_liver_H3K36me3_1 Histone H3K36me3 source mouse_testis_H3K36me3_1 RNA polymerase RNA polymerase I source mouse_liver_pol1_3 RNA polymerase RNA polymerase II source mouse_liver_pol2_1 RNA polymerase RNA polymerase I source mouse_testis_pol1_1 Others Mybl1 source mouse_testis_MybL1_1 Histone H3K4me3 source mouse_liver_H3K4me3_1 RNA polymerase RNA polymerase I source mouse_testis_pol1_2 Histone H3K27me3 source mouse_liver_H3K27me3_2 Histone H3K36me3 source mouse_testis_H3K36me3_3 Histone H3K4me3 source mouse_testis_H3K4me3_2 Others Mybl1 source mouse_liver_MybL1_1 RNA polymerase RNA polymerase III source mouse_testis_pol3_1 Input control Input control source mouse_liver_input_2 Unclassified Unclassified ERS1063830 Unclassified Unclassified source ERS132603 Unclassified Unclassified source ERS132602 Unclassified Unclassified source ERS132601 Unclassified Unclassified source ERS132600 Unclassified Unclassified source ERS004854 RNA polymerase RNA polymerase II Anti RNA Polymerase II. Abcam 8WG16 source ERS004851 Others Cxxc1 anti-Cfp1 source ERS023718 Others Cxxc1 anti-Cfp1 source ERS023717 Histone H3K4me3 H3K4me3 source ERS023716 Histone H3K4me3 H3K4me3 source ERS023715 RNA polymerase RNA polymerase II RNA Pol II source ERS023714 RNA polymerase RNA polymerase II RNA Pol II source ERS023713 Unclassified Unclassified source ERS026037 Histone H3K9K14ac Anti H3 Acetyl K9, K14 (Millipore 06-499) source ERS095007 Histone H3K9K14ac Anti H3 Acetyl K9, K14 (Millipore 06-499) source ERS095006 Histone H3K9K14ac Anti H3 Acetyl K9, K14 (Millipore 06-499) source ERS095005 Histone H3K9K14ac Anti H3 Acetyl K9, K14 (Millipore 06-499) source ERS095004 Histone H3K9K14ac Anti H3 Acetyl K9, K14 (Millipore 06-499) source ERS095003 Histone H3K9K14ac Anti H3 Acetyl K9, K14 (Millipore 06-499) source ERS095002 Unclassified Unclassified to be provided source ERS149520 Unclassified Unclassified to be provided source ERS149519 Unclassified Unclassified to be provided source ERS149518 Unclassified Unclassified to be provided source ERS149517 Unclassified Unclassified to be provided source ERS149516 Unclassified Unclassified to be provided source ERS149515 Unclassified Unclassified source ERS018870 Unclassified Unclassified source ERS018868 Unclassified Unclassified source ERS018869 Unclassified Unclassified source ERS018867 Unclassified Unclassified source ERS005087 Unclassified Unclassified source ERS005089 Unclassified Unclassified source ERS005084 Unclassified Unclassified source ERS005080 Unclassified Unclassified source ERS005011 Unclassified Unclassified source ERS005010 Unclassified Unclassified source ERS004848 Unclassified Unclassified source ERS004847 Unclassified Unclassified source ERS004850 Unclassified Unclassified source ERS004849 Unclassified Unclassified source ERS004235 Unclassified Unclassified source ERS004245 Unclassified Unclassified source ERS004243 Unclassified Unclassified source ERS004241 Unclassified Unclassified source ERS004240 Unclassified Unclassified source ERS004242 Unclassified Unclassified source ERS004239 Unclassified Unclassified source ERS004237 Unclassified Unclassified source ERS004238 Unclassified Unclassified source ERS004244 Histone H3K4me3 H3K4me3 source ERS071955 Others MethylCap anti-MBD source ERS002963 Others MethylCap anti-MBD source ERS002961 Others MethylCap anti-MBD source ERS002960 RNA polymerase RNA polymerase II RNA Pol II source ERS002653 RNA polymerase RNA polymerase II RNA Pol II source ERS002652 RNA polymerase RNA polymerase II RNA Pol II source ERS002651 RNA polymerase RNA polymerase II RNA Pol II source ERS002650 RNA polymerase RNA polymerase II RNA Pol II source ERS002649 RNA polymerase RNA polymerase II RNA Pol II