Comment[ArrayExpressAccession]	E-GEOD-45471
MAGE-TAB Version	1.1						
Public Release Date	2013-03-26
Investigation Title	SNP data from OX1 human fibroblasts and induced Pluripotent Stem cells						
Comment[Submitted Name]	SNP data from OX1 human fibroblasts and induced Pluripotent Stem cells
Experiment Description	human induced Pluripotent Stem cells (hiPSc) and their differentiated progeny have great potential for modelling disease. To realise this potential, robust protocols need to be developed for deriving authentic differentiated cell lineages and these lineages need to be rigorously characterised. We have generated hiPSc using retrovirus-mediated delivery of reprogramming factors, and have used them for assessing the efficiency of a defined protocol for differentiation to monocytes and macrophages. hiPSc lines have been screened using SNP array to assess chromosomal stability, and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets. van Wilgenburg B, Browne C and Cowley SA, submitted for publication human iPSc lines were derived from normal human dermal fibroblasts.						
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	Cowley	van Wilgenburg	Browne	Cowley			
Person First Name	Sally	Bonnie	Cathy	Sally			
Person Mid Initials	A			A			
Person Email	sally.cowley@path.ox.ac.uk						
Person Affiliation	University of Oxford						
Person Phone	+44 (0) 1865 275600						
Person Fax	+44 (0) 01865 275515						
Person Address	Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, United Kingdom						
Person Roles	submitter						
Protocol Name	P-GSE45471-1	P-GSE45471-6	P-GSE45471-5	P-GSE45471-2	P-GSE45471-3	P-GSE45471-4	P-GSE45471-7
Protocol Description	ID_REF =  VALUE = Genotype (AA, AB, BB, NC); GC score; Theta; B allele frequency; LogR ratio GC Score =  Theta =  R =  B Allele Freq =  Log R Ratio = 	Standard Illumina scanning protocol for BeadChip Arrays	Standard Illumina hybridisation protocol	untreated cell samples; Fibroblasts grown in ADMEM + 10% FCS; iPSc lines all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest	genomic DNA was extracted using QIAGEN DNeasy blood and tissue kit	Standard Illumina labelling protocol	The scanned data files were processed by GenomeStudio Genotyping module v1.9, using the cluster file HumanCytoSNP-12v2-1_H.egt provided by Illumina. Raw data was also uploaded to KaryoStudio (Illumina) for generation of karyotype reports (see publication).
Protocol Type	bioassay_data_transformation	image_aquisition	hybridization	specified_biomaterial_action	nucleic_acid_extraction	labeling	feature_extraction
Experimental Factor Name	CELL TYPE	CULTURE					
Experimental Factor Type	cell type	culture					
Comment[SecondaryAccession]	GSE45471						
Comment[GEOReleaseDate]	2013-03-26						
Comment[ArrayExpressSubmissionDate]	2013-03-25						
Comment[GEOLastUpdateDate]	2013-03-26						
Comment[AEExperimentType]	genotyping by array						
Comment[AdditionalFile:Data1]	GSE45471_Matrix_signal_intensities.txt						
SDRF File	E-GEOD-45471.sdrf.txt