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).



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

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: 1 Oct 2018