nepal13, Zebrafish TSS landscape during development


CAGE and histone modification maps in zebrafish during embryonic development.

Overview of samples:

Filename Description Feature GEO-ID
1 unfertilized_egg.sga CAGE from unfertilised egg CAGE -
2 fertilized_egg.sga CAGE from fertilised egg CAGE -
3 64_cells_embryo.sga CAGE from 64-cell embryo CAGE -
4 512_cells_embryo.sga CAGE from 512-cell embryo CAGE -
5 high_embryo.sga CAGE from high embryo CAGE -
6 oblong_embryo.sga CAGE from oblong embryo CAGE -
7 sphere-dome_embryo.sga CAGE from sphere-dome embryo CAGE -
8 dome30_epiboly_embryo.sga CAGE from dome-30%-epiboly embryo CAGE -
9 shield_embryo.sga CAGE from shield embryo CAGE -
10 14somites_embryo.sga CAGE from 14 somites embryo CAGE -
11 prim6_embryo.sga CAGE from prim-6 embryo CAGE -
12 prim20_embryo.sga CAGE from prim-20 embryo CAGE -
13 H2AZ_dome30_epiboly_embryo.sga H2A.Z from dome-30%-epiboly embryo H2AZ -
14 H3K4me3_512_cells_embryo.sga H3K4me3 from 512-cell embryo H3K4me3 -
15 H3K4me3_oblong_embryo.sga H3K4me3 from oblong embryo H3K4me3 -
16 H3K4me3_dome30_epiboly_embryo_run1.sga H3K4me3 from dome-30%-epiboly embryo, rep1 H3K4me3 -
17 H3K4me3_dome30_epiboly_embryo_run2.sga H3K4me3 from dome-30%-epiboly embryo, rep2 H3K4me3 -
18 H3K4me3_prim6_embryo.sga H3K4me3 from prim-6 embryo, rep1 H3K4me3 -
19 H3K4me3_prim6_embryo_run1.sga H3K4me3 from prim-6 embryo, rep2 H3K4me3 -
20 Control_dome30_epiboly_embryo.sga Control from dome-30%-epiboly embryo Control -
21 Control_prim6_embryo.sga Control from prim-6 embryo Control -

Technical Notes

Raw data was downloaded from NCBI SRA database (ID SRA055273) and mapped to Zv9/danRer7 genome using Bowtie aligner. The resulting SAM files were converted to BED using SAMtools and BEDtools. Final conversion to SGA files was done using ChIP-Seq.


Nepal C, Hadzhiev Y, Previty C, Haberle V, Li N, Takahashi H, Suzuki AM, Sheng Y, Abdelhamid R, Anand S, Gehrig J, Akalin A, Kockx C, van der Sloot A, van Ijcken W, Armant O, Rastegar S, Straehle U, Stupka E, Carninci P, Lenhard B, Muller F.
Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. Genome Res. 2013 Sep 3. [Epub ahead of print] PubMed PMID: 24002785

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