Gaffney 2012, Controls of nucleosome positioning in the human genome.

Paired-end sequenceing of MNase-treated chromatin of seven lymphoblastoid cell lines. Two of the cell lines have been also single-end sequenced for comparison.

• Raw data was downloaded from: SRA
• Input file format: SRA
• Download date: 26-9-2016

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

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	GSM907783.sga	GM18507 - MNase-seq	MNase	GSM907783
2	GSM907784.sga	GM18508 - MNase-seq	MNase	GSM907784
3	GSM907786.sga	GM18516 - MNase-seq	MNase	GSM907786
4	GSM907788.sga	GM18522 - MNase-seq	MNase	GSM907788
5	GSM907789.sga	GM19193 - MNase-seq	MNase	GSM907789
6	GSM907790.sga	GM19238 - MNase-seq	MNase	GSM907790
7	GSM907791.sga	GM19239 - MNase-seq	MNase	GSM907791
8	allSamples147.sga	All Paired-end samples - 147bp fragments	MNase	GSM907791
9	GSM907783_147.sga	GM18507 - 147bp fragments	MNase	GSM907783
10	GSM907784_147.sga	GM18508 - 147bp fragments	MNase	GSM907784
11	GSM907786_147.sga	GM18516 - 147bp fragments	MNase	GSM907786
12	GSM907788_147.sga	GM18522 - 147bp fragments	MNase	GSM907788
13	GSM907789_147.sga	GM19193 - 147bp fragments	MNase	GSM907789
14	GSM907790_147.sga	GM19238 - 147bp fragments	MNase	GSM907790
15	GSM907791_147.sga	GM19239 - 147bp fragments	MNase	GSM907791
16	GSM907785.sga	GM18516 - MNase-seq - Single-end	MNase	GSM907785
17	GSM907787.sga	GM18522 - MNase-seq - Single-end	MNase	GSM907787

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. 1.5.3).

• Gaffney DJ, McVicker G, Pai AA, Fondufe-Mittendorf YN, Lewellen N, Michelini K, Widom J, Gilad Y, Pritchard JK
  Controls of nucleosome positioning in the human genome. PLoS Genet. 2012;8(11):e1003036. doi: 10.1371/journal.pgen.1003036. Epub 2012 Nov 15. 23166509