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	Wu	Hoyle
Person First Name	Neil	Charles	George	Alan
Person Mid Initials	D.	M.		P.
Person Email	hayes@med.unc.edu	cperou@med.unc.edu	georgewu@med.unc.edu	alanh@unc.edu
Person Phone	919-966-3786	919-843-5740	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"

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
Person Roles	investigator	investigator	submitter	submitter

Date of Experiment	20141203

Public Release Date	20141203

Experiment Description	TCGA level 3 analysis of RNASeq data produced on Illumina HiSeq 2000 sequencers

Protocol Name	unc.edu:library_preparation:IlluminaHiSeq_RNASeqV2:3	unc.edu:DNA_Sequencing:IlluminaHiSeq_RNASeqV2:3	unc.edu:consensus_mRNA:IlluminaHiSeq_RNASeqV2:3	unc.edu:exon_expression:IlluminaHiSeq_RNASeqV2:3	unc.edu:splice_junction_expression:IlluminaHiSeq_RNASeqV2:3	unc.edu:RSEM_isoforms_normalized:IlluminaHiSeq_RNASeqV2:3	unc.edu:RSEM_genes_normalized:IlluminaHiSeq_RNASeqV2:3	unc.edu:RSEM_isoforms:IlluminaHiSeq_RNASeqV2:3	unc.edu:RSEM_genes:IlluminaHiSeq_RNASeqV2:3	unc.edu:library_preparation:IlluminaHiSeq_RNASeqV2:2	unc.edu:DNA_Sequencing:IlluminaHiSeq_RNASeqV2:2	unc.edu:consensus_mRNA:IlluminaHiSeq_RNASeqV2:2	unc.edu:exon_expression:IlluminaHiSeq_RNASeqV2:2	unc.edu:splice_junction_expression:IlluminaHiSeq_RNASeqV2:2	unc.edu:RSEM_isoforms_normalized:IlluminaHiSeq_RNASeqV2:2	unc.edu:RSEM_genes_normalized:IlluminaHiSeq_RNASeqV2:2	unc.edu:RSEM_isoforms:IlluminaHiSeq_RNASeqV2:2	unc.edu:RSEM_genes:IlluminaHiSeq_RNASeqV2:2	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	gene_expression	gene_expression	library_preparation	DNA sequencing	consensus_mRNA	gene_expression	gene_expression	gene_expression	gene_expression	gene_expression	gene_expression	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	MGED Ontology	MGED Ontology	NCI EVS	NCI EVS	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology	NCI EVS	NCI EVS	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology
Protocol Description	Illumina TruSeq Kit	Paired-end Sequencing on Illumina HiSeq2000	Alignment of reads to genome (TCGA hg19) in the SeqWare framework via the MapSpliceRSEM workflow (http://seqware.sourceforge.net)	Read counts and RPKM per composite exon (GAF TCGA hg19 June 2011 build) calculated using the SeqWare framework via the MapSpliceRSEM workflow	Read counts and RPKM per splice junction (GAF TCGA hg19 June 2011 build) calculated using the SeqWare framework via the MapSpliceRSEM workflow	"Upper quartile normalized read counts per isoform (GAF TCGA hg19 June 2011 build) calculated using the SeqWare framework via the RSEM algorithm (Li and Dewey, BMC Bioinformatics 2011)"	"Upper quartile normalized gene counts per isoform (GAF TCGA hg19 June 2011 build) calculated using the SeqWare framework via the RSEM algorithm (Li and Dewey, BMC Bioinformatics 2011)"	"Counts per isoform (GAF TCGA hg19 June 2011 build) calculated using the SeqWare framework via the RSEM algorithm (Li and Dewey, BMC Bioinformatics 2011)"	"Counts per genes (GAF TCGA hg19 June 2011 build) calculated using the SeqWare framework via the RSEM algorithm (Li and Dewey, BMC Bioinformatics 2011)"	Illumina TruSeq Kit	Paired-end Sequencing on Illumina HiSeq2000	Alignment of reads to genome (TCGA hg19) in the SeqWare framework via the MapSpliceRSEM workflow (http://seqware.sourceforge.net)	Read counts and RPKM per composite exon (GAF TCGA hg19 June 2011 build) calculated using the SeqWare framework via the MapSpliceRSEM workflow	Read counts and RPKM per splice junction (GAF TCGA hg19 June 2011 build) calculated using the SeqWare framework via the MapSpliceRSEM workflow	"Upper quartile normalized read counts per isoform (GAF TCGA hg19 June 2011 build) calculated using the SeqWare framework via the RSEM algorithm (Li and Dewey, BMC Bioinformatics 2011)"	"Upper quartile normalized gene counts per isoform (GAF TCGA hg19 June 2011 build) calculated using the SeqWare framework via the RSEM algorithm (Li and Dewey, BMC Bioinformatics 2011)"	"Counts per isoform (GAF TCGA hg19 June 2011 build) calculated using the SeqWare framework via the RSEM algorithm (Li and Dewey, BMC Bioinformatics 2011)"	"Counts per genes (GAF TCGA hg19 June 2011 build) calculated using the SeqWare framework via the RSEM algorithm (Li and Dewey, BMC Bioinformatics 2011)"	Illumina TruSeq Kit	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;MapSpliceRSEM=0.7.5	SeqWareVersion=0.7.0;MapSpliceRSEM=0.7.5	SeqWareVersion=0.7.0;MapSpliceRSEM=0.7.5	SeqWareVersion=0.7.0;MapSpliceRSEM=0.7.5	SeqWareVersion=0.7.0;MapSpliceRSEM=0.7.5	SeqWareVersion=0.7.0;MapSpliceRSEM=0.7.5	SeqWareVersion=0.7.0;MapSpliceRSEM=0.7.5	SeqWareVersion=0.7.0;MapSpliceRSEM=0.7.5	SeqWareVersion=0.7.0;MapSpliceRSEM=0.7.5	SeqWareVersion=0.7.0;MapSpliceRSEM=0.7.4	SeqWareVersion=0.7.0;MapSpliceRSEM=0.7.4	SeqWareVersion=0.7.0;MapSpliceRSEM=0.7.4	SeqWareVersion=0.7.0;MapSpliceRSEM=0.7.4	SeqWareVersion=0.7.0;MapSpliceRSEM=0.7.4	SeqWareVersion=0.7.0;MapSpliceRSEM=0.7.4	SeqWareVersion=0.7.0;MapSpliceRSEM=0.7.4	SeqWareVersion=0.7.0;MapSpliceRSEM=0.7.4	SeqWareVersion=0.7.0;MapSpliceRSEM=0.7.4SeqWareVersion=0.7.0;RNASeqAlignmentBWAWorfklowVersion=0.7.x;RNASeqQuantificationWorfklowVersion=0.7.0	SeqWareVersion=0.7.0;RNASeqAlignmentBWAWorfklowVersion=0.7.10;RNASeqQuantificationWorfklowVersion=0.7.0

SDRF Files	unc.edu_KIRP.IlluminaHiSeq_RNASeqV2.1.17.0.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
