Investigation Title	RNA-Seq Analysis of TCGA ESCA Samples using Illumina HiSeq
Experimental Design	transcript_identification_design	is_expressed_design
Experimental Design Term Source REF	MGED Ontology	MGED Ontology
Experimental Factor Name	Esophageal carcinoma
Experimental Factor Type	disease_state_design
Experimental Factor Type Term Source REF	MGED Ontology
							
Person Last Name	Marra	Mungall	Bowlby	He
Person First Name	Marco	Andrew	Reanne	An
Person Mid Initials							
Person Email	mmarra@bcgsc.ca	amungall@bcgsc.ca	rbowlby@bcgsc.ca	ahe@bcgsc.ca
Person Phone	604-707-5900 extn 67-6082	604-675-8000 extn 66-7937
Person Address	"100-570 W 7th Ave, Vancouver, BC, V5Z 4S6, Canada"	"675 W 10th Ave, Vancouver, BC, V5Z 1L3, Canada"	"100-570 W 7th Ave, Vancouver, BC, V5Z 4S6, Canada"	"100-570 W 7th Ave, Vancouver, BC, V5Z 4S6, Canada"
Person Affiliation	"Genome Sciences Centre, BCCA"	"Genome Sciences Centre, BCCA"	"Genome Sciences Centre, BCCA"	"Genome Sciences Centre, BCCA"
Person Roles	investigator	investigator	submitter;investigator	submitter
							
Date of Experiment	2015-04-22
Public Release Date	2015-04-22
							
Experiment Description	RNA-Seq Analysis of TCGA ESCA Samples using Illumina HiSeq
Protocol Name	bcgsc.ca:reverse_transcription:IlluminaHiSeq_RNASeq:01	bcgsc.ca:library_preparation:IlluminaHiSeq_RNASeq:01	bcgsc.ca:DNA_Sequencing:IlluminaHiSeq_RNASeq:01	bcgsc.ca:alignment:IlluminaHiSeq_RNASeq:01	bcgsc.ca:gene_expression:IlluminaHiSeq_RNASeq:01	bcgsc.ca:gene_expression:IlluminaHiSeq_RNASeq:01	bcgsc.ca:snv:IlluminaHiSeq_RNASeq:01	bcgsc.ca:indel:IlluminaHiSeq_RNASeq:01
Protocol Type	reverse_transcription	library_preparation	DNA sequencing	consensus_mRNA	gene_expression	gene_expression	gene_expression	snv	Indel Mutation
Protocol Type	Term Source REF	MGED Ontology	NCI EVS	NCI EVS	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology	Genome Sciences Centre, BCCA	NCI EVS
Protocol Description	Ligation of linkers and reverse transcription of mRNAs	"PCR with sequencing primers, size fractionation"	Sequencing on Illumina HiSeq	Alignment of reads to reference genome plus exon junction sequences	Read counts and RPKM per composite gene	Read counts and RPKM per composite exon	Read counts per splice junction	Single nucleotide variant (see DESCRIPTION.txt)	Insertion and/or deletion events called from mRNAs
							
SDRF Files	bcgsc.ca_ESCA.IlluminaHiSeq_RNASeq.sdrf.txt
							
Term Source Name	MGED Ontology	NCI EVS	Genome Sciences Centre, BCCA
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://evs.nci.nih.gov/	http://www.bcgsc.ca
Term Source Version	1.3.1.1	2010-09	-