source ERS002648 Others MethylCap anti-MBD source ERS005091 Others MethylCap anti-MBD source ERS005093 Others MethylCap anti-MBD2 source ERS004954 Others MethylCap anti-MBD2 source ERS004952 Histone H3ac H3Ac source ERS004951 Histone H3ac H3Ac source ERS004950 Others MethylCap anti-MBD2 source ERS004871 Others MethylCap anti-MBD source ERS004869 Others MethylCap anti-MBD source ERS004868 Others MethylCap anti-MBD source ERS004867 Others MethylCap anti-MBD2 source ERS004870 Others MethylCap anti-MBD source ERS004872 Others MethylCap anti-MBD source ERS004368 Others MethylCap anti-MBD source ERS004371 Others MethylCap anti-MBD source ERS004375 Others MethylCap anti-MBD source ERS004373 Others MethylCap anti-MBD source ERS004374 Others MethylCap anti-MBD source ERS004379 Others MethylCap anti-MBD source ERS004369 Others MethylCap anti-MBD source ERS004372 Unclassified Unclassified ERS1052383 Input control Input control source TCF3-IgG Others Tcf3 source TCF3 Input control Input control source TCF1-IgG Others Tcf7 source TCF1 Input control Input control source R152_Input Histone H3K4me3 source R152_H3K4me3 Histone H3K27me3 source R152_H3K27me3 Input control Input control source MO467_Input Histone H3K4me3 source MO467_H3K4me3 Histone H3K27me3 source MO467_H3K27me3 Unclassified Unclassified ERS1006286 Unclassified Unclassified ERS1006285 Unclassified Unclassified ERS1006284 Unclassified Unclassified ERS1006283 Unclassified Unclassified ERS1006282 Unclassified Unclassified ERS1006281 Unclassified Unclassified ERS1006280 Unclassified Unclassified ERS1006279 Unclassified Unclassified ERS1006278 Unclassified Unclassified ERS1006277 Unclassified Unclassified ERS1006276 Unclassified Unclassified ERS1006275 Unclassified Unclassified ERS1006274 Unclassified Unclassified ERS1006273 RNA polymerase RNA polymerase III Pol III (RPC1/155) source Hepa1c1c7_rep2 RNA polymerase RNA polymerase III Pol III (RPC1/155) source Hepa1c1c7_rep1 RNA polymerase RNA polymerase III Pol III (RPC1/155) source Hepa1_6_rep2 RNA polymerase RNA polymerase III Pol III (RPC1/155) source Hepa1_6_rep1 Others Tbx20 source Tbx20-GFP IP RNA polymerase RNA polymerase II source RNAP2 ChIP 1 Others Cebpa source Rad21+/- CEBPA ChIP 1 Histone H3K4me1 source H3K4me1 ChIP 1 Others Crebbp source CBP ChIP 1 Others Ncor2 source CTCF ChIP 1 Histone H3K36me3 source H3K36me3 ChIP 1 Others Hnf4a source Rad21+/- HNF4A ChIP 2 Others Hnf4a source Rad21+/- HNF4A ChIP 1 Others Ep300 source Rad21+/- CEBPA ChIP 2 Others Ncor2 source CTCF ChIP 2 Others Rad21 source Rad21+/- RAD21 ChIP 2 Others Ep300 source p300 ChIP 2 Histone H3K79me2 source H3K79me2 ChIP 1 Histone H3K4me3 source H3K4me3 ChIP 1 RNA polymerase RNA polymerase II source RNAP2 ChIP 2 Others Stag2 source STAG2 ChIP 1 Others Onecut1 source Rad21+/- HNF6 ChIP 2 Others Foxa1 source FOXA1 ChIP 2 Histone H2AK5sc source H2AK5ac ChIP 1 Input control Input control source input 3 Others Foxa1 source FOXA1 ChIP 1 Others Rest source NRSF/REST ChIP 1 Others E2f4 source E2F4 ChIP 1 Others Rad21 source Rad21+/- RAD21 ChIP 1 Others Rad21 source RAD21 ChIP 1 Input control Input control source Rad21+/- input 2 Others Onecut1 source Rad21+/- HNF6 ChIP 1 Input control Input control source Rad21+/- input 1 Unclassified Unclassified source PREP1 ChIP 1 Others Stag1 source STAG1 ChIP 2 Others Ep300 source p300 ChIP 1 Others Foxa2 source FOXA2 ChIP 2 Input control Input control source input 2 Input control Input control source input 1 Unclassified Unclassified source ESC_WT2 Unclassified Unclassified source ESC_WT1 Unclassified Unclassified source ESC_KO2 Unclassified Unclassified source ESC_KO1 Unclassified Unclassified source EPISC_WT2 Unclassified Unclassified source EPISC_WT1 