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

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.

• Raw data was downloaded from GEO: GSE15188
• Input file format: SRA
• Download date: 29-03-2016

From S. cerevisiae (Apr 2011 R64/sacCer3).

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

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).

• Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K
  Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol. 2009 Aug;16(8):847-52. doi: 10.1038/nsmb.1636. Epub 2009 Jul 20. 19620965
• GEO series GSE15188: Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo