Hesselberth 2009, Global mapping of protein-DNA interactions. .

Protein occupancy on genomic DNA in yeast by dense mapping of individual DNase I cleavages from intact nuclei.

• Raw data was downloaded from: SRA
• Input file format: SRA
• Download date: 13-4-2017

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

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	yeast_digital_genomic_footprinting.sga	Yeast DNaseI	DNaseI	-
2	yeast_purified_DNA.sga	Yeast purified DNA	purDNA	-

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).

• Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, Kuehn MS, Noble WS, Fields S, Stamatoyannopoulos JA
  Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods. 2009 Apr;6(4):283-9. doi: 10.1038/nmeth.1313. Epub 2009 Mar 22. 19305407