Comment[ArrayExpressAccession]	E-GEOD-24471
MAGE-TAB Version	1.1		
Public Release Date	2010-10-01
Investigation Title	ChIP-Seq data in secondary fibroblast with dox-inducible cassettes for Oct4, Sox2 and Klf4.		
Comment[Submitted Name]	ChIP-Seq data in secondary fibroblast with dox-inducible cassettes for Oct4, Sox2 and Klf4.
Experiment Description	The conversion of fibroblasts to induced pluripotent stem cells (iPS) by forced expression of Oct4, Sox2 and Klf4 is among the earliest demonstrations of reprogramming to a pluripotent state by forced expression of transcription factors. To gain insights into the transcriptional state of genes required for reprogramming, we profiled RNA polymerase II, H3K27me3 and E2F4. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibodies to RNA polymerase II, H3K27me3 and E2F4.		
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl	
Person Last Name	Young	Bilodeau	Young
Person First Name	Richard	Steve	Richard
Person Mid Initials	A		A
Person Email	young_computation@wi.mit.edu		
Person Affiliation	Whitehead Institute for Biomedical Research		
Person Phone	617-258-5219		
Person Address	Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA, USA		
Person Roles	submitter		
Protocol Name	P-GSE24471-2	P-GSE24471-1	P-GSE24471-3
Protocol Description	Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 350bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.	Oct4/Klf4/Sox2-inducible iPS cells with Oct4-selectable cassette were derived in the presence of Wnt3a-conditioned medium and were injected into BDF2 blastocysts. Secondary fibroblasts were harvested from the resulting chimeric embryos at 13.5dpc. Fibroblasts derived from the injected iPS cells were selected for with 2M-5g/ml puromycin for 48 hours. Cells were cultured in DulbeccoM-bM-^@M-^Ys modified Eagle medium supplemented with 10% cosmic calf serum, M-NM-2-mercaptoethanol, nonessential amino acids, L glutamine and penicillin/streptomycin.	Images analysis and base calling was done using the solexa pipeline. For all samples reads were aligned to their indicated build using bowtie. For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Protocol Type	nucleic acid library construction protocol	grow	feature_extraction
Experimental Factor Name	ANTIBODY CATALOG NUMBER	CHIP ANTIBODY	
Experimental Factor Type	antibody catalog number	chip antibody	
Comment[SecondaryAccession]	GSE24471		
Comment[GEOReleaseDate]	2010-10-01		
Comment[ArrayExpressSubmissionDate]	2010-09-30		
Comment[GEOLastUpdateDate]	2013-02-26		
Comment[AEExperimentType]	ChIP-seq		
Comment[SecondaryAccession]	SRP003667		
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR067348-SRR067352		
SDRF File	E-GEOD-24471.sdrf.txt