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.

• Raw data was downloaded from: GEO
• Input file format: SRA
• Download date: n/a

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

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).

• Zhang Y, Vastenhouw NL, Feng J, Fu K, Wang C, Ge Y, Pauli A, van Hummelen P, Schier AF, Liu XS
  Canonical nucleosome organization at promoters forms during genome activation. Genome Res. 2014 Feb;24(2):260-6. doi: 10.1101/gr.157750.113. Epub 2013 Nov 27. 24285721
• GEO series GSE44269: Canonical Nucleosome Organization at Promoters Forms During Genome Activation