West 2014, Nucleosome occupancy during cell differentiation and reprogramming.

Paired-end seqiencing of MNase-treated chromatin from mouse Embryonic stem cells (ESC), induced-pluripotent stem cells (iPSC, derived from tail-tip-fibroblasts, TTF), somatic tail-tip-fibroblasts (TTF) and somatic liver (Liv).

• Raw data was downloaded from: SRP044041
• Input file format: SRA
• Download date: 21-3-2017

From M. musculus (July 2007 NCBI37/mm9).

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	GSM1425441.sga	ESC|Nucleosomes|rep1	MNase	GSM1425441
2	GSM1425442.sga	ESC|Nucleosomes|rep2	MNase	GSM1425442
3	GSM1425447.sga	Liv|Nucleosomes|rep1	MNase	GSM1425447
4	GSM1425448.sga	Liv|Nucleosomes|rep2	MNase	GSM1425448
5	GSM1425445.sga	TTF|Nucleosomes|rep1	MNase	GSM1425445
6	GSM1425446.sga	TTF|Nucleosomes|rep2	MNase	GSM1425446
7	GSM1425443.sga	iPSC|Nucleosomes|rep1	MNase	GSM1425443
8	GSM1425444.sga	iPSC|Nucleosomes|rep2	MNase	GSM1425444

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)