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.



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

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).


Last update: 9 Mar 2017