Unclassified Unclassified source EPISC_KO2 Unclassified Unclassified source EPISC_KO1 Others Trim24 source 11Feb-Trim24-iR2 Others Trim24 source 11Feb-Trim24-iR1 Others Trim24 source 11Feb-Trim24-fR2 Others Trim24 source 11Feb-Trim24-fR1 Unclassified Unclassified source 11Feb-InpFBS-R2 Unclassified Unclassified source 11Feb-InpFBS-R1 Unclassified Unclassified source 11Feb-Inp2i-R2 Unclassified Unclassified source 11Feb-Inp2i-R1 Others Foxa2 source Foxa2_input_1 Others Foxa2 source Foxa2_input_2 Others Foxa2 source Foxa2_ChIP_2 Others Foxa2 source Foxa2_ChIP_1 Unclassified Unclassified source tc1_28.3_m11_and_28.4_m12 Unclassified Unclassified source tc1_R024 Unclassified Unclassified source tc1_m1 Unclassified Unclassified source tc1_28.1_m9 Unclassified Unclassified source tc1_28.1_m9_AND_28.2_m10_liver RNA polymerase RNA polymerase II source Cell culture 2 SMRT-KD RNA-PolII Others Ncor2 source Cell culture 5 SMRT RNA polymerase RNA polymerase II source Cell culture 1 GFP-KD RNA-PolII Others Ncor1 source Cell culture 2 NCoR1 Others Ncor1 source Cell culture 1 NCoR1 Histone H3K4me3 H3K4me3 source ERS002497 Input control Input control input_DNA source ERS002498 Input control Input control input_DNA source ERS002484 Histone H3K4me3 H3K4me3 source ERS002485 Input control Input control input_DNA source ERS002488 Histone H3K4me3 H3K4me3 source ERS002495 Input control Input control input_DNA source ERS002496 Histone H3K4me3 H3K4me3 source ERS002483 Histone H3K4me3 H3K4me3 source ERS002487 Histone H3K4me3 H3K4me3 source ERS002489 Input control Input control input_DNA source ERS002490 Histone H3K4me3 H3K4me3 source ERS002491 Input control Input control input_DNA source ERS002492 Histone H3K4me3 H3K4me3 source ERS002493 Input control Input control input_DNA source ERS002494 Histone H3K4me3 H3K4me3 source ERS002012 Input control Input control input_DNA source ERS002021 Input control Input control input_DNA source ERS002013 Histone H3K4me3 H3K4me3 source ERS002014 Input control Input control input_DNA source ERS002015 Input control Input control input_DNA source ERS002017 Histone H3K4me3 H3K4me3 source ERS002018 Input control Input control input_DNA source ERS002019 Histone H3K4me3 H3K4me3 source ERS002020 Input control Input control input_DNA source ERS001681 Histone H3K4me3 H3K4me3 source ERS001680 Input control Input control input_DNA source ERS001677 Histone H3K4me3 H3K4me3 source ERS001676 Unclassified Unclassified source Treated-Male-Control Unclassified Unclassified source Treated-Female-Mutant Unclassified Unclassified source Untreated-Female-Control Unclassified Unclassified source Untreated-Male-Control Unclassified Unclassified source Treated-Male-Mutant Unclassified Unclassified source Treated-Female-Control Others Smad3 source TGFbeta treated Smad3 Others Kdm6b source TGFbeta treated JMJD3 Input control Input control source TGFbeta treated input Unclassified Unclassified source 46C-2 Others Gtf3c2 source TFIIIC110 Others Brf1 source BRF1 RNA polymerase Polr3a source RPC1 Others Gtf3c1 source TFIIIC220 Others Gtf3c4 source TFIIIC90 RNA polymerase Polr3d source RPC4 Others Brf2 source BRF2 Others Tcea1 source TCEA1 Unclassified Unclassified source 46C Unclassified Unclassified source mmu0SQ121 Unclassified Unclassified source mmu491_liver Unclassified Unclassified source mmu490 Unclassified Unclassified source mmu0ON490 Others Ctcf source TC1 ChIP 2 Unclassified Unclassified source mouse ChIP 2 Input control Input control source TC1 input 2 Input control Input control source mouse input 2 Others Ctcf source TC1 ChIP 3 Others Ctcf source TC1 ChIP 1 Unclassified Unclassified ERS017292 Unclassified Unclassified ERS017291 Unclassified Unclassified