Zhang 2009, In-vitro assembled nucleosomes on fragmented yeast genome.

Description

Nucleosome from Drosophila embryos were purified using salt dialysis and in-vitro assembled with sonicated yeast genome alone (salt dialysis sample) or with the help on the ACF assembly factor (ACF sample). The resulting chromatin was digested with micrococcal nuclease to release core particles and sequenced. The control sample derive from sonicated genome.

Source

Samples

From Yeast Apr 2011 (NCBI3.1/sacCer3) Assembly.

DNase FAIRE data:

Filename Description Feature GEO-ID
1 GSM379239.sga Strain BY4730|Nucleosomes|Salt dialysis nucleosomes GSM379239
2 GSM379240.sga Strain BY4730|Nucleosomes|ACF nucleosomes GSM379240
3 GSM379241.sga Strain BY4730|Control nucleosomes GSM379241

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. 1.5.2).

References

Last update: 30 Mar 2016