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/a | zhang14 | 24285721 |
2 | MNase (dome) | centered MNase-seq tagsa | 25 | n/a | GSE44269 | SRA | n/a | dome | n/a | zhang14 | 24285721 |
3 | Dome H3K4me3 | centered H3K4me3 ChIP-seq tagsb | 10 | n/a | GSM1081556 | SRA | n/a | dome | n/a | zhang14 | 24285721 |
4 | Dome Pol2 | centered RNA Pol II ChIP-seq tagsc | 10 | n/a | GSM1081560, GSM1081559 | SRA | n/a | dome | n/a | zhang14 | 24285721 |
5 | All CAGE (+) | 5′ end of CAGE reads | 1 | + | SRP013950 | SRA | n/a | all stages merged | n/a | nepal13 | 24002785 |
track subset: CAGE reads at various stages | |||||||||||
6 | (+) Unfert. Egg | 5′ end of CAGE reads | 1 | + | SRX156307 | SRA | n/a | unfertilized egg | n/a | nepal13 | 24002785 |
7 | (+) Fert. Egg | 5′ end of CAGE reads | 1 | + | SRX156325 | SRA | n/a | fertilized egg | n/a | nepal13 | 24002785 |
8 | (+) 64 Cell Em. | 5′ end of CAGE reads | 1 | + | SRX156334 | SRA | n/a | 64-cell embryo | n/a | nepal13 | 24002785 |
9 | (+) 512 Cell Em. | 5′ end of CAGE reads | 1 | + | SRX156336 | SRA | n/a | 512-cell embryo | n/a | nepal13 | 24002785 |
10 | (+) High Em. | 5′ end of CAGE reads | 1 | + | SRX156337 | SRA | n/a | high embryo | n/a | nepal13 | 24002785 |
11 | (+) Oblong Em. | 5′ end of CAGE reads | 1 | + | SRX156338 | SRA | n/a | oblong embryo | n/a | nepal13 | 24002785 |
12 | (+) Sphere Em. | 5′ end of CAGE reads | 1 | + | SRX156347 | SRA | n/a | sphere/dome embryo | n/a | nepal13 | 24002785 |
13 | (+) Dome 30 Em. | 5′ end of CAGE reads | 1 | + | SRX156349 | SRA | n/a | dome/30% epiboly | n/a | nepal13 | 24002785 |
14 | (+) Shield Em. | 5′ end of CAGE reads | 1 | + | SRX156350 | SRA | n/a | shield embryo | n/a | nepal13 | 24002785 |
15 | (+) 14 Somites Em. | 5′ end of CAGE reads | 1 | + | SRX156352 | SRA | n/a | 14-somite embryo | n/a | nepal13 | 24002785 |
16 | (+) Prim-6 Em. | 5′ end of CAGE reads | 1 | + | SRX156355 | SRA | n/a | prim-6 embryo | n/a | nepal13 | 24002785 |
17 | (+) Prim-20 Em. | 5′ end of CAGE reads | 1 | + | SRX156356 | SRA | n/a | prim-20 embryo | n/a | nepal13 | 24002785 |
18 | (-) Unfert. Egg | 5′ end of CAGE reads | 1 | − | SRX156307 | SRA | n/a | unfertilized egg | n/a | nepal13 | 24002785 |
19 | (-) Fert. Egg | 5′ end of CAGE reads | 1 | − | SRX156325 | SRA | n/a | fertilized egg | n/a | nepal13 | 24002785 |
20 | (-) 64 Cell Em. | 5′ end of CAGE reads | 1 | − | SRX156334 | SRA | n/a | 64-cell embryo | n/a | nepal13 | 24002785 |
21 | (-) 512 Cell Em. | 5′ end of CAGE reads | 1 | − | SRX156336 | SRA | n/a | 512-cell embryo | n/a | nepal13 | 24002785 |
22 | (-) High Em. | 5′ end of CAGE reads | 1 | − | SRX156337 | SRA | n/a | high embryo | n/a | nepal13 | 24002785 |
23 | (-) Oblong Em. | 5′ end of CAGE reads | 1 | − | SRX156338 | SRA | n/a | oblong embryo | n/a | nepal13 | 24002785 |
24 | (-) Sphere Em. | 5′ end of CAGE reads | 1 | − | SRX156347 | SRA | n/a | sphere/dome embryo | n/a | nepal13 | 24002785 |
25 | (-) Dome 30 Em. | 5′ end of CAGE reads | 1 | − | SRX156349 | SRA | n/a | dome/30% epiboly | n/a | nepal13 | 24002785 |
26 | (-) Shield Em. | 5′ end of CAGE reads | 1 | − | SRX156350 | SRA | n/a | shield embryo | n/a | nepal13 | 24002785 |
27 | (-) 14 Somites Em. | 5′ end of CAGE reads | 1 | − | SRX156352 | SRA | n/a | 14-somite embryo | n/a | nepal13 | 24002785 |
28 | (-) Prim-6 Em. | 5′ end of CAGE reads | 1 | − | SRX156355 | SRA | n/a | prim-6 embryo | n/a | nepal13 | 24002785 |
29 | (-) Prim-20 Em. | 5′ end of CAGE reads | 1 | − | SRX156356 | SRA | n/a | prim-20 embryo | n/a | nepal13 | 24002785 |
30 | All CAGE (-) | 5′ end of CAGE reads | 1 | − | SRP013950 | SRA | n/a | all stages merged | n/a | nepal13 | 24002785 |
31 | EPDnew promoters | EPDnew promoters v. 001 | 1d | n/ae | n/a | n/a | n/a | n/a | n/a | epd | 23193273 |
These tracks are available at UCSC as a public hub named "EPD Viewer Hub".