ERS011161 Unclassified Unclassified The sample was fixed with 0.5% formaldehyde for 5 min. Differentiation from myoblast state was done by transferring to Dulbecco's modified Eagle's medium containing 2% horse serum upon reaching confluence. Unclassified Unclassified The sample was fixed with 0.5% formaldehyde for 5 min. Histone H3K27ac E14TG2a ESCs derived from 129/Ola were cultured in GMEM supplemented non-essential amino acids, 10% Knockout Serum Replacement, sodium pyruvate, L-glutamine, 2-mercaptoethanol, penicillin, streptomycin, and leukemia inhibitory factor without feeder cells. ChIP experiment with anti-H3K27ac antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Others Rest E14TG2a ESCs derived from 129/Ola were cultured in GMEM supplemented non-essential amino acids, 10% Knockout Serum Replacement, sodium pyruvate, L-glutamine, 2-mercaptoethanol, penicillin, streptomycin, and leukemia inhibitory factor without feeder cells. ChIP experiment with anti-Rest antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Histone H3ac E14TG2a ESCs derived from 129/Ola were cultured in GMEM supplemented non-essential amino acids, 10% Knockout Serum Replacement, sodium pyruvate, L-glutamine, 2-mercaptoethanol, penicillin, streptomycin, and leukemia inhibitory factor without feeder cells. ChIP experiment with anti-H3ac antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Histone H3K4me3 E14TG2a ESCs derived from 129/Ola were cultured in GMEM supplemented non-essential amino acids, 10% Knockout Serum Replacement, sodium pyruvate, L-glutamine, 2-mercaptoethanol, penicillin, streptomycin, and leukemia inhibitory factor without feeder cells. ChIP experiment with anti-H3K4me3 antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Histone H3K4me1 E14TG2a ESCs derived from 129/Ola were cultured in GMEM supplemented non-essential amino acids, 10% Knockout Serum Replacement, sodium pyruvate, L-glutamine, 2-mercaptoethanol, penicillin, streptomycin, and leukemia inhibitory factor without feeder cells. ChIP experiment with anti-H3K4me1 antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Histone H3K27me3 E14TG2a ESCs derived from 129/Ola were cultured in GMEM supplemented non-essential amino acids, 10% Knockout Serum Replacement, sodium pyruvate, L-glutamine, 2-mercaptoethanol, penicillin, streptomycin, and leukemia inhibitory factor without feeder cells. ChIP experiment with anti-H3K27me3 antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Others Sin3a E14TG2a ESCs derived from 129/Ola were cultured in GMEM supplemented non-essential amino acids, 10% Knockout Serum Replacement, sodium pyruvate, L-glutamine, 2-mercaptoethanol, penicillin, streptomycin, and leukemia inhibitory factor without feeder cells. ChIP experiment with anti-Sin3a antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Histone H3K9me3 E14TG2a ESCs derived from 129/Ola were cultured in GMEM supplemented non-essential amino acids, 10% Knockout Serum Replacement, sodium pyruvate, L-glutamine, 2-mercaptoethanol, penicillin, streptomycin, and leukemia inhibitory factor without feeder cells. ChIP experiment with anti-H3K9me3 antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Histone H3K9me2 E14TG2a ESCs derived from 129/Ola were cultured in GMEM supplemented non-essential amino acids, 10% Knockout Serum Replacement, sodium pyruvate, L-glutamine, 2-mercaptoethanol, penicillin, streptomycin, and leukemia inhibitory factor without feeder cells. ChIP experiment with anti-H3K9me2 antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. RNA polymerase RNA polymerase II E14TG2a ESCs derived from 129/Ola were cultured in GMEM supplemented non-essential amino acids, 10% Knockout