MAGE-TAB Version	1.1						
Investigation Title	TARGET ALL Phase II Gene Expression Profiling						
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)	Harvey	Willman	Hunger	Loh	
Person First Name			Richard	Cheryl	Stephen	Mignon	
Person Mid Initials			C	L	P		
Person Email	ocg@mail.nih.gov	ncicbiit@mail.nih.gov	rharvey@salud.unm.edu	cwillman@salud.unm.edu 	hungers@chop.edu	lohm@peds.ucsf.edu	
Person Phone	+1 301 451 8027	+1 888 478 4423	505-272-6793	505-272-5622 		415-476-3831	
Person Fax	+1 301 480 4368			505-272-4039 			
Person Address	31 Center Dr, Rm 10A07, Bethesda, MD 20892	9609 Medical Center Dr, Rockville, MD 20850	MSC08-4640, 1201 Camino de Salud NE, Albuquerque, NM 87131	MSC07-4025, 1201 Camino de Salud NE, Albuquerque, NM 87131	3401 Civic Center Blvd Philadelphia, PA 19104	Box 0106, UCSF
San Francisco, CA 94143-0106	
Person Affiliation	National Cancer Institute	National Cancer Institute	University of New Mexico School of Medicine	Univeristy of New Mexico School of Medicine	Children's Hospital of Philadelphia	UCSF Benioff Children's Hospital	
Person Roles	funder	data coder;curator	investigator;data analyst;submitter	investigator	investigator	investigator	
Person Roles Term Source REF	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	Gene expression data were generated for pediatric patients with early relapses in order to study whether expression patterns predicted outcome or other critical clinical features.  These data are intended to be merged with copy-number analysis and sequencing of the same samples to create the most predictive parameters.						
Protocol Name	stjude.org:Protocol:RNA-Extraction-Trizol:01	stjude.org:Protocol:GeneExpressionArray-Labeling-Affymetrix-OneCycle:01	stjude.org:Protocol:GeneExpressionArray-Hybridization-Affymetrix-IVTExpress:01	stjude.org:Protocol:GeneExpressionArray-Scan-Affymetrix-U133Plus2:01	stjude.org:Protocol:GeneExpressionArray-Scanning-Affymetrix-U133Plus2:01	stjude.org:Protocol:GeneExpressionArray-DataNormalization-MAS5:01	stjude.org:Protocol:GeneExpressionArray-Expression-CollapseDataset:01
Protocol Type	nucleic acid extraction protocol	nucleic acid labeling 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	EFO
Protocol Description	"RNA was extracted by the method of Trizol according to the manufacturer's instructions (Invitrogen).  Briefly, cryopreserved cells were thawed and gently pelleted.  The supernatant was removed and the pellet was dispersed while adding Trizol with vortexing (1 mL Trizol/1e7 cells).  Vortexing was continued until the lysate was homogeneous and clear."	"cRNA for hybridization to U133_Plus_2.0 arrays was performed according to Affymetrix's recommendations (GeneChip Expression Analysis Technical Manual).  First, 300 ng of total RNA was converted to cDNA.  Biotinylated cRNA was generated from the cDNA and 15 µg was subjected to fragmentation.  Affymetrix One-Cycle Target Labeling Kit was used."	"cRNA for hybridization to U133_Plus_2.0 arrays was performed according to Affymetrix's recommendations (GeneChip Expression Analysis Technical Manual).  First, 300 ng of total RNA was converted to cDNA.  Biotinylated cRNA was generated from the cDNA and 15 µg was subjected to fragmentation.  Affymetrix 3' IVT Express Kit was used.  This v02 labeling protcol differs from v01 because the labeling kit changed. Affymetrix changed the IVT kit between 2008 and 2009.  While most of the gene expression patterns remain the same, there are some pronounced differences that may result in set effects when trying to merge data generated from the different labeling kits."	"Hybridization of 12.5 µg fragmented biotinylated cRNA was performed according to Affymetrix's recommendations (GeneChip Expression Analysis Technical Manual)."	"Scanning of the microarrays was performed according to Affymetrix's recommended protocol  (GeneChip Expression Analysis Technical Manual)."	"Data were masked according to the method outlined in Harvey et al, Blood 116:4874-4884, (2010) in order to remove uninformative probe pairs.  Default MAS 5.0 normalization was performed on the masked data using Expression Console software (Affymetrix)."	"The non-collapsed GCT file is simply the masked MAS 5.0 data from the CHP files formatted as a GCT file.  Level 3 data were generated by using the CollapseDataset algorithm of GenePattern:  http://www.broadinstitute.org/cancer/software/genepattern/.  In applying this software, the "maximum" (as opposed to "median") probeset setting was used, and the gene-to-probeset associations were obtained from the file AFFYMETRIX.chip downloaded from ftp://gseaftp.broadinstitute.org/pub/gsea/annotations/. 
"

Protocol Parameters							
Protocol Hardware							
Protocol Software							
Protocol Contact							
SDRF File	TARGET_ALL_GeneExpressionArray_Phase2_20160812.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							