Comment[ArrayExpressAccession]	E-GEOD-43190
MAGE-TAB Version	1.1					
Public Release Date	2012-12-29
Investigation Title	Serum predictors of susceptibility to infection with West Nile virus					
Comment[Submitted Name]	Serum predictors of susceptibility to infection with West Nile virus
Experiment Description	West Nile virus (WNV) is a mosquito-borne RNA flavivirus and the cause of more than 31,000 cases in the USA from 1999-2011 including 1, 262 fatalities. WNV infections are typically asymptomatic, but some patients, especially the elderly and immunocompromised, may experience severe neurological disease and even death. Control of WNV infection by the immune system is multifactorial. We profiled antibody, cytokine responses and gene expression from a stratified cohort of WNV subjects to define immune responses that contribute to disease severity and outcome. Differential gene expression by human PBMCs from asymptomatic and severe patients with WNV infection were generated by microarray.					
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	Meng	Montgomery	Qian	Meng	Kleinstein	
Person First Name	Hailong	Ruth	Feng	Hailong	Steven	
Person Email	geo@ncbi.nlm.nih.gov					
Person Affiliation	Yale University					
Person Address	Yale University, 300 George Str, New Haven, CT, USA					
Person Roles	submitter					
Protocol Name	P-GSE43190-1	P-GSE43190-5	P-GSE43190-4	P-GSE43190-2	P-GSE43190-3	P-GSE43190-6
Protocol Description	ID_REF =  VALUE = quantile and then log2 normalized Detection Pval = 	Standard Illumina scanning protocol	Standard Illumina hybridization protocol	Total RNA from PBMC samples was extracted using the RNeasy mini kit (Qiagen, CA)	Preparation of cDNA, cRNA, and labeling were carried out by the Yale Center for Genomic Analysis using the standard Illumina protocols. Hybridization buffer from the BeadChip kit (Illumina) was mixed with 1500 ng of biotin-labeled cRNA, heated to 65°C for 5 minutes, and then loaded onto the BeadChip. The BeadChips were sealed in a hybridization chamber and placed in an oven at 58°C with a rocker for 16-20 hours. After the hybridization, the BeadChips were washed and stained in a series of washes and stains as outlined in the Illumina protocol. The BeadChips were scanned on the Illumina Iscan.	The data were normalised using quantile normalisation with lumi (lumi_2.4.0) in R version 2.13.2 (2011-09-30)
Protocol Type	bioassay_data_transformation	image_aquisition	hybridization	nucleic_acid_extraction	labeling	feature_extraction
Experimental Factor Name	OUTCOME	BATCH	DISEASE STATUS	SEX	AGE	
Experimental Factor Type	outcome	batch	disease status	sex	age	
Comment[SecondaryAccession]	GSE43190					
Comment[GEOReleaseDate]	2012-12-29					
Comment[ArrayExpressSubmissionDate]	2012-12-28					
Comment[GEOLastUpdateDate]	2012-12-31					
Comment[AEExperimentType]	transcription profiling by array					
Comment[AdditionalFile:Data1]	GSE43190_non-normalized.txt					
SDRF File	E-GEOD-43190.sdrf.txt