Serum Replacement, sodium pyruvate, L-glutamine, 2-mercaptoethanol, penicillin, streptomycin, and leukemia inhibitory factor without feeder cells. ChIP experiment with anti-Pol2 antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Others Kdm1a E14TG2a ESCs derived from 129/Ola were cultured in GMEM supplemented non-essential amino acids, 10% Knockout Serum Replacement, sodium pyruvate, L-glutamine, 2-mercaptoethanol, penicillin, streptomycin, and leukemia inhibitory factor without feeder cells. ChIP experiment with anti-Lsd1 antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Input control Input control E14TG2a ESCs derived from 129/Ola were cultured in GMEM supplemented non-essential amino acids, 10% Knockout Serum Replacement, sodium pyruvate, L-glutamine, 2-mercaptoethanol, penicillin, streptomycin, and leukemia inhibitory factor without feeder cells.ChIP experiment with whole cell extract was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Others Rest EpiSC cells were cultured on murine fibroblast feeders in DMEM/F12 supplemented with 20% KSR, bFGF, nonessential amino acids, b-mercaptoethanol, L-glutamax, penicillin, and streptomycin.ChIP experiment with anti-Rest antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Others Sin3a EpiSC cells were cultured on murine fibroblast feeders in DMEM/F12 supplemented with 20% KSR, bFGF, nonessential amino acids, b-mercaptoethanol, L-glutamax, penicillin, and streptomycin.ChIP experiment with anti-Sin3a antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Histone H3K27ac EpiSC cells were cultured on murine fibroblast feeders in DMEM/F12 supplemented with 20% KSR, bFGF, nonessential amino acids, b-mercaptoethanol, L-glutamax, penicillin, and streptomycin.ChIP experiment with anti-H3K27ac antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Histone H3ac EpiSC cells were cultured on murine fibroblast feeders in DMEM/F12 supplemented with 20% KSR, bFGF, nonessential amino acids, b-mercaptoethanol, L-glutamax, penicillin, and streptomycin.ChIP experiment with anti-H3ac antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. RNA polymerase RNA polymerase II EpiSC cells were cultured on murine fibroblast feeders in DMEM/F12 supplemented with 20% KSR, bFGF, nonessential amino acids, b-mercaptoethanol, L-glutamax, penicillin, and streptomycin.ChIP experiment with anti-Pol2 antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Histone H3K27ac EpiSC cells were cultured on murine fibroblast feeders in DMEM/F12 supplemented with 20% KSR, bFGF, nonessential amino acids, b-mercaptoethanol, L-glutamax, penicillin, and streptomycin.ChIP experiment with anti-H3k27Ac antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Others Cdyl EpiSC cells were cultured on murine fibroblast feeders in DMEM/F12 supplemented with 20% KSR, bFGF, nonessential amino acids, b-mercaptoethanol, L-glutamax, penicillin, and streptomycin.ChIP experiment with anti-CDYL antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Others Sin3a EpiSC cells were cultured on murine fibroblast feeders in DMEM/F12 supplemented with 20% KSR, bFGF, nonessential amino acids, b-mercaptoethanol, L-glutamax, penicillin, and streptomycin.ChIP experiment with anti-SIN3A antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Others Ehmt2 EpiSC cells were cultured on murine fibroblast feeders in DMEM/F12 supplemented with 20% KSR, bFGF, nonessential amino acids, b-mercaptoethanol, L-glutamax, penicillin, and streptomycin.ChIP experiment with anti-G9a antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Others Rcor2 EpiSC cells were cultured on murine fibroblast feeders in DMEM/F12 supplemented with 20% KSR, bFGF, nonessential amino