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EPD viewer for A. thaliana (Feb 2011 TAIR10/araTha1), version 004

The EPD viewer for A. thaliana 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 GSM1216733 SRA n/a seedling n/ali14 24606212
2 GFP H3K4me3 centered H3K4me3 ChIP-seqb 20 n/a GSM2302418 SRA root n/a GFPdeLucas16 27650334
3 All CAGE (+) 5′ end of PEAT reads 1 + megraw.cgr... BAM root n/a n/amorton14 25035402
4 All CAGE (-) 5′ end of PEAT reads 1 megraw.cgr... BAM root n/a n/amorton14 25035402
5 EPDnew promoters EPDnew promoters v. 004 1c n/ad n/a n/a n/a n/a n/aepd 23193273
6 RefSeq genes RefSeq gene annotation 1 n/a arabidopsi... GFF n/a n/a n/an/a 22121212
atags were centered by 73 bp (ends were shifted 73 bp downstream or upstream if on the + or − strand respectively)
btags were centered by 60 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