Investigation Title	TCGA Analysis of SNPs and Copy Number Variations for COAD/READ Using Affymetrix Genome-Wide SNP Array 6.0											
Experimental Design	comparative_genome_hybridization_design											
Experimental Design Term Source REF	MGED Ontology											
Experimental Factor Name	Colon/Rectal adenocarcinoma											
Experimental Factor Type	disease_state											
Experimental Factor Type Term Source REF	MGED Ontology											
												
Person Last Name	Meyerson	Gabriel	Submission									
Person First Name	Matthew	Stacey	GAP									
Person Mid Initials												
Person Email	meyerson@broadinstitute.org	stacey@broadinstitute.org	gap-sub@broadinstitute.org									
Person Phone	(617) 632-4768	617-714-7620	(617) 252-1142									
Person Fax												
Person Address	7 Cambridge Center, Cambridge, MA 02142, USA	7 Cambridge Center, Cambridge, MA 02142, USA	7 Cambridge Center, Cambridge, MA 02142, USA									
Person Affiliation	Broad Institute	Broad Institute	Broad Institute									
Person Roles	investigator	investigator	submitter									
Person Roles Term Source REF	MGED Ontology	MGED Ontology	MGED Ontology									
												
Quality Control Types												
Quality Control Types Term Source REF												
Replicate Type												
Replicate Type Term Source REF												
Normalization Type												
Normalization Term Source REF												
Date of Experiment	2/20/2009											
Public Release Date	3/4/2009											
Comment[ArrayExpressSubmissionDate]												
												
PubMed ID												
Publication DOI												
Publication Author List												
Publication Title												
Publication Status												
Publication Status Term Source REF												
Experiment Description	TCGA Analysis of SNPs and Copy Number Variations for Colon/Rectal adenocarcinoma Using Affymetrix Genome-Wide SNP Array 6.0											
												
Protocol Name	broad.mit.edu:labeling:Genome_Wide_SNP_6:01	broad.mit.edu:hybridization:Genome_Wide_SNP_6:01	broad.mit.edu:image_acquisition:Genome_Wide_SNP_6:01	broad.mit.edu:invariantset_medianpolish:Genome_Wide_SNP_6:01	broad.mit.edu:birdseed_genotype:Genome_Wide_SNP_6:01	broad.mit.edu:copynumber_byallele:Genome_Wide_SNP_6:01	broad.mit.edu:copy_number:Genome_Wide_SNP_6:01	broad.mit.edu:no_outlier_copy_number:Genome_Wide_SNP_6:01	broad.mit.edu:after_tangent_copy_number:Genome_Wide_SNP_6:01	broad.mit.edu:segmented_cna:Genome_Wide_SNP_6:01	broad.mit.edu:loss_of_heterozygosity:Genome_Wide_SNP_6:01	broad.mit.edu:loh_segmented_cna:Genome_Wide_SNP_6:01
Protocol Type	labeling	hybridization	image_acquisition	invariantset_medianpolish	birdseed	copynumber_byallele	copynumber	no_outlier_copynumber	after_tangent_copynumber	segmented_cna	loss_of_heterozygosity	loh_segmented_cna
Protocol Description	https://www.affymetrix.com/support/downloads/manuals/genomewidesnp6_manual.pdf	https://www.affymetrix.com/support/downloads/manuals/genomewidesnp6_manual.pdf	https://www.affymetrix.com/support/downloads/manuals/genomewidesnp6_manual.pdf	See DESCRIPTION.txt	See DESCRIPTION.txt	See DESCRIPTION.txt	See DESCRIPTION.txt	See DESCRIPTION.txt	See DESCRIPTION.txt	See DESCRIPTION.txt	See DESCRIPTION.txt	See DESCRIPTION.txt
Protocol Parameters												
Protocol Hardware	GeneChip(R) Fluidics Station	hybridization_station	GeneChip(R) Scanner									
Protocol Software	Affymetrix GeneChip Operating Software Version 1.4		Affymetrix GeneChip Operating Software Version 1.4	GenePattern - SNPFileCreator module	Affymetrix Power Tools	GenePattern	GenePattern	GenePattern	GenePattern	GenePattern	GenePattern	GenePattern
Protocol Contact	https://www.affymetrix.com/	https://www.affymetrix.com/	https://www.affymetrix.com/	http://www.broadinstitute.org/cancer/software/genepattern/	https://www.affymetrix.com/support/developer/powertools/index.affx	http://www.broadinstitute.org/cancer/software/genepattern/	http://www.broadinstitute.org/cancer/software/genepattern/	http://www.broadinstitute.org/cancer/software/genepattern/	http://www.broadinstitute.org/cancer/software/genepattern/	http://www.broadinstitute.org/cancer/software/genepattern/	http://www.broadinstitute.org/cancer/software/genepattern/	http://www.broadinstitute.org/cancer/software/genepattern/
Protocol Term Source REF	MGED Ontology	MGED Ontology	MGED Ontology	The Broad Institute of MIT and Harvard	The Broad Institute of MIT and Harvard	The Broad Institute of MIT and Harvard	The Broad Institute of MIT and Harvard	The Broad Institute of MIT and Harvard	The Broad Institute of MIT and Harvard	The Broad Institute of MIT and Harvard	The Broad Institute of MIT and Harvard	The Broad Institute of MIT and Harvard
												
SDRF Files	crc_snp6_magetab_sdrf.txt											
												
Term Source Name	MGED Ontology	caArray	BCR	Affymetrix	The Broad Institute of MIT and Harvard							
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://caarraydb.nci.nih.gov/	http://www.tgen.org	https://www.affymetrix.com/	http://www.broadinstitute.org							
Term Source Version	1.3.1.1	1.4	-	-	-							

