Investigation Title	TCGA Analysis of SNPs and Copy Number Variations for Breast invasive carcinoma Using Affymetrix Genome-Wide SNP Array 6.0		
Experimental Design	comparative_genome_hybridization_design		
Experimental Design Term Source REF	MGED Ontology		
Experimental Factor Name	Breast invasive carcinoma		
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	2009/02/20		
Public Release Date	2009/03/04		
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 Breast invasive carcinoma 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_5NN_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_5NN_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	broad.mit.edu_BRCA.Genome_Wide_SNP_6.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	-	-	-
