EPD viewer for Z. mays (Oct 2013 B73 RefGen_v3/zm3), version 001

The EPD viewer for Z. mays 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 Shoot H3K4me3 centered H3K4me3 ChIP-seq tagsa 25 n/a GSM381695 SRA shoot n/a n/awang09 19376930
2 All CAGE (+) 5′ end of CAGE reads 1 + GSE70251 SRA root and shoot merged n/a B73 and Mo17 lines mergedguerra15 26628745
3 All CAGE (-) 5′ end of CAGE reads 1 − GSE70251 SRA root and shoot merged n/a B73 and Mo17 lines mergedguerra15 26628745
4 EPDnew promoters EPDnew promoters v. 001 1b n/ac n/a n/a n/a n/a n/aepd 23193273
5 RefSeq genes RefSeq gene annotation 1 n/a ftp.ncbi.n... GFF n/a n/a n/an/a 22121212
atags were centered by 50 bp (ends were shifted 50 bp downstream or upstream if on the + or − strand respectively)
bthe thick part represents the TSS plus the 10 bp downstream while the thin part represents the 49 bp upstream of the TSS
cpromoters 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