Soufi 2012, Yamanaka factors ChIP-seq in fibroblasts.

Description

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.

Source

Samples

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

ChIP-seq data:

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

ChIP-seq peaks files:

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

Notes on samples nomenclature:

"Mock" refers to uninfected cells which were cultured for 48 hours with dox and "48h" to cells 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 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. 1.5.3).

References

Last update: 16 Mar 2017