MAGE-TAB Version	1.1000000000000001								
Investigation Title	TARGET Analysis of Gene Expression for Neuroblastoma using Affymetrix Human Exon Array Platform								
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	disease state								
Experimental Factor Term Source REF	EFO								
Person Last Name	NCI Office of Cancer Genomics (OCG)	NCI Center for Biomedical Informatics and Information Technology (CBIIT)	Asgharzadeh	Maris					
Person First Name			Shahab	John					
Person Mid Initials				M					
Person Email	ocg@mail.nih.gov	ncicbiit@mail.nih.gov	shahab@chla.usc.edu	maris@chop.edu					
Person Phone	+1 301 451 8027	+1 888 478 4423	323-361-6477	215-590-5244					
Person Fax	+1 301 480 4368			267-426-0685					
Person Address	31 Center Dr, Rm 10A07, Bethesda, MD 20892	9609 Medical Center Dr, Rockville, MD 20850	Children's Hospital Los Angeles, 4650 Sunset Blvd MS57, Los Angeles, CA 90027	3501 Civic Center Blvd CTRB 3060, Philadelphia, PA 19104					
Person Affiliation	National Cancer Institute	National Cancer Institute	University of Southern California	Children's Hospital of Philadelphia and Perelmen School of Medicine at the University of Pennsylvania					
Person Roles	funder	data coder;curator	submitter;investigator;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									
Protocol Name	chla.org:Protocol:RNA-Extraction-Trizol:01	chop.edu:Protocol:RNA-Extraction-Trizol:01	chla.org:Protocol:GeneExpressionArray-Labeling-Affymetrix-HuExon:01	chla.org:Protocol:GeneExpressionArray-Hybridization-Affymetrix-HuExon:01	chla.org:Protocol:GeneExpressionArray-Scanning-Affymetrix-HuExon:01	chla.org:Protocol:GeneExpressionArray-DataNormalization-RMASketch:01	chla.org:Protocol:GeneExpressionArray-DataTransformation-GLM:01	chla.org:Protocol:GeneExpressionArray-Affymetrix-TranscriptAnnotation:01	chla.org:Protocol:GeneExpressionArray-Affymetrix-GeneAnnotation:01
Protocol Type	nucleic acid extraction protocol	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol 	array scanning protocol	normalization data transformation protocol	data transformation protocol	data transformation protocol	data transformation protocol
Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO	EFO	EFO	EFO	EFO
Protocol Description	"RNA was extracted from OCT embedded primary tumor tissues using TRIZOL based methods with QIAGEN RNAeasy clean up at  Children's Hospital Los Angeles."	"RNA was extracted from OCT embedded primary tumor tissues using TRIZOL based methods with QIAGEN RNAeasy clean up at  Children's Hospital of Philadelphia."	"Affymetrix Human Exon Array Labeled Extract"	"Affymetrix Human Exon Array Hybridization Protocol"	"Affymetrix Human Exon Array Scan Protocol"	"Level 2 data from normalization and summariztion using rma-skectch analysis of Affymetrix APT tools (version 1.16.0)."	"Level 2 batch effect corrected (BER) data were obtained by removing the batch effect observed related to RNA source of the specimens. Generalized linear model (glm() - R version 3.10) was used to remove institutional batch effect by fitting a model for each of the Human Exon array probeset regions (PSR) to the batch effect (RNA source by institution). This GLM model was adjusted for risk groups based on stage and MYCN amplification status.  This Level 2 data was used to generate  all subsequent data transformations."	"Level 3 based on PSRs that are part of the 'core', 'extended', and 'full' annotation.  The data was derived from Level 2 BER data.  First PSRs with low expression (less than median expression level of entire dataset) and low coefficient of variation (less than median cv of entire dataset) were removed (~10% of PSRs) prior to averaging of PSRs by Transcript ID (based on Affymetrix Annotation)."	"Level 3 based on PSRs that are part of the 'core', 'extended', and 'full' annotation.  The data was derived from Level 3 BER transcript data set where PSRs with low expression (less than median expression level of entire dataset) and low coefficient of variation (less than median cv of entire dataset) were removed (~10% of PSRs) prior to averaging of PSRs by Gene Symbol (based on BioCore Package Affymetrix huex10 annotation data - huex10stprobeset.db. Mappings were based on data provided by: Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/DATA With a date stamp from the source of: 2014-Mar13)."
Protocol Parameters									
Protocol Hardware									
Protocol Software									
Protocol Contact									
SDRF File	TARGET_NBL_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									