Yardimci 2014, DNase-seq of naked DNA from two different cell types.

DNase-seq experiments on deproteinized naked genomic DNA isolated from two different cell types (K562 and MCF7) to determine sequence cleavage bias associated with the DNase-seq protocol.

• Raw data was downloaded from: GEO
• Input file format: SRA
• Download date: 9-3-2017

From H. sapiens (Feb 2009 GRCh37/hg19).

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	GSM1496625.sga	K562|Deproteinized DNase	DNase	GSM1496625
2	GSM1496626.sga	MCF7|Deproteinized DNase	DNase	GSM1496626

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).

• Yardimci GG, Frank CL, Crawford GE, Ohler U
  Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection. Nucleic Acids Res. 2014 Oct 29;42(19):11865-78. doi: 10.1093/nar/gku810. Epub 2014 Oct 7. 25294828
• GEO series GSE61105: Explicit DNase sequence bias modeling enables high resolution transcription factor footprint detection