MAGE-TAB Version	1.1000000000000001					
Investigation Title	TARGET Analysis of DNA Methylation for NBL using Illumina Infinium HumanMethylation450 Platform					
Experimental Design	disease state design					
Experimental Design Term Source REF	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)	Laird	Maris		
Person First Name			Peter	John		
Person Mid Initials			W	M		
Person Email	ocg@mail.nih.gov	ncicbiit@mail.nih.gov	plaird@usc.edu	maris@chop.edu		
Person Phone	+1 301 451 8027	+1 888 478 4423	323.442.7890	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	USC Epigenome Center, University of Southern California, CA 90033, USA	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	investigator;submitter;data analyst	investigator		
Person Roles Term Source REF	EFO	EFO;EFO	EFO;EFO;EFO	EFO		
Quality Control Type	real_time_PCR_quality_control					
Quality Control Term Source REF	MO					
Replicate Type	bioassay_replicate_reduction					
Replicate Term Source REF	MO					
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	usc.edu:Protocol:DNA-Extraction:01	usc.edu:Protocol:MethylationArray-Labeling-Illumina-450k:01	usc.edu:Protocol:MethylationArray-Hybridization-Illumina-450k:01	usc.edu:Protocol:MethylationArray-Scanning-Illumina-450k:01	usc.edu:Protocol:MethylationArray-DataNormalization-Methylumi:01	usc.edu:Protocol:MethylationArray-GeneAnnotation: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	""	"Illumina Infinium HumanMethylation450 Labeling Protocol"	"Illumina HumanMethylation450 Hybridization Protocol"	"Illumina Infinium HumanMethylation450 Scan Protocol"	"Level 2 data contain background-corrected methylated (M) and unmethylated (U) summary intensities as extracted by the methylumi package.  Non-detection probabilities (P-values) were computed as the minimum of the two values (one per allele) for the empirical cumulative density function of the negative control probes in the appropriate color channel. Background correction is performed via normal-exponential deconvolution using out-of-band probes (Triche, Jr. et al, Nucl. Acids Res 2013). Multiple-batch archives have the intensities in each of the two channels multiplicatively scaled to match a reference sample (sample with R/G ratio of normalization control probes closest to 1.0.)."	"Level 3 data contain derived summary measures (beta values: M/(M+U) for each interrogated locus) with annotations (based on Illumina's manifest on GEO, GPL13534) for gene symbol, chromosome (UCSC hg19, Feb 2009), and CpG/CpH coordinate (UCSC hg19, Feb 2009). Probes having a common SNP (common SNP is a SNP with Minor Allele Frequency &gt; 1% as defined by the UCSC snp135common track) within 10bp of the interrogated CpG site or having 15bp from the interrogated CpG site overlap with a REPEAT element (as defined by RepeatMasker and Tandem Repeat Finder Masks based on UCSC hg19, Feb 2009) are masked as NA across all samples, and probes with a non-detection probability (P-value) greater than 0.05 in a given sample are masked as NA on that chip. Probes that are mapped to multiple sites on hg19 are annotated as NA for chromosome and 0 for CpG/CpH coordinate."
Protocol Parameters						
Protocol Hardware						
Protocol Software						
Protocol Contact						
SDRF File	TARGET_NBL_MethylationArray_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						