Comment[ArrayExpressAccession]	E-GEOD-42073
MAGE-TAB Version	1.1							
Public Release Date	2012-11-07
Investigation Title	Expression data of PTK7+ and PTK7- cells from differentiated pluripotent stem cells (PSC), and expression data from undifferentiated PSC and definitive endoderm							
Comment[Submitted Name]	Expression data of PTK7+ and PTK7- cells from differentiated pluripotent stem cells (PSC), and expression data from undifferentiated PSC and definitive endoderm
Experiment Description	As PSCs differentiate, they display characteristics of EMT as well as PTK7 expression.  We sought to discover novel markers and regulators of this process by comparing purified PTK7+ and PTK7- populations We used microarrays to detail the global program of gene expression underlying this EMT process and identified distinct classes of up-regulated genes during this process. PTK7+ and PTK7- populations were purified by FACS and subjected to lysis and RNA extraction.  Undifferentiated PSCs and definitive endoderm were washed with PBS, then subjected to lysis and RNA extraction							
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	Chan	Chan	Lowry					
Person First Name	David	David	William					
Person Mid Initials		N	E					
Person Email	geo@ncbi.nlm.nih.gov							
Person Affiliation	UCLA							
Person Address	MCDB, UCLA, 621 Charles E Young Drive South, Los Angeles, CA, USA							
Person Roles	submitter							
Protocol Name	P-GSE42073-1	P-GSE42073-6	P-GSE42073-3	P-GSE42073-8	P-GSE42073-7	P-GSE42073-2	P-GSE42073-4	P-GSE42073-5
Protocol Description	ID_REF =  VALUE = RMA signal	Affymetrix GeneChip Hybridization oven 645; overnight 16 hours	Pluripotent stem cells were cultured in standard conditions as described	Affymetrix Expression Console version 1.2 with TGT=500 The data were processed and normalized in GeneSpring and 3 separate normalizations were performed (for FFH9 ES PTK7- and FFH9 ES PTK7+; XFiPSC2 ES PTK7- and XFiPSC2 ES PTK7+; HSF1-undiff d0 and HSF1-endo d5). We made use of the raw RMA signals after the normalization.	Affymetrix G7 scanner	Spontaneous differentiation by culturing in low bFGF conditions, Definitive endoderm derivation by culturing in 100ng/mL ActivinA	Total RNA was extracted with Qiagen RNeasy micro kit or mini kit according to manufacturer's protocol	Ambion MessageAmp(tm) Premier RNA Amplification Protocol or Nugen Ovation(r) Pico WTA System V2
Protocol Type	bioassay_data_transformation	hybridization	grow	feature_extraction	image_aquisition	specified_biomaterial_action	nucleic_acid_extraction	labeling
Experimental Factor Name	DIFFERENTIATION	FACS POPULATION	CELL POPULATION	LENGTH OF DIFFERENTIATION				
Experimental Factor Type	differentiation	facs population	cell population	length of differentiation				
Comment[SecondaryAccession]	GSE42073							
Comment[GEOReleaseDate]	2012-11-07							
Comment[ArrayExpressSubmissionDate]	2012-11-06							
Comment[GEOLastUpdateDate]	2012-11-08							
Comment[AEExperimentType]	transcription profiling by array							
SDRF File	E-GEOD-42073.sdrf.txt