MAGE-TAB Version	1.1					
Investigation Title	Characterization of the Transcriptome in Clear Cell Sarcoma of the Kidney					
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		
Person First Name			Samantha	Elizabeth		
Person Mid Initials			L	J		
Person Email	ocg@mail.nih.gov	ncicbiit@mail.nih.gov	sgadd@luriechildrens.org	eperlman@luriechildrens.org 		
Person Phone	+1 301 451 8027	+1 888 478 4423	773-755-6392	312-227-3967		
Person Fax	+1 301 480 4368					
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 Avenue, Chicago, IL 60611		
Person Affiliation	National Cancer Institute	National Cancer Institute	Lurie Children's Hospital of Chicago Research Center  	Ann &amp; Robert H. Lurie Children's Hospital of Chicago		
Person Roles	funder	data coder;curator	submitter;data analyst	investigator		
Person Roles Term Source REF	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	The NCI TARGET initiative seeks to identify therapeutic targets for high-risk pediatric tumors through genomic sequencing supported by copy number, gene expression, and epigenetic analyses. The aim of this study was to use the AffyMetrix U133plus2 chip to determine the transcriptomic status of clear cell sarcoma of the kidney to characterize the gene expression pattern of these tumors and for use in subsequent integrative analyses.					
Protocol Name	nationwidechildrens.org:Protocol:RNA-Extraction:01	luriechildrens.org:Protocol:GeneExpressionArray-Labeling-Affymetrix-IVTExpress:01	luriechildrens.org:Protocol:GeneExpressionArray-Hybridization-Affymetrix-U133Plus2:01	luriechildrens.org:Protocol:GeneExpressionArray-Scanning-Affymetrix-U133Plus2:01	luriechildrens.org:Protocol:GeneExpressionArray-DataNormalization-RMA:01	luriechildrens.org:Protocol:GeneExpressionArray-CollapseDataset:01
Protocol Type	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol 	array scanning protocol	normalization data transformation protocol	data transformation protocol
Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO	EFO
Protocol Description	"RNA was extracted from tumor samples at  Nationwide Children's BioPathology Center (BPC) by using the standard BPC protocol. RNA quality was assessed by a bioanalyzer and RNA samples were required to have a RIN &gt; 7. Total RNA was provided to Lurie Children's Hospital Research Center at a concentration of 150 ng/ul (2 ug total). "	"250 ng of total RNA was labeled by using the Affymetrix GeneChip 3' IVT Express Kit at Lurie Children's Hospital Research Center.  All procedures, including 1st strand reverse transcription, 2nd strand synthesis, in vitro transcription of aRNA, aRNA purification, quantitation, and fragmentation were performed according to the manufacturer's protocol."	"Nucleic acid hybridization to the array was performed at Lurie Children's Hospital Research Center by using the AffyMetrix GeneChip Hybridization, Wash and Stain Kit per the manufacturer's instructions."	"The arrays were scanned at Lurie Children's Hospital Research Center by using the Gene-Chip Operating Software (GCOS).  Each .dat file was visually inspected for large scratches and/or misalignment of the grid. "	"GeneChip Operating Software (GCOS) was used to generate .chp files, which represent the consolidation of all individual probes within a probeset, from .cel files. From .chp files, GCOS was used to generate .rpt files, which show probe intensity values and QC values. All samples were inspected for several parameters: Background &lt; 45, Noise (Raw Q) &lt; 1.35, Scaling Factor &lt; 65%, Present call &gt; 35%, 3'/5' GAPDH &lt; 3.92. All .cel files were imported into the Broad Institute's GenePattern server and Robust Multichip Average (RMA) normalization was performed using the ExpressionFileCreator module. Data were exported as a single .txt file containing probeset information for each individual tumor within a single spreadsheet. Several analytic quality control steps were performed. Principle component analysis (PCA) was performed to ensure that none of the samples were outliers."	"A collapsed data file was created by using the Broad Insitute's GenePattern CollapseDataset module with the default parameters and the maximum probe collapse method."
Protocol Parameters						
Protocol Hardware						
Protocol Software						
Protocol Contact						
SDRF File	TARGET_CCSK_GeneExpressionArray_20160819.sdrf.txt					
Term Source Name	NCBITaxon	NCIt	MO	EFO	OBI	
Term Source File	http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html	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						