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EPD viewer for M. musculus (March 2012 GRCm38/mm10), version 003

The EPD viewer for M. musculus 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
track subset: Nucleosomes
1 Liver nucleosomes centered MNase tagsa 20 n/a GSM1425447, GSM1425448 SRA liver n/a n/awest14 25158628
2 ESC nucleosomes centered MNase tagsa 20 n/a GSM1425441, GSM1425442 SRA embryonic stem cells n/a n/awest14 25158628
3 iPSC nucleosomes centered MNase tagsa 20 n/a GSM1425443, GSM1425444 SRA induced pluripotent stem cells n/a n/awest14 25158628
4 TTF nucleosomes centered MNase tagsa 20 n/a GSM1425445, GSM1425446 SRA tail-tip fibroblasts n/a n/awest14 25158628
track subset: Selected Histone Marks
5 Myoblasts H3K4me1 centered H3K4me1 ChIP-seq tagsb 10 n/a GSM721288 TXT myoblasts n/a n/aasp11 21551099
6 Myoblasts H3K4me3 centered H3K4me3 ChIP-seq tagsb 10 n/a GSM721292 TXT myoblasts n/a n/aasp11 21551099
7 Myoblasts Pol2 centered RNA Pol II ChIP-seq tagsc 10 n/a GSM721286 TXT myoblasts n/a n/aasp11 21551099
8 All CAGE (+) 5′ end of CAGE reads 1 + FANTOM5 BAM all adult tissues merged n/a n/afantom5 24670764
9 Fantom5 CAGE 5′ end of CAGE reads 1 +/− FANTOM5 BAM 508 tissuesd n/a n/afantom5 24670764
10 All CAGE (-) 5′ end of CAGE reads 1 − FANTOM5 BAM all adult tissues merged n/a n/afantom5 24670764
11 EPDnew promoters EPDnew promoters v. 003 1e n/af n/a n/a n/a n/a n/aepd 23193273
12 EPDnewNC promoters EPDnewNC promoters v. 001 1e n/af n/a n/a n/a n/a n/aepd-nc 23193273
athe midpoint between paired-end fragments was used
btags were centered by 75 bp (ends were shifted 75 bp downstream or upstream if on the + or − strand respectively)
ctags were centered by 50 bp
dbiological and technical replicates were merged
ethe thick part represents the TSS plus the 10 bp downstream while the thin part represents the 49 bp upstream of the TSS
fpromoters 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". Tracks with green background are composite tracks composed of a large number of tissues, of which a specific panel may be selected in the genome browser using track configuration.

Last update November 2024