Comment[ArrayExpressAccession]	E-GEOD-41328
MAGE-TAB Version	1.1						
Public Release Date	2012-10-03
Investigation Title	Colorectal adenocaricinomas and matched normal colonic tissues						
Comment[Submitted Name]	Colorectal adenocaricinomas and matched normal colonic tissues
Experiment Description	Five colorectal adenocarcinomas and matched normal colonic tissues were analyzed with Affymetrix HG-U133-Plus-2.0 microarrays. Two labs independently generated microarray data with the same array platform on the same biological samples. Colorectal adenocarcinomas and matched normal colonic RNA sample were purchased from Oncomatrix, Inc., San Diego, CA. The RNA from each biological sample was distributed to and processed in two laboratories at Stanford University.						
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	Chen	Lin	He	Ji	Shi	Davis	Zhong
Person First Name	Chieh-Chun	Guixian	Xuming	Hanlee	Leming	Ronald	Sheng
Person Email	cchen63@illinois.edu						
Person Affiliation	University of illinois						
Person Address	Bioengineering, University of illinois, 1206 West Gregory Drive, Urbana, Illinois, USA						
Person Roles	submitter						
Protocol Name	P-GSE41328-1	P-GSE41328-5	P-GSE41328-4	P-GSE41328-2	P-GSE41328-3	P-GSE41328-6	
Protocol Description	ID_REF =  VALUE = BioConductor-calculated PLIER Signal intensity with the addition of an offset value of 16	GeneChips were scanned using the Affymetrix scanner.	20 µg of cRNA was hybridized to each individual microarray (HG-U133-Plus-2.0). The microarrays were hybridized for 16 hours at 45°C, stained, and washed according to an Affymetrix protocol (EukGE-WS2v4) using an Affymetrix fluidics station.	Colorectal adenocarcinomas and matched normal colonic RNA sample were purchased from Oncomatrix, Inc., San Diego, CA.	5 µg of total RNA was used to synthesize cRNA for each sample.	The CEL file data were analyzed with BioConductor to generate probeset level data using the justPlier() function. Probe-level data were quantile normalized before PLIER summarization per test site (10 arrays). An offset value of 16 was then added to each probeset-level data point.	
Protocol Type	bioassay_data_transformation	image_aquisition	hybridization	nucleic_acid_extraction	labeling	feature_extraction	
Experimental Factor Name	LAB	ORGANISM PART					
Experimental Factor Type	lab	organism part					
Publication Title	Reproducibility Probability Score--incorporating measurement variability across laboratories for gene selection.						
Publication Author List	Lin G, He X, Ji H, Shi L, Davis RW, Zhong S						
PubMed ID	17160039						
Publication DOI	10.1038/nbt1206-1476						
Comment[SecondaryAccession]	GSE41328						
Comment[GEOReleaseDate]	2012-10-03						
Comment[ArrayExpressSubmissionDate]	2012-10-03						
Comment[GEOLastUpdateDate]	2012-10-12						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-41328.sdrf.txt