
Investigation Title	TCGA level 3 analysis of RNASeq data produced on Illumina GAII sequencers for COAD samples. 						
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	Neil	Charles	Derek	Brian			
Person First Name	Hayes	Perou	Chiang	O'Connor			
Person Mid Initials	D.	M.	D.	D.			
Person Email	hayes@med.unc.edu	cperou@med.unc.edu	Derek_Chiang@med.unc.edu	brianoc@email.unc.edu			
Person Phone	919-966-3786	919-843-5740	919-843-7887	919-966-3786			
Person Address	Lineberger Comprehensive Cancer Center, UNC, Chapel Hill, NC 27599-7264	Lineberger Comprehensive Cancer Center, UNC, Chapel Hill, NC 27599-7264	Lineberger Comprehensive Cancer Center, UNC, Chapel Hill, NC 27599-7264	Lineberger Comprehensive Cancer Center, UNC, Chapel Hill, NC 27599-7264			
Person Affiliation	University of North Carolina, Chapel Hills	University of North Carolina, Chapel Hills	University of North Carolina, Chapel Hills	University of North Carolina, Chapel Hills			
Person Roles	investigator	investigator	investigator	submitter			
							
Date of Experiment	20110727
						
Public Release Date	20110727
						
Experiment Description	TCGA level 3 analysis of RNASeq data produced on Illumina GAII sequencers for COAD samples. 						
							
Protocol Name	unc.edu:reverse_transcription:IlluminaGA_RNASeq:01	unc.edu:library_preparation:IlluminaGA_RNASeq:01	unc.edu:DNA_Sequencing:IlluminaGA_RNASeq:01	unc.edu:consensus_mRNA:IlluminaGA_RNASeq:01	unc.edu:gene_expression:IlluminaGA_RNASeq:01	unc.edu:exon_expression:IlluminaGA_RNASeq:01	unc.edu:splice_junction_expression:IlluminaGA_RNASeq:01	unc.edu:coverage:IlluminaGA_RNASeq:01
Protocol Type	reverse_transcription	library_preparation	DNA sequencing	consensus_mRNA	gene_expression	gene_expression	gene_expression	gene_expression
Protocol Term Source REF	MGED Ontology	NCI EVS	NCI EVS	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology
Protocol Description	Ligation of linkers and reverse transcription of mRNAs	PCR with sequencing primers, size fractionation	Sequencing on Illumina GAII	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_COAD.IlluminaGA_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				
