Comment[ArrayExpressAccession]	E-GEOD-49082
MAGE-TAB Version	1.1					
Public Release Date	2013-07-23
Investigation Title	Genomic alteration in MRC5-derived induced pluripotent stem (MRC5-iPS) cell line, Tic					
Comment[Submitted Name]	Genomic alteration in MRC5-derived induced pluripotent stem (MRC5-iPS) cell line, Tic
Experiment Description	Disease-specific induced pluripotent stem (iPS) cells have been used for a model to analyze pathogenesis of the disease. We generated iPS cells derived from a fibroblastic cell line of ataxia telangiectasia (AT-iPS cells). In analysis of AT-iPS cells, the human wild-type iPS cell line (MRC5-iPS) was generated and cultured in the same conditions as the diseased iPS cell lines. It is an ideal control cell line for the disease and patient-specific iPS cell lines.  Because MRC5-iPS cells exhibited considerable chromosomal abnormalities in vitro, we performed a structural alteration analysis by using a SNP genotyping array for MRC5-iPS cell line, Tic,  at passage 15,  passage 30, and  passage 37. The parental MRC-5 fibroblast cells and MRC-iPS 25 (Tic)  were subjected to Illumina HumanCytoSNP-12 v2.1 BeadChip analysis.					
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	Umezawa	Masashi	Nakabayashi	Okamura	Hata	Umezawa
Person First Name	Akihiro	Toyoda	Kazuhiro	Kohji	Kenichiro	Akihiro
Person Email	umezawa@1985.jukuin.keio.ac.jp					
Person Affiliation	National Center for Child Health and Development					
Person Phone	81-3-5494-7047					
Person Fax	81-3-5494-7048					
Person Address	Reproductive Biology, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, Japan					
Person Roles	submitter					
Protocol Name	P-GSE49082-1	P-GSE49082-4	P-GSE49082-5	P-GSE49082-2	P-GSE49082-3	P-GSE49082-6
Protocol Description	Genomic DNA extracted from breast tumors was genotyped using HumanCytoSNP-12 v2.1 DNA Analysis BeadChip Kit (Illumina). ID_REF =  VALUE = Genotype: AA,AB,BB,or NC (no call) GC_SCORE =  Theta =  R =  B_Allele_Freq =  Log_R_Ratio = 	Illumina's standard protocol	DNA was amplified, fragmented and hybridized to each BeadChip arrays according to the manufacturer's instructions.	All cultures were maintained at 37°C in a humidified atmosphere containing 95% air and 5% CO2. When the cultures reached subconfluence, the cells were harvested with Trypsin-EDTA Solution (cat# 23315, IBL CO., Ltd, Gunma, Japan), and re-plated at a density of 5 x 105 cells in a 100-mm dish. Medium changes were carried out twice a week thereafter.	Genomic DNA extracted from cells using QIAamp DNA Mini Kit (Qiagen).	The BeadChip array was scanned using the iScan (Illumina)
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	CELL LINE					
Experimental Factor Type	cell line					
Comment[SecondaryAccession]	GSE49082					
Comment[GEOReleaseDate]	2013-07-23					
Comment[ArrayExpressSubmissionDate]	2013-07-22					
Comment[GEOLastUpdateDate]	2013-07-23					
Comment[AEExperimentType]	comparative genomic hybridization by array					
Comment[AEExperimentType]	genotyping by array					
Comment[AdditionalFile:Data1]	GSE49082_non-normalized.txt					
SDRF File	E-GEOD-49082.sdrf.txt