Nepal 2013, Zebrafish TSS landscape during development.


CAGE and histone modification maps during zebrafish embryonic development.



From D. rerio (July 2010 Zv9/danRer7).

ChIP-seq data:

Filename Description Feature GEO-ID
1 H2AZ_dome30_epiboly_embryo.sga H2A.Z from dome-30%-epiboly embryo H2AZ -
2 H3K4me3_512_cells_embryo.sga H3K4me3 from 512-cell embryo H3K4me3 -
3 H3K4me3_oblong_embryo.sga H3K4me3 from oblong embryo H3K4me3 -
4 H3K4me3_dome30_epiboly_embryo_run1.sga H3K4me3 from dome-30%-epiboly embryo, rep1 H3K4me3 -
5 H3K4me3_dome30_epiboly_embryo_run2.sga H3K4me3 from dome-30%-epiboly embryo, rep2 H3K4me3 -
6 H3K4me3_prim6_embryo.sga H3K4me3 from prim-6 embryo, rep1 H3K4me3 -
7 H3K4me3_prim6_embryo_run1.sga H3K4me3 from prim-6 embryo, rep2 H3K4me3 -
8 Control_dome30_epiboly_embryo.sga Control from dome-30%-epiboly embryo Control -
9 Control_prim6_embryo.sga Control from prim-6 embryo Control -


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 -

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie v0.12.8. SAM files were then converted into bam using samtools v0.1.14 and to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using (ChIP-Seq v. 1.5.3).


Last update: 1 Oct 2018