Zhang 2014, Nucleosome organisation at promoters during genome activation.


The chromatin organisation around promotrs is investigated using ChIP-seq and MNase-seq in two developmental stages (256-cell and dome) that are characterised by the shift between mathernal and zigotic mRNA usage.



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

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM1081560.sga dome|PolII|rep1 PolII GSM1081560
2 GSM1081559.sga dome|PolII|rep2 PolII GSM1081559
3 GSM1081558.sga dome|H3K36me3 H3K36me3 GSM1081558
4 GSM1081557.sga dome|H3K27me3 H3K27me3 GSM1081557
5 GSM1081556.sga dome|H3K4me3 H3K4me3 GSM1081556
6 GSM1081562.sga 256-cell|H3K4me3 H3K4me3 GSM1081562
7 GSM1081561.sga oblong|H3K4me3 H3K4me3 GSM1081561

DNase FAIRE data:

Filename Description Feature GEO-ID
1 GSM1081555.sga dome|nucleosome|rep1 MNase GSM1081555
2 GSM1081554.sga dome|nucleosome|rep2 MNase GSM1081554
3 GSM1081553.sga 256-cell|nucleosome|rep1 MNase GSM1081553
4 GSM1081552.sga 256-cell|nucleosome|rep2 MNase GSM1081552

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 bed2sga.pl (ChIP-Seq v. 1.5.3).


Last update: 1 Oct 2018