EPD viewer for H. sapiens (Dec 2013 GRCh38/hg38), version 006

The EPD viewer for H. sapiens is made of the tracks given in the table below. Note that when strand is n/a, it means that signal applies to both strands.

UCSC track name Track description Track resolution [bp] Strand Original dataset Raw format Tissue Stage/Time point Condition MGA series name PMID
track subset: Selected histone marks
1 H3K4me1 centered H3K4me1 ChIP-seq tagsa 20 n/a SRP000201 BED CD4+ T cells n/a n/abarski07 17512414
2 H3K4me3 centered H3K4me3 ChIP-seq tagsa 20 n/a SRP000201 BED CD4+ T cells n/a n/abarski07 17512414
3 Pol2 centered RNA Pol II ChIP-seq tagsb 20 n/a SRP000201 BED CD4+ T cells n/a n/abarski07 17512414
4 Roadmap histones centered ChIP-seq tags for 31 histone marksc 20 or 100d n/a ftp.ncbi.n... BED 116 tissues n/a n/aroadmap 25693562
5 All CAGE (+) 5′ end of CAGE reads 1 + GSE34448 BAM all cell lines merged n/a n/aGSE34448 22955620
6 ENCODE CAGE 5′ end of CAGE reads 1 +/− GSE34448 BAM 35 cell linese n/a n/aGSE34448 22955620
7 All CAGE (-) 5′ end of CAGE reads 1 − GSE34448 BAM all cell lines merged n/a n/aGSE34448 22955620
8 All RAMPAGE (+) 5′ end of RAMPAGE reads 1 + encodeproj... BAM all samples merged n/a n/arampage 22936248
9 All RAMPAGE (-) 5′ end of RAMPAGE reads 1 − encodeproj... BAM all samples merged n/a n/arampage 22936248
10 All Fantom5 (+) 5′ end of CAGE reads 1 + fantom.gsc... BAM all samples merged n/a n/afantom5 24670764
11 Fantom5 CAGE 5′ end of CAGE reads 1 +/− fantom.gsc... BAM 555 tissuesf n/a n/afantom5 24670764
12 All Fantom5 (-) 5′ end of CAGE reads 1 − fantom.gsc... BAM all samples merged n/a n/afantom5 24670764
13 EPDnew promoters EPDnew promoters v. 006 1g n/ah n/a n/a n/a n/a n/aepd 23193273
14 EPDnewNC promoters EPDnewNC promoters v. 001 1g n/ah n/a n/a n/a n/a n/aepd-nc 23193273
atags were centered by 73 bp (ends were shifted 73 bp downstream or upstream if on the + or − strand respectively)
btags were centered by 40 bp
ctags were centered by 70 bp
da 20-bp resolution was used for H3K4 methylations and for all acetylations
ecellular long poly-A(+) samples only
fbiological and technical replicates were merged
gthe thick part represents the TSS plus the 10 bp downstream while the thin part represents the 49 bp upstream of the TSS
hpromoters on the + and − strands are combined in a single track, with promoter orientation defined by the position of the thick part relative to the thin part

These tracks are available at UCSC as a public hub named "EPD Viewer Hub". Tracks with green background are composite tracks composed of a large number of tissues, of which a specific panel may be selected in the genome browser using track configuration.

Last update October 2019