Comment[ArrayExpressAccession]	E-GEOD-53299
MAGE-TAB Version	1.1						
Public Release Date	2014-03-08
Investigation Title	Expression data from mouse protein iPS cells compared to mouse embryonic stem cells and mouse hepatocyte.						
Comment[Submitted Name]	Expression data from mouse protein iPS cells compared to mouse embryonic stem cells and mouse hepatocyte.
Experiment Description	Increased genomic integrity an improved protein-based iPS cell method compared to current viral induced strategies We used microarrays to detail the global gene expression of protein-based iPS cells Total RNAs were prepared from mH, mES, miPS cells usingTRIzol reagent (Invitrogen, Carlsbad, CA) and their cDNAs were allowed to hybridize to Affymetrix Mouse Expression Array 430 containing over 43,000 mouse transcripts at the Harvard Partners Center for Genomics and Genetics.						
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	Kim						
Person First Name	Kwang-Soo						
Person Email	geo@ncbi.nlm.nih.gov						
Person Affiliation	McLean Hospital/Harvard Medical School						
Person Address	McLean Hospital/Harvard Medical School, 115 Mill St., Belmont, MA, USA						
Person Roles	submitter						
Protocol Name	P-GSE53299-1	P-GSE53299-5	P-GSE53299-6	P-GSE53299-2	P-GSE53299-3	P-GSE53299-4	P-GSE53299-7
Protocol Description	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. ID_REF =  VALUE = Signal ABS_CALL = indicating whether the transcript was present (P), absent (A), or marginal (M) DETECTION P-VALUE = 	protocol performed at Harvard Partners Center for Genomics and Genetics	protocol performed at Harvard Partners Center for Genomics and Genetics	Cells were harvested by treating trypsin/EDTA.	Primary mouse hepatocytes (mH) were isolated from 13.5-day-pregnant C57/BL6J mice and cultured in DulbeccoM-bM-^@M-^Ysmodified Minimal Essential Medium (DMEM, Invitrogen, Carlsbad, CA), supplemented with 10ng/ml of epidermal growth factor (EGF) (Pepprotech), 15% fetal bovine serum (FBS, Hyclone, Thermo Scientific, Logan UT), 100 U/ml penicillin and 100 M-NM-<g/ml streptomycin (Invitrogen, Grand island, NY). Reprogramming was initiated with proteins or viruses when cultures reached 10-20% confluence. Cultures were maintainedat 37M-0C and 5% CO2, and media changed everyother day. mESCs derived from murine strain C57/BL6J were purchased from Millipore (Cat No. SF-CMT1-2) and maintained in mouse ES medium (DMEM supplemented with 2mM L-glutamine (Invitrogen), 1mM M-NM-2-mercaptoethanol, 1x non-essential amino acids (NEAA; Invitrogen, Carlsbad, CA), 15% fetal bovine serum (FBS, Hyclone, Thermo Scientific, Logan UT), 100 U/ml penicillin, 100 M-NM-<g/ml streptomycin (Invitrogen), 1500U/ml (Millipore)). miPSCs were generated and maintained in mouse ES media. miPSCs were maintained on MEF feeder cells treated with mitomycin C (10M-NM-<g/ml media, Sigma-Aldrich, St. Lake, MO) and passaged by washing twice with PBS, followed by dissociation with 1X trypsin-EDTA solution (Invitrogen; 10 mins). Cells were suspended in an appropriate volume of medium and transferred onto MEF feeder cells in a new dish.	Trizol extraction of total RNA was performed according to the manufacturer's instructions.	protocol performed at Harvard Partners Center for Genomics and Genetics
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	CELL TYPE						
Experimental Factor Type	cell type						
Comment[SecondaryAccession]	GSE53299						
Comment[GEOReleaseDate]	2014-03-08						
Comment[ArrayExpressSubmissionDate]	2013-12-13						
Comment[GEOLastUpdateDate]	2014-03-13						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-53299.sdrf.txt