Comment[ArrayExpressAccession]	E-GEOD-48252
MAGE-TAB Version	1.1								
Public Release Date	2013-07-22
Investigation Title	Inducing pluripotency from mouse somatic cells by small-molecule compounds [RNA-Seq]								
Comment[Submitted Name]	Inducing pluripotency from mouse somatic cells by small-molecule compounds [RNA-Seq]
Experiment Description	Pluripotent stem cells can be induced from somatic cells, providing an unlimited cell resource for regenerative medicine. However, genetic manipulation and difficult-to-manufacture strategies used in reprogramming limit their clinical applications. Here, we show pluripotency can be induced from mouse somatic cells by specific small-molecule compounds. The completely chemically-induced pluripotent stem cells (CiPSCs) can be stably maintained in embryonic stem cell (ESC) culture medium and resemble ESCs in terms of their gene expression profiles, epigenetic status, and potential for differentiation and germline transmission. These findings suggest that exogenous master genes are dispensable for cell fate reprogramming and pave the way for the clinical application of somatic reprogramming techniques. Chemicals' acronym: V, VPA; C, CHIR; 6, 616452; T, tranylcypromine; F, FSK; Z, DZNep; P, PGE2; R, RG108; S, SRT1720; M, 2-Me-5HT; D, D4476; B, Sodium butyrate. mRNA expression analysis of mouse embryonic fibroblasts (MEFs), GFP- cells, GFP+ clusters,GFP+ colonies, embryonic stem cells (ESCs) and CiPSCs by RNA sequencing.								
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	liu	Hou	Li	Zhang	Liu	Guan	Li	Zhao	Deng
Person First Name	chun	Pingping	Yanqin	Xu	Chun	Jingyang	Honggang	Yang	Hongkui
Person Email	dabai22222@163.com								
Person Affiliation	Peking University								
Person Phone	13621043040								
Person Address	Peking University, beijing, beijing, beijing, China								
Person Roles	submitter								
Protocol Name	P-GSE48252-4	P-GSE48252-1	P-GSE48252-3	P-GSE48252-2					
Protocol Description	Tophat 1.3.0. to align the clean reads to the mm9 RefSeq, and gene expression was analyzed by the RPKM method. FDR < 0.01 and the absolute ratio of log2 > 1 as the threshold for the differential expresion of genes. Genome_build: MGSCv37 Supplementary_files_format_and_content: Tab-delimited text file. RPKM values and GeneIDs.	GFP- cells, GFP+ clusters and GFP+ colonies were picked up and collected for RNA isolation.	Total RNA extracted by QIAGEN Rneasy Kit following manufacturer's instructions. RNA libraries were prepared and sequenced following Illumina protocol	MEFs were cultured in DMEM/High Glucose (Hyclone) containing 10% fetal bovine serum (Invitrogen). Mouse ESCs (R1 and TT2) and CiPSCs were maintained on feeder layers of mitomycin C-treated MEFs in ESC culture medium.					
Protocol Type	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol	growth protocol					
Experimental Factor Name	STRAIN OR LINE	CELL TYPE	CHEMICAL TREATMENT CONDITION						
Experimental Factor Type	strain or line	cell type	chemical treatment condition						
Publication Title	Pluripotent stem cells induced from mouse somatic cells by small-molecule compounds.								
Publication Author List	Hou P, Li Y, Zhang X, Liu C, Guan J, Li H, Zhao T, Ye J, Yang W, Liu K, Ge J, Xu J, Zhang Q, Zhao Y, Deng H								
PubMed ID	23868920								
Publication DOI	10.1126/science.1239278								
Comment[SecondaryAccession]	GSE48252								
Comment[GEOReleaseDate]	2013-07-22								
Comment[ArrayExpressSubmissionDate]	2013-06-24								
Comment[GEOLastUpdateDate]	2013-09-04								
Comment[AEExperimentType]	RNA-seq of coding RNA								
Comment[AdditionalFile:Data1]	GSE48252_rnaseq_processed.txt								
Comment[SecondaryAccession]	SRP026281								
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR921473-SRR921485								
SDRF File	E-GEOD-48252.sdrf.txt