EPD viewer for R. norvegicus (Jul 2014 Rnor_6.0/rn6), version 001

The EPD viewer for R. norvegicus 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 All CAGE (+) 5′ end of CAGE reads 1 + FANTOM5 BAM all tissues merged n/a n/alizio17 29182598
track subset: Selected FANTOM CAGE samples
2 (+) AortSmMuscDiff 5′ end of CAGE reads 1 + FANTOM5 BAM aortic smooth muscle cells n/a differentiatedlizio17 29182598
3 (+) AortSmoothMusc 5′ end of CAGE reads 1 + FANTOM5 BAM aortic smooth muscle cells n/a undifferentiatedlizio17 29182598
4 (+) Hepatocytes 5′ end of CAGE reads 1 + FANTOM5 BAM hepatocytes n/a n/alizio17 29182598
5 (+) MesencStmCells 5′ end of CAGE reads 1 + FANTOM5 BAM mesenchymal stem cells n/a n/alizio17 29182598
6 (+) Universal RNA 5′ end of CAGE reads 1 + FANTOM5 BAM universal RNA n/a n/alizio17 29182598
7 (-) AorticSmMuscDiff 5′ end of CAGE reads 1 − FANTOM5 BAM aortic smooth muscle cells n/a differentiatedlizio17 29182598
8 (-) AortSmMuscle 5′ end of CAGE reads 1 − FANTOM5 BAM aortic smooth muscle cells n/a undifferentiatedlizio17 29182598
9 (-) Hepatocytes 5′ end of CAGE reads 1 − FANTOM5 BAM hepatocytes n/a n/alizio17 29182598
10 (-) MesencStmCells 5′ end of CAGE reads 1 − FANTOM5 BAM mesenchymal stem cells n/a n/alizio17 29182598
11 (-) Universal RNA 5′ end of CAGE reads 1 − FANTOM5 BAM universal RNA n/a n/alizio17 29182598
12 All CAGE (-) 5′ end of CAGE reads 1 − FANTOM5 BAM all tissues merged n/a n/alizio17 29182598
13 EPDnew promoters EPDnew promoters v. 001 1a n/ab n/a n/a n/a n/a n/aepd 23193273
athe thick part represents the TSS plus the 10 bp downstream while the thin part represents the 49 bp upstream of the TSS
bpromoters 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