Comment[ArrayExpressAccession]	E-GEOD-32464
Public Release Date	2011-10-23						
Investigation Title	Global gene expression analysis in murine iPS cells derived with mouse and human Nanog orthologs						
Comment[Submitted Name]	Global gene expression analysis in murine iPS cells derived with mouse and human Nanog orthologs
Experiment Description	Nanog null neural stem (NS) cells were reprogrammed to naive pluripotency in 2i/LIF conditions with mouse (m) Nanog and human (h) Nanog. Global gene expression in resulting iPS cells was compared to embryonic stem (ES) cells and nanog null NS cells. Murine iPS cells derived with mouse nanog iPS and human nanog iPS and then compared to embryonic stem cells and nanog null neural stem cells (3 replicates each).						
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Term Source Name	EFO
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Term Source File	http://www.ebi.ac.uk/efo/efo.owl						
Person Last Name	Theunissen	Theunissen	Silva				
Person First Name	Thorold	Thorold	Jose				
Person Mid Initials		W	C				
Person Email	twt22@cam.ac.uk						
Person Affiliation	Wellcome Trust Centre for Stem Cell Research						
Person Phone	+44 (0)1223 760226						
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Person Address	Biochemistry, Wellcome Trust Centre for Stem Cell Research, Tennis Court Road, Cambridge, United Kingdom						
Person Roles	submitter						
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Protocol Name	P-GSE32464-1	P-GSE32464-6	P-GSE32464-5	P-GSE32464-3	P-GSE32464-2	P-GSE32464-4	P-GSE32464-7
Protocol Description	ID_REF = <br>VALUE = Quantile normalized<br>DETECTION PVAL = 	Staining and scanning were performed according to the Whole Genome Gene Expression Direct Hybridization Guide on the MouseWG-6 v2.0 Expression BeadChip (Illumina).	Hybrization were performed according to the Whole Genome Gene Expression Direct Hybridization Guide on the MouseWG-6 v2.0 Expression BeadChip (Illumina).	Total RNA was extracted using Rneasy kit (Qiagen)	iPS and ES cells were cultured in N2B27 medium (Stem Cell Sciences, SCS-SF-NB-02) supplemented with LIF and 2i inhibitors (Ying et al., 2008), CHIR99021 (3μM) and PD0325901 (1μM).	Amplification and labeling of RNA were performed according to the TotalPrep-96 RNA Amplification Kit for the Illumina platform (Ambion).	The data were filtered removing any probes with a detection p-value above 0.01 for all the samples in the set. This remove any probes not detected at all in the set. It has been done before transformation via variance stabilisation and normalisation in order to reduce the noise of the set before normalisation. The data were then transformed using VST (Variance Stabilizing Transform) and normalised by quantile normalisation.
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Protocol Type	bioassay_data_transformation	image_aquisition	hybridization	nucleic_acid_extraction	grow	labeling	feature_extraction
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Experimental Factor Name	CELL TYPE						
Experimental Factor Type	cell type						
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Comment[SecondaryAccession]	GSE32464						
Comment[GEOLastUpdateDate]	2011-10-24
Comment[AEExperimentType]	transcription profiling by array						
Comment[GEOReleaseDate]	2011-10-22
Comment[ArrayExpressSubmissionDate]	2011-09-27
SDRF File	E-GEOD-32464.sdrf.txt