acids, b-mercaptoethanol, L-glutamax, penicillin, and streptomycin.ChIP experiment with anti-COREST antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Others Rest EpiSC cells were cultured on murine fibroblast feeders in DMEM/F12 supplemented with 20% KSR, bFGF, nonessential amino acids, b-mercaptoethanol, L-glutamax, penicillin, and streptomycin.ChIP experiment with anti-REST antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. RNA polymerase RNA polymerase II EpiSC cells were cultured on murine fibroblast feeders in DMEM/F12 supplemented with 20% KSR, bFGF, nonessential amino acids, b-mercaptoethanol, L-glutamax, penicillin, and streptomycin.ChIP experiment with anti-pol2 antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Histone H3ac EpiSC cells were cultured on murine fibroblast feeders in DMEM/F12 supplemented with 20% KSR, bFGF, nonessential amino acids, b-mercaptoethanol, L-glutamax, penicillin, and streptomycin.ChIP experiment with anti-H3Ac antibody was performed as we have described previously. Samples destined for ChIP seq by Illumina HiSeq were prepared according to the manufacturers instructions. Input control Input control Input DNA analysis of ChIP from N2A cells treated with siRNAs against Fus, Ewsr1 and Taf15. Input control Input control Input DNA analysis of ChIP from N2A cells treated with siRNA against Fus. Input control Input control Input DNA analysis of ChIP from N2A cells treated with control siRNA. Unclassified Unclassified ChIP-seq analysis of N2A cells treated with siRNAs against Fus, Ewsr1 and Taf15. Unclassified Unclassified ChIP-seq analysis of N2A cells treated with siRNA against Fus. Unclassified Unclassified ChIP-seq analysis of N2A cells treated with control siRNA. Input control Input control Input DNA from adult Leydig cells Others Gata3 3xFlag-tagged Gata3-expressing mouse Th2 cell clone, D10G4.1 cells weresubjected to ChIP-seq analysis for anti-Flag mAb. This sample is control libray. Others Gata3 3xFlag-tagged Gata3-expressing mouse Th2 cell clone, D10G4.1 cells weresubjected to ChIP-seq analysis for anti-Flag mAb. Histone H3.3 ZHBTc4 is derived from ZHTc6 and maintained by tetracycline (Tc)-regulatable Oct-3/4 transgene. Both of Oct-3/4 locus are disrupted by IRES-zeocin and IRES-BSD KO vectors. It should be cultured in the absence of tetraycline to maintain the undifferentiated state. pCAGGS vector was used to generate the transgenic ES cell lines constitutively expressing Flag-H3.3 variant. A DNA fragment coding the histone variant tagged with Flag on its N-terminal was inserted into EcoRI site of the pCAGGS vector. Puromycin N-acetyl-transferase (Pac) gene obtained from salI digestion of pCre-Pac was inserted into the salI site of the vectors. The vector coding a Flag-histone variant was transfected into the ZHBTc4 cells by lipofection, and the cells were selected in the ES medium with 100 ??g/mL of puromycin. A single colony of the cells thus obtained for the variant was picked up and cultured. Histone H3.2 ZHBTc4 is derived from ZHTc6 and maintained by tetracycline (Tc)-regulatable Oct-3/4 transgene. Both of Oct-3/4 locus are disrupted by IRES-zeocin and IRES-BSD KO vectors. It should be cultured in the absence of tetraycline to maintain the undifferentiated state. pCAGGS vector was used to generate the transgenic ES cell lines constitutively expressing Flag-H3.2 variant. A DNA fragment coding the histone variant tagged with Flag on its N-terminal was inserted into EcoRI site of the pCAGGS vector. Puromycin N-acetyl-transferase (Pac) gene obtained from salI digestion of pCre-Pac was inserted into the salI site of the vectors. The vector coding a Flag-histone variant was transfected into the ZHBTc4 