West 2014, Nucleosome occupancy during cell differentiation and reprogramming.

Paired-end sequencing of MNase-treated chromatin from human Embryonic stem cells (hESC), induced-pluripotent stem cells (hiPSC) and fibroblasts (differentiated from hESC).

• Raw data was downloaded from: SRP044041
• Input file format: SRA
• Download date: 17-3-2017

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

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	GSM1425449.sga	hESC|Nucleosomes|rep1	MNase	GSM1425449
2	GSM1425450.sga	hESC|Nucleosomes|rep2	MNase	GSM1425450
3	GSM1425451.sga	hESC|Nucleosomes|rep3	MNase	GSM1425451
4	GSM1425452.sga	hiPSC|Nucleosomes|rep1	MNase	GSM1425452
5	GSM1425453.sga	hiPSC|Nucleosomes|rep2	MNase	GSM1425453
6	GSM1425454.sga	hFib|Nucleosomes|rep1	MNase	GSM1425454
7	GSM1425455.sga	hFib|Nucleosomes|rep2	MNase	GSM1425455
8	GSM1425456.sga	hFib|Nucleosomes|rep3	MNase	GSM1425456
9	GSM1425457.sga	hFib|Nucleosomes|rep4	MNase	GSM1425457

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) with the option --split-3. Paired-end reads were 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).

• West JA, Cook A, Alver BH, Stadtfeld M, Deaton AM, Hochedlinger K, Park PJ, Tolstorukov MY, Kingston RE
  Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming. Nat Commun. 2014 Aug 27;5:4719. doi: 10.1038/ncomms5719. 25158628
• GEO series GSE59062: Nucleosome occupancy changes in mammalian cell differentiation and reprogramming (Mnase-Seq)