Comment[ArrayExpressAccession]	E-GEOD-42452
MAGE-TAB Version	1.1				
Public Release Date	2013-12-03
Investigation Title	Comparison of gene expression profilings between SFEBq differentiation-defective clones and good clones				
Comment[Submitted Name]	Comparison of gene expression profilings between SFEBq differentiation-defective clones and good clones
Experiment Description	It remains controversial whether human induced pluripotent stem cells (hiPSCs) are distinct from human embryonic stem cells (hESCs) in their molecular signatures and differentiation properties. We examined the gene expression and DNA methylation of 49 hiPSC and 10 hESC lines and identified no molecular signatures that distinguished hiPSCs from hESCs. Comparisons of the in vitro directed neural differentiation of 40 hiPSC and four hESC lines showed that most hiPSC clones were comparable to hESCs. However, in seven hiPSC clones, significant amount of undifferentiated cells persisted even after neural differentiation and resulted in teratoma formation when transplantated into mouse brains. These differentiation-defective hiPSC clones were marked by higher expression of several genes, including those expressed from long terminal repeats of human endogenous retroviruses. These data demonstrated that many hiPSC clones are indistinguishable from hESCs, while some defective hiPSC clones need to be eliminated prior to their application for regenerative medicine. We extracted total RNA from 10 hESCs and 40 hiPSCs, and hybridized them to Agilent gene expression microarrays.				
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	Koyanagi-Aoi	Narita		
Person First Name	Shinya	M	M		
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-GSE42452-1	P-GSE42452-3	P-GSE42452-4	P-GSE42452-2	P-GSE42452-5
Protocol Description	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	Agilent standard protocol	Agilent standard protocol	Total RNA was isolated by Trizol reagent (Life Technologies) according to the manufacturer's instruction.	Agilent standard protocol
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction 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]	GSE42452				
Comment[GEOReleaseDate]	2013-12-03				
Comment[ArrayExpressSubmissionDate]	2012-11-21				
Comment[GEOLastUpdateDate]	2013-12-03				
Comment[AEExperimentType]	transcription profiling by array				
SDRF File	E-GEOD-42452.sdrf.txt