cells by lipofection, and the cells were selected in the ES medium with 100 ??g/mL of puromycin. A single colony of the cells thus obtained for the variant was picked up and cultured. Histone H3.1 ZHBTc4 is derived from ZHTc6 and maintained by tetracycline (Tc)-regulatable Oct-3/4 transgene. Both of Oct-3/4 locus are disrupted by IRES-zeocin and IRES-BSD KO vectors. It should be cultured in the absence of tetraycline to maintain the undifferentiated state. pCAGGS vector was used to generate the transgenic ES cell lines constitutively expressing Flag-H3.1 variant. A DNA fragment coding the histone variant tagged with Flag on its N-terminal was inserted into EcoRI site of the pCAGGS vector. Puromycin N-acetyl-transferase (Pac) gene obtained from salI digestion of pCre-Pac was inserted into the salI site of the vectors. The vector coding a Flag-histone variant was transfected into the ZHBTc4 cells by lipofection, and the cells were selected in the ES medium with 100 ??g/mL of puromycin. A single colony of the cells thus obtained for the variant was picked up and cultured. Histone macroH2A2 ZHBTc4 is derived from ZHTc6 and maintained by tetracycline (Tc)-regulatable Oct-3/4 transgene. Both of Oct-3/4 locus are disrupted by IRES-zeocin and IRES-BSD KO vectors. It should be cultured in the absence of tetraycline to maintain the undifferentiated state. pCAGGS vector was used to generate the transgenic ES cell lines constitutively expressing Flag-MacroH2A variant. A DNA fragment coding the histone variant tagged with Flag on its N-terminal was inserted into EcoRI site of the pCAGGS vector. Puromycin N-acetyl-transferase (Pac) gene obtained from salI digestion of pCre-Pac was inserted into the salI site of the vectors. The vector coding a Flag-histone variant was transfected into the ZHBTc4 cells by lipofection, and the cells were selected in the ES medium with 100 ??g/mL of puromycin. A single colony of the cells thus obtained for the variant was picked up and cultured. Histone H2A.Z ZHBTc4 is derived from ZHTc6 and maintained by tetracycline (Tc)-regulatable Oct-3/4 transgene. Both of Oct-3/4 locus are disrupted by IRES-zeocin and IRES-BSD KO vectors. It should be cultured in the absence of tetraycline to maintain the undifferentiated state. pCAGGS vector was used to generate the transgenic ES cell lines constitutively expressing Flag-H2A.Z variant. A DNA fragment coding the histone variant tagged with Flag on its N-terminal was inserted into EcoRI site of the pCAGGS vector. Puromycin N-acetyl-transferase (Pac) gene obtained from salI digestion of pCre-Pac was inserted into the salI site of the vectors. The vector coding a Flag-histone variant was transfected into the ZHBTc4 cells by lipofection, and the cells were selected in the ES medium with 100 ??g/mL of puromycin. A single colony of the cells thus obtained for the variant was picked up and cultured. Histone H2A.X ZHBTc4 is derived from ZHTc6 and maintained by tetracycline (Tc)-regulatable Oct-3/4 transgene. Both of Oct-3/4 locus are disrupted by IRES-zeocin and IRES-BSD KO vectors. It should be cultured in the absence of tetraycline to maintain the undifferentiated state. pCAGGS vector was used to generate the transgenic ES cell lines constitutively expressing Flag-H2A.X variant. A DNA fragment coding the histone variant tagged with Flag on its N-terminal was inserted into EcoRI site of the pCAGGS vector. Puromycin N-acetyl-transferase (Pac) gene obtained from salI digestion of pCre-Pac was inserted into the salI site of the vectors. The vector coding a Flag-histone variant was transfected into the ZHBTc4 cells by lipofection, and the cells were selected in the ES medium with 100 ??g/mL of