Investigation Title	TCGA level 3 analysis of RNASeq data produced on Illumina HiSeq 2000 sequencers 						
Experimental Design	transcript_identification_design	is_expressed_design					
Experimental Design Term Source REF	MGED Ontology	MGED Ontology					
Experimental Factor Type	disease_state_design 						
Experimental Factor Type Term Source REF	MGED Ontology						
							
Person Last Name	Hayes	Perou	Chiang	Wu	Hoyle		
Person First Name	Neil	Charles	Derek	George	Alan                    		
Person Mid Initials	D.	M.	D.		P.		
Person Email	hayes@med.unc.educ	perou@med.unc.edu	Derek_Chiang@med.unc.edu	georgewu@med.unc.edu	alanh@unc.edu		
Person Phone	919-966-3786	919-843-5740	919-843-7887	919-843-6669	919-966-9678		
Person Address	"Lineberger Comprehensive Cancer Center, UNC-CH, Chapel Hill, NC 27599-7264"	"Lineberger Comprehensive Cancer Center, UNC-CH, Chapel Hill, NC 27599-7264"	"Lineberger Comprehensive Cancer Center, UNC-CH, Chapel Hill, NC 27599-7264"	"Lineberger Comprehensive Cancer Center, UNC-CH, Chapel Hill, NC 27599-7264"	"Lineberger Comprehensive Cancer Center, UNC-CH, Chapel Hill, NC 27599-7264"		
							
Person Affiliation	The University of North Carolina at Chapel Hill	The University of North Carolina at Chapel Hill	The University of North Carolina at Chapel Hill	The University of North Carolina at Chapel Hill	The University of North Carolina at Chapel Hill		
Person Roles	investigator	investigator	investigator	submitter	submitter		
							
Date of Experiment	20111207						
							
Public Release Date	20111207						
							
Experiment Description	TCGA level 3 analysis of RNASeq data produced on Illumina HiSeq 2000 sequencers 						
							
Protocol Name	unc.edu:library_preparation:IlluminaHiSeq_RNASeq:01	unc.edu:DNA_Sequencing:IlluminaHiSeq_RNASeq:01	unc.edu:consensus_mRNA:IlluminaHiSeq_RNASeq:01	unc.edu:gene_expression:IlluminaHiSeq_RNASeq:01	unc.edu:exon_expression:IlluminaHiSeq_RNASeq:01	unc.edu:splice_junction_expression:IlluminaHiSeq_RNASeq:01	unc.edu:coverage:IlluminaHiSeq_RNASeq:01
Protocol Type	library_preparation	DNA sequencing	consensus_mRNA	gene_expression	gene_expression	gene_expression	gene_expression
Protocol Term Source REF	NCI EVS	NCI EVS	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology
Protocol Description	Illumina TruSeq Kit	2x50 paired-end Sequencing on Illumina HiSeq2000	Alignment of reads to reference transcriptome (UCSC genes Dec 2009 build) with subsequent mapping to the whole genome (UCSC hg19 based on GRCh37) calculated using the SeqWare framework via the RNASeqAlignmentBWA workflow (http://seqware.sourceforge.net)	Read counts and RPKM per composite gene (UCSC genes Dec 2009 build) calculated using the SeqWare framework via the RNASeqAlignmentBWA workflow (http://seqware.sourceforge.net)	Read counts and RPKM per composite exon (UCSC genes Dec 2009 build) calculated using the SeqWare framework via the RNASeqAlignmentBWA workflow (http://seqware.sourceforge.net)	Read counts per splice junction (UCSC genes Dec 2009 build) calculated using the SeqWare framework via the RNASeqAlignmentBWA workflow (http://seqware.sourceforge.net)	Gene expression density plots based on the alignment of reads to reference transcriptome (UCSC genes Dec 2009 build) with subsequent mapping to the whole genome (UCSC hg19 based on GRCh37) calculated using the SeqWare framework via the RNASeqAlignmentBWA workflow (http://seqware.sourceforge.net)
							
Protocol Parameters	SeqWareVersion=0.7.0;RNASeqAlignmentBWAWorfklowVersion=0.7.10;RNASeqQuantificationWorfklowVersion=0.7.0	SeqWareVersion=0.7.0;RNASeqAlignmentBWAWorfklowVersion=0.7.10;RNASeqQuantificationWorfklowVersion=0.7.0	SeqWareVersion=0.7.0;RNASeqAlignmentBWAWorfklowVersion=0.7.10;RNASeqQuantificationWorfklowVersion=0.7.0	SeqWareVersion=0.7.0;RNASeqAlignmentBWAWorfklowVersion=0.7.10;RNASeqQuantificationWorfklowVersion=0.7.0	SeqWareVersion=0.7.0;RNASeqAlignmentBWAWorfklowVersion=0.7.10;RNASeqQuantificationWorfklowVersion=0.7.0		
							
SDRF Files	unc.edu_KIRC.IlluminaHiSeq_RNASeq.2.sdrf.txt						
Term Source Name	MGED Ontology	NCI EVS	NCBI Taxonomy				
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://evs.nci.nih.gov/	http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/				
Term Source Version	1.3.1.1	2010-09	2010-09				
