MAGE-TAB Version	1.1
Investigation Title	TARGET: Kidney - Clear Cell Sarcoma of the Kidney (CCSK) mRNA-seq
Experimental Design	disease state design	transcript identification design	is expressed design
Experimental Design Term Source REF	EFO	EFO	EFO
Experimental Factor Name
Experimental Factor Type
Experimental Factor Term Source REF
Person Last Name	NCI Office of Cancer Genomics (OCG)	NCI Center for Biomedical Informatics and Information Technology (CBIIT)	Gadd	Perlman	Khan
Person First Name			Samantha	Elizabeth	Javed
Person Mid Initials			L	J	
Person Email	ocg@mail.nih.gov	ncicbiit@mail.nih.gov	sgadd@luriechildrens.org	eperlman@luriechildrens.org	javed.khan@nih.gov
Person Phone	+1 301 451 8027	+1 888 478 4423	+1 773 755 6392	+1 312 227 3967	+1 301 435 2937
Person Fax	+1 301 480 4368				+1 301 480 0314
Person Address	31 Center Dr, Rm 10A07, Bethesda, MD 20892	9609 Medical Center Dr, Rockville, MD 20850	2430 N Halsted St, Room C366 Chicago, IL 60614	225 E Chicago Ave, Chicago, IL 60611	37 Convent Dr Rm 2016B, Bethesda MD 20892
Person Affiliation	National Cancer Institute	National Cancer Institute	Lurie Children's Hospital of Chicago Research Center	Ann & Robert H. Lurie Children's Hospital of Chicago	National Cancer Institute
Person Roles	funder;investigator	data coder;curator	investigator;data analyst	investigator	investigator;data analyst;submitter
Person Roles Term Source REF	EFO;EFO	EFO;EFO	EFO;EFO	EFO	EFO;EFO;EFO
Quality Control Type
Quality Control Term Source REF
Replicate Type
Replicate Term Source REF
Normalization Type
Normalization Term Source REF
Date of Experiment
Public Release Date
PubMed ID
Publication DOI
Publication Author List
Publication Title
Publication Status
Publication Status Term Source REF
Experiment Description	"To further explore some more aggressive subtypes in pediatric cancer already under study in OCG, CGCI is partnering with TARGET initiative to support extensive sequencing analysis of three hard to treat childhood cancers: refractory to treatment cases of acute myeloid leukemia and two rare kidney tumors; clear cell sarcoma of the kidney (CCSK) and rhabdoid tumor. CCSK is a rare, aggressive kidney tumor that usually occurs in children younger than 3 years of age and little is known about the biology of this disease. There are 13 patient cases in the CCSK dataset, each with gene expression, methylation and comprehensive next-generation sequencing to include whole genome sequencing of tumor/normal pairs and mRNA-seq. All cases can be sorted according to data type via the Case Matrix on the TARGET Data Matrix. Please visit the TARGET website listed above for additional information on this and other TARGET genomics projects. Please see the TARGET Publication... (for more see dbGaP study page.)"
Protocol Name	nationwidechildrens.org:Protocol:RNA-Extraction-Qiagen-AllPrep:01	nci.nih.gov:CCR.Khan.Protocol:mRNAseq-LibraryPrep-Illumina-Unstranded:01	nci.nih.gov:CCR.Khan.Protocol:mRNAseq-Sequence-Illumina-HiSeq2000:01	nci.nih.gov:CCR.Khan.Protocol:mRNAseq-BaseCall-Illumina:01	nci.nih.gov:CCR.Khan.Protocol:mRNAseq-Expression:02	nci.nih.gov:CCR.Khan.Protocol:mRNAseq-Fusion-DeFuse:01
Protocol Type	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	data transformation protocol	normalization data transformation protocol	data transformation protocol
Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO	EFO
Protocol Description	"RNA was prepared from using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). Please see https://ocg.cancer.gov/programs/target/target-methods for full extraction protocol details."	"Illumina TruSeq paired-end RNA-seq libraries were prepared using Illumina TruSeq Stranded Total RNA Sample Preparation kits according to the manufacturer's protocol. Briefly, ribosomal RNA was removed using Ribo-Zero Gold beads. After purification, total RNA was fragmented to 200nt pieces and then reverse-transcribed using reverse transcriptase and random primers. Second strand cDNA was synthesized using DNA polymerase I and RNase H. These cDNA fragments was added a singl e base and ligated with adaptors. The products were purified and enriched with PCR to create the final RNA-seq libraries."	"Illumina TruSeq paired-end sequencing of RNA libraries were sequenced on Illumina HiSeq2000 using 100bp paired-end sequencing according to the manufacturer's protocol."		"Gene and isoform expression from RNA-seq data was generated using Cufflinks version 2.1.1. with default options and supplied reference annotation (Homo_sapiens.GRCh37.71.gtf) for estimation of expression. Cufflinks will not assemble novel transcripts, and it will ignore alignments not structurally compatible with any reference transcript. RPKM for a given exon is determined by: ( (raw base counts / median read length) * 10^9) / (total reads * exon length). The raw base counts for a given exon is the total number of bases aligned to that genomic segment. Raw base counts are used instead of raw read counts because in many cases only a portion of a read will align to a given exon."	"Gene fusion file was generated using DeFuse version 0.6.1 with default parameters and with reference annotation Homo_sapiens.GRCh37.69."
Protocol Parameters						
Protocol Hardware			Illumina HiSeq 2000			
Protocol Software						
Protocol Contact
SDRF File	TARGET_CCSK_mRNA-seq_20170609.sdrf.txt
Term Source Name	NCBITaxon	NCIt	MO	EFO	OBI
Term Source File	http://www.ncbi.nlm.nih.gov/taxonomy	http://ncit.nci.nih.gov/	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo	http://purl.obolibrary.org/obo/obi
Term Source Version
Comment[SRA_STUDY]	SRP012001
Comment[BioProject]	PRJNA89537
Comment[dbGaP Study]	phs000466
