Comment[ArrayExpressAccession]	E-GEOD-49053
MAGE-TAB Version	1.1														
Public Release Date	2013-12-03
Investigation Title	Differentiation defective phenotypes revealed by large scale analyses of human pluripotent stem cells														
Comment[Submitted Name]	Differentiation defective phenotypes revealed by large scale analyses of human pluripotent stem cells
Experiment Description	This SuperSeries is composed of the SubSeries listed below. Refer to individual Series														
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	Yamanaka														
Person First Name	Shinya														
Person Email	yamanaka@cira.kyoto-u.ac.jp														
Person Affiliation	Center for iPS Cell Research and Applicaton (CiRA), Kyoto University														
Person Phone	81-75-366-7041														
Person Address	Center for iPS Cell Research and Applicaton (CiRA), Kyoto University, 53 Kawahara-machi, Shogoin, Sakyo-ku, Kyoto, Japan														
Person Roles	submitter														
Protocol Name	P-GSE49053-4	P-GSE49053-3	P-GSE49053-1	P-GSE49053-2	P-GSE49053-13	P-GSE49053-6	P-GSE49053-10	P-GSE49053-11	P-GSE49053-7	P-GSE49053-14	P-GSE49053-5	P-GSE49053-9	P-GSE49053-15	P-GSE49053-8	P-GSE49053-12
Protocol Description	The exon array data analysis was performed using the Gene Spring GX11.5.1 software. Summarization algorithme:ExonPLIER16 with core and extended probe sets. probe group file: HuEx-1_0-st-v2_na32_hg19_2011-06-23 ID_REF =  VALUE = Quantile normalized gene level expression values from Gene Spring GX	Illumina GenomeStudio software Unmethylated(Signal_A) and methylated(Signal_B) signal intensities ID_REF =  VALUE = Average Beta Detection Pval = 	The data were analyzed using the Gene Spring GX 11.5.1 software program (Agilent Technologies).The data processing was performed as follows; (i) Threshold raw signals were set to 1.0, (ii) Log base 2 transformation was performed, (iii) 75th percentile normalization was chosen as the normalized algorithm. ID_REF =  VALUE = Normalized signal intensity	The data were analyzed using the Gene Spring GX 11.5.1 software program (Agilent Technologies).The data processing was performed as follows; (i) Threshold raw signals were set to 1.0, (ii) Log base 2 transformation was performed, (iii) 90th percentile normalization was chosen as the normalized algorithm. ID_REF =  VALUE = Normalized signal intensity	Samples were enzymatically fragmented and biotinylated using the WT Terminal labeling Kit (Affymetrix).	Agilent standard protocol	Standard Illumina protocol	bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol.	Agilent standard protocol	Approximately 5.5ug of labeled DNA target was hybridized to the Affymetrix GeneChip Human Exon 1.0 ST Array at 45℃ for 17 hrs according to the manufacturer's recommendation.	Total RNA was isolated by Trizol reagent (Life Technologies) according to the manufacturer's instruction.	Genomic DNA extraction and purification from cultured cells was carried out using a Gentra Puregene kit (QIAGEN).	Hybridized arrays were washed and satined on a GeneChip Fluidics Satation 450 and scanned on a GCS3000 Scanner (Affymetrix).	Agilent standard protocol	Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.
Protocol Type	normalization data transformation protocol	normalization data transformation protocol	normalization data transformation protocol	normalization data transformation protocol	labelling protocol	labelling protocol	labelling protocol	hybridization protocol	hybridization protocol	hybridization protocol	nucleic acid extraction protocol	nucleic acid extraction protocol	array scanning protocol	array scanning protocol	array scanning protocol
Experimental Factor Name	CELL TYPE	TRANSDUCTION	METHOD	SFEBQ	CELL ORIGIN										
Experimental Factor Type	cell type	transduction	method	sfebq	cell origin										
Publication Title	Differentiation-defective phenotypes revealed by large-scale analyses of human pluripotent stem cells.														
Publication Author List	Koyanagi-Aoi M, Ohnuki M, Takahashi K, Okita K, Noma H, Sawamura Y, Teramoto I, Narita M, Sato Y, Ichisaka T, Amano N, Watanabe A, Morizane A, Yamada Y, Sato T, Takahashi J, Yamanaka S														
PubMed ID	24259714														
Publication DOI	10.1073/pnas.1319061110														
Comment[SecondaryAccession]	GSE49053														
Comment[GEOReleaseDate]	2013-12-03														
Comment[ArrayExpressSubmissionDate]	2013-07-19														
Comment[GEOLastUpdateDate]	2013-12-03														
Comment[AEExperimentType]	transcription profiling by array														
Comment[AEExperimentType]	methylation profiling by array														
SDRF File	E-GEOD-49053.sdrf.txt