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Data name ⇅ Database name ⇅ DOI ⇅ Description of data contents ⇅ Data file ⇅ Simple search URL ⇅ Data acquisition method ⇅ Data analysis method ⇅ Number of data entries ⇅ Data detail
(reprocessed)HeliscopeCAGE sequencing, Delve mapping and CAGE TSS aggregation FANTOM5 10.18908/lsdba.nbdc01389-008.V003

Time course and snapshot data by HeliScopeCAGE
Human and mouse reads are re-mapped to new reference genome sequences (hg38/mm10).
"basic" directory contains the following:
 

00_.assay_sdrf.txt:
Experimental information for each sample (tabbed text)
*.bam:
Binary read mapping results (BAM format)
*.bam.bai:
Indexes of BAM files
*.ctss.bed.gz:
TSS (CTSS) identified by CAGE tag analysis (BED format)
*.rdna.fa.gz:
rDNA sequences (FASTA format)

 fantom5_rp_exp_details.zip
(237 KB) 		http://togodb.biosciencedbc.jp/togodb/view/fantom5_rp_exp_details#en

HeliScopeCAGE (http://fantom.gsc.riken.jp/protocols/heliscope.html)
Delve (Alignment software for short read) (http://fantom.gsc.riken.jp/jp/software/)

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Data detail open_in_full
(reprocessed)pooled_ctss FANTOM5 10.18908/lsdba.nbdc01389-013.V003

Mapping results of the all CAGE tags used from phase1.0 to phase2.0
Human and mouse reads are re-mapped for new reference sequences (hg38/mm10).

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(6.5 GB) 		-

Human: 2 files / Mouse: 2 files
Data detail open_in_full
CAGE peaks FANTOM5 10.18908/lsdba.nbdc01389-002.V003

Data about CAGE peak regions and RNA transcriptional initiation activities measured by CAGE

 CAGE_peaks
(4.1 GB) 		-

CAGE
DPI (Decomposition-based peak identification)

 35 files
Data detail open_in_full
CAGE peaks identified as true TSS by TSS classifier FANTOM5 10.18908/lsdba.nbdc01389-007.V003

Evaluation of CAGE peaks
It shows that the sequence close to CAGE peak has "TSS-like" or not. "TSS_human.bed.gz" and "TSS_mouse.bed.gz" contain identified TSS.

 TSS_classifier
(32 MB) 		-

TSS Classifier（http://sourceforge.net/p/tometools/wiki/TssClassifier/）

 4 files
Data detail open_in_full
CAGE_peaks_annotation FANTOM5 10.18908/lsdba.nbdc01389-010.V003

Annotation of human and mouse CAGE peaks and RNA transcriptional initiation activities by CAGE

 CAGE_peaks_annotation
(195 MB) 		-

CAGE

 9 files
Data detail open_in_full
Data name Database name DOI Description of data contents Data file Simple search URL Data acquisition method Data analysis method Number of data entries Data detail