Soufi 2012, Yamanaka factors ChIP-seq in fibroblasts.


Assesment of Oct4, Sox2, Klf4 and c-Myc binding using ChIP-seq during fibroblasts reprogramming into induced pluripotent cells. Human foreskin fibroblast JB cells were transduced with retroviral constructs containing Oct4, Sox2, Klf4 and c-Myc under the control of a doxycycline (dox) inducible promoter. Cells were induced for 48h with dox and were then collected for ChIP-seq. Uninfected cells induced for 48h with dox were used as a control.



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

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM1000576.sga fibroblast|c-Myc|Mock c-Myc GSM1000576
2 GSM1000575.sga fibroblast|Oct4|Mock Oct4 GSM1000575
3 GSM896989.sga fibroblast|Input|48h DNA GSM896989
4 GSM896988.sga fibroblast|c-Myc|48h c-Myc GSM896988
5 GSM896987.sga fibroblast|Klf4|48h Klf4 GSM896987
6 GSM896986.sga fibroblast|Sox2|48h Sox2 GSM896986
7 GSM896985.sga fibroblast|Oct4|48h Oct4 GSM896985

ChIP-seq peaks files:

Filename Description Feature GEO-ID
1 GSM1000576_peaks.sga fibroblast|c-Myc|Mock c-Myc_p GSM1000576
2 GSM1000575_peaks.sga fibroblast|Oct4|Mock Oct4_p GSM1000575
3 GSM896988_peaks.sga fibroblast|c-Myc|48h c-Myc_p GSM896988
4 GSM896987_peaks.sga fibroblast|Klf4|48h Klf4_p GSM896987
5 GSM896986_peaks.sga fibroblast|Sox2|48h Sox2_p GSM896986
6 GSM896985_peaks.sga fibroblast|Oct4|48h Oct4_p GSM896985

Notes on samples nomenclature:

"Mock" refers to uninfected fibroblasts which were cultured for 48 hours with dox and "48h" to fibroblasts which were infected with a lentivirus construct containing Oct4, Sox2, Klf4 and c-Myc, and induced with dox for 48h.

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the hg19 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 (ChIP-Seq v. 1.5.3).


Last update: 1 Oct 2018