Comment[ArrayExpressAccession]	E-GEOD-55319
MAGE-TAB Version	1.1						
Public Release Date	2014-02-26
Investigation Title	Whole Blood Gene Expression Profiling Predicts Therapeutic Response in Polyarticular Juvenile Idiopathic Arthritis at 4 Months						
Comment[Submitted Name]	Whole Blood Gene Expression Profiling Predicts Therapeutic Response in Polyarticular Juvenile Idiopathic Arthritis at 4 Months
Experiment Description	To determine whether gene expression profiles from peripheral whole blood could be used to determine therapeutic outcome in a cohort of children with newly diagnosed polyarticular JIA. 19 samples were obtained from healthy childhood controls and 93 samples from patients with juvenile idiopathic arthritis. For patient samples, they were collected prior to treatment (month 0) or 4 months after treatment.						
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl					
Person Last Name	Frank	Jiang	Sawle	Frank	Chen	Wallace	Jarvis
Person First Name	Bart	Kaiyu	Ashley	Mark	Yanmin	Carol	James
Person Mid Initials			D	B		A	N
Person Email	frank@omrf.org						
Person Affiliation	OMRF						
Person Address	OMRF, 825 NE 13 St, Oklahoma City, OK, USA						
Person Roles	submitter						
Protocol Name	P-GSE55319-1	P-GSE55319-4	P-GSE55319-5	P-GSE55319-2	P-GSE55319-3	P-GSE55319-6	
Protocol Description	Because of microarray product changes in the course of the study, raw data were reduced to contain 39426 common probes between the microarrays. Data in Matrix (raw) table contain values from Illumina's Genome Studio software and detection p-values above background. Sample tables contain variance stabilized and robust spline values from the lumi package. Batch effects were removed using the ComBat algorithm in the sva package. ID_REF =  VALUE = normalized data	cRNA was produced from reverse transcribed cDNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Austin).	cRNA was hybridized to Illumina WG-6 v3 or Illumina HT-12 v4 human whole genome microarrays, and stained according to the manufacturer’s directions.	2.5 ml of blood was collected in a PAXgene tube (PreAnalytiX GmbH, Hilden, Germany). Samples were stored at -80 C prior to RNA extraction.	RNA was purified from whole blood PAXgene specimens using a PAXgene Blood RNA kit (Qiagen,Valencia, CA) as recommended by the manufacturer, including a DNAse (Qiagen) step to remove genomic DNA. Globin transcripts were reduced using GLOBINclear-Human (Ambion , Austin, TX ).	Scanning was performed using Illumina's iScan scanner	
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	array scanning protocol	
Experimental Factor Name	PATIENT ID	GROUP	MONTH OF VISIT	SEX			
Experimental Factor Type	patient id	group	month of visit	Sex			
Comment[SecondaryAccession]	GSE55319						
Comment[GEOReleaseDate]	2014-02-26						
Comment[ArrayExpressSubmissionDate]	2014-02-25						
Comment[GEOLastUpdateDate]	2014-02-26						
Comment[AEExperimentType]	transcription profiling by array						
Comment[AdditionalFile:Data1]	GSE55319.txt						
Comment[AdditionalFile:Data2]	GSE55319_non-normalized.txt						
SDRF File	E-GEOD-55319.sdrf.txt