Microarray analysis

Expression oligonucleotide arrays were performed on RNA isolated from spleen and liver tissues from strain and time-matched mock infected mice and WNV-infected WT, Mavs^−/−, Ifnar^−/−, and Mavs^−/−×Ifnar^−/− DKO mice. RNA was prepared as previously described [13]. Raw data were loaded into a custom-designed laboratory information management system (LIMS). Data were warehoused in a Labkey system (Labkey, Inc., Seattle, WA) and analyzed using GeneData Analyst 2.2.1 software (GeneData Solutions In Silico, San Francisco, CA), and TIBCO Spotfire with Integromics. Raw microarray data have been deposited in NCBI's Gene Expression Omnibus under GEO Series accession number GSE39259 and also are accessible via the Katze Laboratory website (www.viromics.washington.edu) in accordance with proposed Minimum Information About a Microarray Experiment (MIAME) standards. A student's t-test was performed to determine the genes that had different expression levels after WNV infection compared to mock infection for each of the four mouse strains.