Investigation Title	Gene Expression Analysis of TCGA samples																																					
Experimental Design	reference_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	Topal	Hoadley																																				
Person First Name	Michael	Katherine																																				
Person Email	michael_topal@med.unc.edu	hoadley@med.unc.edu																																				
Person Phone	919.966.8208	919.966.1752																																				
Person Address	"CB 7225 Lineberger Cancer Center, UNC, Chapel Hill, NC 27599"	"CB 7225 Lineberger Cancer Center, UNC, Chapel Hill, NC "																																				
Person Affiliation	Lineberger Cancer Center	Lineberger Cancer Center																																				
Person Roles	investigator	investigator																																				
Person Roles Term Source REF	MGED Ontology	MGED Ontology																																				
Date of Experiment	8/20/2010																																					
Public Release Date	8/20/2010																																					
																																						
Experiment Description	Gene Expression Analysis of TCGA  samples using Agilent Expression 244K microarrays. 
Protocol Name	unc.edu:split:AgilentG4502A_07_3:01	unc.edu:store:AgilentG4502A_07_3:01	tgen.org:biopsy:clin:01	tgen.org:nucleic_acid_extraction:clin:01	unc.edu:labeling:AgilentG4502A_07_3:01	unc.edu:hybridization:AgilentG4502A_07_3:01	unc.edu:feature_extraction:AgilentG4502A_07_3:01	unc.edu:unc_lowess_normalization_probe_level:AgilentG4502A_07_3:01	unc.edu:unc_lowess_normalization_gene_level:AgilentG4502A_07_3:01																													
Protocol Type	split	store	biopsy	nucleic_acid_extraction	labeling	hybridization	feature_extraction 	Normalization	Normalization																													
Protocol Description	split into aliquots 	store/freeze aliquots 	Standard BCR biopsy	Standard BCR DNA extraction	document available at http://bioinfostore.unc.edu/tcga/Agilent_Files/G4140-90050_Two-Color_GE_5.7.pdf and part of first archive.	document available at http://bioinfostore.unc.edu/tcga/Agilent_Files/G4140-90050_Two-Color_GE_5.7.pdf and part of first archive.	document available at http://bioinfostore.unc.edu/tcga/Agilent_Files/G4140-90050_Two-Color_GE_5.7.pdf and part of first archive.  	"Lowess normalized data, replicate probes were collapsed by averaging. lookup http://genome.unc.edu for lowess information"	Lowess normalized data at Gene Level.Lookup http://genome.unc.edu/ for lowess information																													
Protocol Parameters	none	none	None	Amplification	None	None	None	None	None																													
Protocol Term Source REF	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology																													
																																						
SDRF Files	unc.edu_BRCA.AgilentG4502A_07_3.sdrf.txt																																					
																																						
Term Source Name	MGED Ontology	caArray	BCR	ncbitax	Agilent																																	
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/	http://www.home.agilent.com																																	
Term Source Version	1.3.0.1	2007-01	2007-01	2007-01	2007-01																																	
