MAGE-TAB Version	1.1					
Investigation Title	Gene Expression Profiling in Pediatric AML					
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)	Meshinchi	Arceci	Ries	
Person First Name			Soheil	Robert	Rhonda	
Person Mid Initials				J	E 	
Person Email	ocg@mail.nih.gov	ncicbiit@mail.nih.gov	smeshinc@fhrc.org	rarceci@phoenixchildrens.com	rries@fhcrc.org	
Person Phone	+1 301 451 8027	+1 888 478 4423	206-667-4077	602-827-2508	206-667-7104	
Person Fax	+1 301 480 4368		206-667-4310	602-271-0264		
Person Address	31 Center Dr, Rm 10A07, Bethesda, MD 20892	9609 Medical Center Dr, Rockville, MD 20850	1100 Fairview Avenue North, D5-380, POB 19024, Seattle, WA  98109	445 N. 5th St, Tgen Building Room 322, Phoenix, AZ 85004	1100 Fairview Avenue North, D2-245, Seattle, WA  98109	
Person Affiliation	National Cancer Institute	National Cancer Institute	Fred Hutchinson Cancer Research Center	University of Arizona College of Medicine	Fred Hutchinson Cancer Research Center	
Person Roles	funder	data coder;curator	investigator	investigator	submitter;data analyst	
Person Roles Term Source REF	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 Profiling and analysis of the TARGET pediatric AML cohort					
Protocol Name	fredhutch.org:Protocol:RNA-Extraction-Qiagen:01	hudsonalpha.org:Protocol:GeneExpressionArray-Labeling-Affymetrix-WT:01	hudsonalpha.org:Protocol:GeneExpressionArray-Hybridization-Affymetrix-HuGene:01	hudsonalpha.org:Protocol:GeneExpressionArray-Scanning-Affymetrix-HuGene:01	fredhutch.org:Protocol:GeneExpressionArray-DataNormalization-RMA:01	fredhutch.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	"Starting with one vial of cryopreserved cells derived from Bone Marrow (or if Bone Marrow unavailable, Peripheral Blood), cells undergo a quick thaw and are adding to a tube containing PBS (to dilute the residual DMSO).  Cells are spun at 1000RPM and pelleted.  The pellet is vortexed and resuspended in lysis buffer from the Qiagen AllPrep DNA/RNA mini kit.  The lysate is added to an RNeasy spin column to isolate RNA while the flow through is added to the DNA spin column for subsequent DNA isolation.  After a series of washes on each column, DNA or RNA is eluted into a tube using elution buffer or RNase-free H20 respectively.  Both nucleic acids are evaluated on the NanoDrop for initial sample concentration and quality.  DNA quantification is then assessed using the Picogreen assay for better accuracy.  RNA quality and quantity is also assessed using the Agilent Bioanalyzer nanochip."	"All microarray experiments were performed according to manufacturer’s protocol using the Ambion WT Expression Kit, the GeneChip WT Terminal Labeling and Controls Kit, and the GeneTitan Hybridization, Wash, and Stain Kit for WT Array Plates. Briefly, 200ng input total RNA was converted to double-stranded cDNA followed by an in-vitro transcription reaction.  The product from the IVT reaction was purified, quantified and normalized to 10ug of cRNA input into a second-cycle, first-strand cDNA synthesis reaction to generate single stranded cDNA.  The cDNA product was purified and 5.5ug was fragmented and labeled for hybridization. The Agilent Bioanalyzer was used to perform quality control bioanalysis of the cDNA, the fragmented cDNA, and labeled cDNA."	"The arrays were hybridized according to manufacturer’s protocol to the Human Gene 1.1 ST 96-Array Plate using the Affymetrix GeneTitan. "	"Arrays were scanned and raw image data (intensity files) were generated using Affymetrix GeneChip Command Console Software."	"Raw intensity files were imported into Affymetrix Expression Console Software and normalized using the Robust Multichip Analysis-sketch workflow to assess quality control parameters and ensure uniform performance across the data set.  All raw files were uploaded into Partek Genomics Suite (St. Louis, MO) and RMA normalized upon import.  "	"To assign a single value per gene ID, multiple cluster IDs mapping to the same gene ID were averaged into one value.  The level 3 file represents the average (if multiple cluster IDs are represented) value per gene."
Protocol Parameters						
Protocol Hardware						
Protocol Software						
Protocol Contact						
SDRF File	TARGET_AML_GeneExpressionArray_20160812.sdrf.txt					
Term Source Name	NCBITaxon	NCIt	MO	EFO		
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		
Term Source Version						