EPD viewer for S. pombe (Aug 2015 ASM294v2/spo2), version 002

The EPD viewer for S. pombe is made of the tracks given in the table below. The genome sequence track is provided by the EPD team (sequence was downloaded here). 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 20 n/a SRP028538 SRA n/a n/a wild-typedegennaro13 24100010
2 H3K4me3 (WT) centered H3K4me3 ChIP-seq tagsb 10 n/a GSM1201989 SRA n/a n/a wild-typedegennaro13 24100010
3 All CAGE (+) 5′ end of CAGE reads 1 + E-MTAB-3188, GSE110976 FASTQ n/a n/a wild-typeli15, thodberg18 25747261
4 All CAGE (-) 5′ end of CAGE reads 1 − E-MTAB-3188, GSE110976 FASTQ n/a n/a wild-typeli15, thodberg18 25747261
5 EPDnew promoters EPDnew promoters v. 002 1c n/ad n/a n/a n/a n/a n/aepd 23193273
6 RefSeq genes RefSeq gene annotation 1 n/a ftp.ncbi.n... GFF n/a n/a n/an/a 22121212
athe midpoint between paired-end fragments was calculated
btags were centered by 50 bp (ends were shifted 50 bp downstream or upstream if on the + or − strand respectively)
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