Kelly 2012, Nucleosome mapping in IMR90 cells.

Nucleosome occupancy data from IMR90 fibroblast cells.

• Raw data was downloaded from: GSM543311
• Input file format: BAM
• Download date: 2-3-2017

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

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	GSM543311.sga	IMR90|MNase	MNase	GSM543311

Note on samples:

The file GSM543311.sga has been generated by concatenating all the files available on GEO for this GSM entry.
Also, be aware that we could not acertain the nature of these data as the descriptions given in the article and those find in GEO do not match.

bam files were converted to sam using samtools v0.1.14, unmapped reads were discarded and sam files were converted back to bam using samtools v0.1.14. and to bed using bamToBed v2.12.0 (bedtools). Files were lifted over to hg19 genome assembly using UCSC LiftOver tool and SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.2).

• Kelly TK, Liu Y, Lay FD, Liang G, Berman BP, Jones PA
  Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res. 2012 Dec;22(12):2497-506. doi: 10.1101/gr.143008.112. Epub 2012 Sep 7. 22960375