ERX008733	SAMEA1022708	CTCF_binding_evolution_in_mammals	ChIP-Seq	GENOMIC	ChIP	0	Application_Read	Forward	1	Illumina_Genome_Analyzer	ERA015135	ERS017355	ERP000395	PRJEB2329	2014-08-12T15:05:18Z	Organism taxonomy_id="10116" taxonomy_name="Rattus norvegicus"	Alias=E-MTAB-437:rat ChIP 1	Broker name=ArrayExpress	CellType=hepatocytes	Description=Protocols: The animal livers were crosslinked with formaldehyde treatment and chromatin fragmented to an average of 300 bp by sonication. Chromatin from an mass equivalent of 1/4 mouse liver was used for each ChIP experiment. Solexa libraries were prepared following the instructions of Illumina (Sample preparation for genomic DNA - version 2.2) with the following modifications. The ChIP-enriched DNA and input DNA were not further fragmented. After end-repair and addition of an A base to the 3 prime ends, the adapters were ligated to the ends of the DNA Fragments using 2 ml of fourtyfold diluted Adapter oligo mix in a total reaction volume of 25 ml. Between these steps, the DNA was purified using the DNA Clean-and-Concentrator-5 kit (Zymo Research). Subsequently, the DNA was amplified by 18 cycles of PCR, purified with QIAquick PCR purification Kit, and eluted with 33.5 ml of 10 mM tris buffer at pH7.0. The PCR-product was sized fractionated on 2 percent agarose gel and a gel slice containing the 200-300 bp fragments was excised. Hepatocytes were prepared by direct perfusion of the liver with buffered salt solution followed by percent formaldehyde. After 10 minutes the tissue was removed and diced in 500 mM glycine buffer to neutralize the formaldehyde. After homogenization the hepatocytes were rinsed with PBS.	INSDC center alias=CRUK-CRI	INSDC center name=CRUK-CRI	INSDC first public=2011-11-01T17:00:25Z	INSDC last update=2018-03-08T15:25:19Z	INSDC status=public	SRA accession=ERS017355	Sample Name=ERS017355	Sex=male	Tissue=liver	Title=rat ChIP 1