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EPD viewer for D. rerio (July 2010 Zv9/danRer7), version 001

The EPD viewer for D. rerio 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 MNase (256-cell) centered MNase-seq tagsa 25 n/a GSE44269 SRA n/a 256-cell embryo n/azhang14 24285721
2 MNase (dome) centered MNase-seq tagsa 25 n/a GSE44269 SRA n/a dome n/azhang14 24285721
3 Dome H3K4me3 centered H3K4me3 ChIP-seq tagsb 10 n/a GSM1081556 SRA n/a dome n/azhang14 24285721
4 Dome Pol2 centered RNA Pol II ChIP-seq tagsc 10 n/a GSM1081560, GSM1081559 SRA n/a dome n/azhang14 24285721
5 All CAGE (+) 5′ end of CAGE reads 1 + SRP013950 SRA n/a all stages merged n/anepal13 24002785
track subset: CAGE reads at various stages
6 (+) Unfert. Egg 5′ end of CAGE reads 1 + SRX156307 SRA n/a unfertilized egg n/anepal13 24002785
7 (+) Fert. Egg 5′ end of CAGE reads 1 + SRX156325 SRA n/a fertilized egg n/anepal13 24002785
8 (+) 64 Cell Em. 5′ end of CAGE reads 1 + SRX156334 SRA n/a 64-cell embryo n/anepal13 24002785
9 (+) 512 Cell Em. 5′ end of CAGE reads 1 + SRX156336 SRA n/a 512-cell embryo n/anepal13 24002785
10 (+) High Em. 5′ end of CAGE reads 1 + SRX156337 SRA n/a high embryo n/anepal13 24002785
11 (+) Oblong Em. 5′ end of CAGE reads 1 + SRX156338 SRA n/a oblong embryo n/anepal13 24002785
12 (+) Sphere Em. 5′ end of CAGE reads 1 + SRX156347 SRA n/a sphere/dome embryo n/anepal13 24002785
13 (+) Dome 30 Em. 5′ end of CAGE reads 1 + SRX156349 SRA n/a dome/30% epiboly n/anepal13 24002785
14 (+) Shield Em. 5′ end of CAGE reads 1 + SRX156350 SRA n/a shield embryo n/anepal13 24002785
15 (+) 14 Somites Em. 5′ end of CAGE reads 1 + SRX156352 SRA n/a 14-somite embryo n/anepal13 24002785
16 (+) Prim-6 Em. 5′ end of CAGE reads 1 + SRX156355 SRA n/a prim-6 embryo n/anepal13 24002785
17 (+) Prim-20 Em. 5′ end of CAGE reads 1 + SRX156356 SRA n/a prim-20 embryo n/anepal13 24002785
18 (-) Unfert. Egg 5′ end of CAGE reads 1 SRX156307 SRA n/a unfertilized egg n/anepal13 24002785
19 (-) Fert. Egg 5′ end of CAGE reads 1 SRX156325 SRA n/a fertilized egg n/anepal13 24002785
20 (-) 64 Cell Em. 5′ end of CAGE reads 1 SRX156334 SRA n/a 64-cell embryo n/anepal13 24002785
21 (-) 512 Cell Em. 5′ end of CAGE reads 1 SRX156336 SRA n/a 512-cell embryo n/anepal13 24002785
22 (-) High Em. 5′ end of CAGE reads 1 SRX156337 SRA n/a high embryo n/anepal13 24002785
23 (-) Oblong Em. 5′ end of CAGE reads 1 SRX156338 SRA n/a oblong embryo n/anepal13 24002785
24 (-) Sphere Em. 5′ end of CAGE reads 1 SRX156347 SRA n/a sphere/dome embryo n/anepal13 24002785
25 (-) Dome 30 Em. 5′ end of CAGE reads 1 SRX156349 SRA n/a dome/30% epiboly n/anepal13 24002785
26 (-) Shield Em. 5′ end of CAGE reads 1 SRX156350 SRA n/a shield embryo n/anepal13 24002785
27 (-) 14 Somites Em. 5′ end of CAGE reads 1 SRX156352 SRA n/a 14-somite embryo n/anepal13 24002785
28 (-) Prim-6 Em. 5′ end of CAGE reads 1 SRX156355 SRA n/a prim-6 embryo n/anepal13 24002785
29 (-) Prim-20 Em. 5′ end of CAGE reads 1 SRX156356 SRA n/a prim-20 embryo n/anepal13 24002785
30 All CAGE (-) 5′ end of CAGE reads 1 SRP013950 SRA n/a all stages merged n/anepal13 24002785
31 EPDnew promoters EPDnew promoters v. 001 1d n/ae n/a n/a n/a n/a n/aepd 23193273
atags were centered by 75 bp (ends were shifted 75 bp downstream or upstream if on the + or − strand respectively)
btags were centered by 80 bp
ctags were centered by 35 bp
dthe thick part represents the TSS plus the 10 bp downstream while the thin part represents the 49 bp upstream of the TSS
epromoters 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