Investigation Title	TCGA Analysis of Copy Number for OV Using Agilent SurePrint G3 Human CGH Microarray Kit 1x1M	
Experimental Design	comparative_genome_hybridization_design	
Experimental Design Term Source REF	MGED Ontology	
Experimental Factor Name	tumor type	
Experimental Factor Type	disease_state_design	 
Experimental Factor Type Term Source REF	MGED Ontology	

Person Last Name	Socci	Ladanyi
Person First Name	Nicholas	Marc
Person Mid Initials	D	
Person Email	socci@cbio.mskcc.org	ladanyim@mskcc.org
Person Phone	646.888.2608	
Person Address	"1275 York Ave., Box460, New York, NY 10021, USA"	"1275 York Ave., New York, NY 10021, USA"
Person Affiliation	Memorial Sloan Kettering Cancer Center	Memorial Sloan Kettering Cancer Center
Person Roles	submitter	investigator
Person Roles Term Source REF	MGED Ontology	MGED Ontology

Quality Control Types									
Quality Control Types Term Source REF									
Date of Experiment	6/1/2009								
Public Release Date	6/12/2009								

PubMed ID									
Experiment Description	TCGA Analysis of Copy Number for OV Using Agilent SurePrint G3 Human CGH Microarray Kit 1x1M								

Protocol Name	mskcc.org:split:CGH-1x1M_G4447A:01	mskcc.org:split:CGH-1x1M_G4447A:02	mskcc.org:labeling:CGH-1x1M_G4447A:01	mskcc.org:hybridization:CGH-1x1M_G4447A:01	mskcc.org:feature_extraction:CGH-1x1M_G4447A:01	mskcc.org:bioassay_data_transformation:CGH-1x1M_G4447A:01	mskcc.org:segmentation_data_computation:CBS	tgen.org:biopsy:clin:01	tgen.org:nucleic_acid_extraction:clin:01
Protocol Type	split	split	labeling	hybridization	feature_extraction	bioassay_data_transformation	bioassay_data_transformation	biopsy	nucleic_acid_extraction
Protocol Term Source REF	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology
Protocol Description	Promega reference genomic DNA was aliquoted at full concentrations into separate tubes	Promega reference genomic DNA was aliquoted to standard concentrations and volumes for Agilent protocol specifications	Standard Agilent labeling protocol http://www.agilent.com	Standard Agilent hybridization protocol http://www.agilent.com	Standard Agilent feature-extraction protocol  http://www.agilent.com	Standard Agilent + MSKCC.org GCNorm bioassay_data_transformation protocol  http://www.cbio.mskcc.org/CGCC	Circular Binary Segmenation Algorithm (ver 1.13.3) http://www.bioconductor.org/packages/2.2/bioc/html/DNAcopy.html	Standard BCR biopsy	Standard BCR DNA extraction
Protocol Parameters		Amplification							Amplification

SDRF Files	mskcc.org_OV.CGH-1x1M_G4447A.9.sdrf.txt								

Term Source Name	MGED Ontology	caArray	BCR	ncbitax
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://caarraydb.nci.nih.gov/	http://www.tgen.org	http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/
Term Source Version	1.3.0.1	2007-01	2007-01	2007-01

