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).



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

Technical Notes

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).


Last update: 21 Mar 2017