Zhang14, Nucleosome organisation at promoters during genome activation

Description

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.

Source

Raw data can be downloaded from: GEO dataset GSE44269

Samples

From D. rerio genome Zv9 (danRer7).

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
8 GSM1081555.sga dome|nucleosome|rep1 MNase GSM1081555
9 GSM1081554.sga dome|nucleosome|rep2 MNase GSM1081554
10 GSM1081553.sga 256-cell|nucleosome|rep1 MNase GSM1081553
11 GSM1081552.sga 256-cell|nucleosome|rep2 MNase GSM1081552

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.

References

Zhang Y, Vastenhouw NL, Feng J, Fu K et al.
Canonical nucleosome organization at promoters forms during genome activation. Genome Res.2014 Feb;24(2):260-6. PubMed PMID: 24285721

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