EPD viewer for C. elegans (May 2008 WS190/ce6), version 001

The EPD viewer for C. elegans 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
1 Nucleosomes centered MNase-seq tagsa 10 n/a GSE20136 SRA n/a all stages merged n/aercan11 21177966
track subset: Nucleosomes at various stages
2 Nucleosomes (MS) centered MNase-seq tags 10 n/a GSM514735 SRA n/a mixed stage embryos n/aercan11 21177966
3 Nucleosomes (GL) centered MNase-seq tags 10 n/a GSM514736 SRA n/a young germline-less adults n/aercan11 21177966
4 Nucleosomes (GC) centered MNase-seq tags 10 n/a GSM590213 SRA n/a young germline-containing adults n/aercan11 21177966
5 Nucleosomes (L3) centered MNase-seq tags 10 n/a GSM590214 SRA n/a L3 stage XO hermaphrodites n/aercan11 21177966
6 H3K4me3 centered H3K4me3 ChIP-seq tagsb 10 n/a GSM1208361, GSM1208362 SRA whole embryo n/a n/achen14 24653213
7 GRO-cap (+) 5′ end of GRO-cap reads 1 + GSE43087 SRA n/a n/a n/akruesi13 23795297
8 GRO-cap (-) 5′ end of GRO-cap reads 1 − GSE43087 SRA n/a n/a n/akruesi13 23795297
9 EPDnew promoters EPDnew promoters v. 001 1c n/ad n/a n/a n/a n/a n/aepd 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 80 bp
cthe thick part represents the TSS plus the 10 bp downstream while the thin part represents the 49 bp upstream of the TSS
dpromoters 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".

Last update October 2019