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EPD viewer for H. vulgare (Apr 2021 GCF_904849725.1/MorexV3), version 000

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 EPDnew Barley promoters from EPDnew version 000a n/a n/ac n/ab n/a n/a n/a n/a epd n/a
2 pavlu23_tcs TSS clusters from Pavlu et al. 2023 1c n/ad Pavlu et al. 2023 Suppl. data file S1 BED-like n/a n/a n/a pavlu23 38173877
3 All CAGE (+) Barley embryo all CAGE(+) 1 + GSE227219 FASTQ all samples merged n/a n/a pavlu23 38173877
4 All CAGE (-) Barley embryo all CAGE(-) 1 − GSE227219 FASTQ all samples merged n/a n/a pavlu23 38173877
5 pavlu_2023_CAGE Barley embryo CAGE 1 +/− GSE227219 FASTQ embryo 3 stages n/a pavlu23 38173877
6 pavlu_2023_MNase Barley embryo ChIP-seq_Mnas 10,25,50e n/a GSE227219 FASTQ embryo 3 stages n/a pavlu23 38173877
a the thick part represents the TSS plus the 10 bp downstream while the thin part represents the 49 bp upstream of the TSS
b promoters 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
c the thick part (1 bp) represents the summit position indicated in the TSS cluster list. The thin part indicates the region cluster region as defined by the start and end position in the BED file
d promoters on the + and − strands are combined in a single track
e 10 for all merged and merged H3k4me3 samples, 25 for individual H3K4me3 and merged H3K9ac,H3k27me3 sammples; 50 for individal H3K9ac,H3k27me3 sammples

These tracks are available at UCSC as a public hub named "EPD Viewer Hub".

Last update November 2024