puromycin. A single colony of the cells thus obtained for the variant was picked up and cultured. Histone H2A ZHBTc4 is derived from ZHTc6 and maintained by tetracycline (Tc)-regulatable Oct-3/4 transgene. Both of Oct-3/4 locus are disrupted by IRES-zeocin and IRES-BSD KO vectors. It should be cultured in the absence of tetraycline to maintain the undifferentiated state. pCAGGS vector was used to generate the transgenic ES cell lines constitutively expressing Flag-H2A variant. A DNA fragment coding the histone variant tagged with Flag on its N-terminal was inserted into EcoRI site of the pCAGGS vector. Puromycin N-acetyl-transferase (Pac) gene obtained from salI digestion of pCre-Pac was inserted into the salI site of the vectors. The vector coding a Flag-histone variant was transfected into the ZHBTc4 cells by lipofection, and the cells were selected in the ES medium with 100 ??g/mL of puromycin. A single colony of the cells thus obtained for the variant was picked up and cultured. Others Six2 The embryonic kidneys (at E16.5) of the wild type mouse were fixed for 30min, sonicated, and mixed with anti-Six2 antibody (Proteintech) at 4C overnight, followed by precipitation by using Dynabeads M-280 conjugated with anti-rabbit IgG (Invitrogen). Others Sall1 The embryonic kidneys (at E16.5) of the wild type mouse were fixed for 30min, sonicated, and mixed with anti-Sall1 antibody (Abcam) at 4C overnight, followed by precipitation by using Dynabeads M-280 conjugated with anti-rabbit IgG (Invitrogen). Input control Input control Mouse na?ve CD4 T cells were stimulated under Th2 conditions for 3 days, this sample is whole cell extract as ChIP-seq cotrol. Input control Input control Mouse na?ve CD4 T cells were stimulated under Th1 conditions for 3 days, this sample is whole cell extract as ChIP-seq cotrol. Others Chd4 Mouse na?ve CD4 T cells were stimulated under Th2 conditions for 3 days, then ChIP-seq for Chd4 was performed. Others Chd4 Mouse na?ve CD4 T cells were stimulated under Th1 conditions for 3 days, then ChIP-seq for Chd4 was performed. Histone H3K27me3 GMPs from Ezh2 KO IP H3K27me3 Input control Input control GMPs from Ezh2 KO input Histone H3K27me3 GMPs from WT IP H3K27me3 Input control Input control GMPs from WT input Histone H3K27me3 GMPs from DKO IP H3K27me3 Input control Input control GMPs from DKO input Histone H3K27me3 GMPs from TET2KO IP H3K27me3 Input control Input control GMPs from TET2 KO input Input control Input control ChIP-seq Input Histone H3K27ac ChIP-seq for H3K27Ac Unclassified Unclassified source:3T3-L1 cells, day 8 of differentiation growth_protocol:3T3-L1 cells were maintained in DMEM, supplemented with 10% FBS. For adipocyte differentiation, two days after confluence, 3T3-L1 cells were treated with dexamethasone (1 uM), IBMX (0.5 mM), and insulin (5 ug/ml) (DMI) for 48 hours, followed by treatment with insulin alone, with medium replacement every two days thereafter. Unclassified Unclassified source:3T3-L1 cells, day 0 of differentiation growth_protocol:3T3-L1 cells were maintained in DMEM, supplemented with 10% FBS. Input control Input control MLL-AF9 induced AML Ezh2 knockout (input) Input control Input control MLL-AF9 induced AML Ezh2 wild type (input) Histone H3K27me3 MLL-AF9 induced AML Ezh2 knockout (H3K27me3) Histone H3K27me3 MLL-AF9 induced AML Ezh2 wild type (H3K27me3) Others Chd2 mouse EB5 cell lines medium condition:rLIF(+) 1% formaldehyde 5min. fixation immunoprecipitated anti-CHD2 moAb Input control Input control mouse EB5 cell lines medium condition:rLIF(+) 1% formaldehyde 5min. fixation input sample Others Chd2 source: C2C12 cells transfected mir5111 targeted Chd2 Unclassified Unclassified source:C2C12 cells