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

Description

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

Source

Samples

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 -

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: 13 Apr 2017