Microarray Gene Expression Analysis

Total RNA was isolated and reverse transcribed for hybridization to the Mouse Gene 1.0 ST Array (GeneChip; Affymetrix, Santa Clara, CA, USA) as described previously.^{33 (link)} Arrays were processed using the Affymetrix GeneChip Fluidic Station 450 (protocol EukGE-WS2v5_450) and scanned using a GeneChip Scanner 3000 G7 (Affymetrix). GeneChip Operating Software (Affymetrix GCOS v.1.4) was used to obtain chip images, with quality control performed using the AffyQCReport software (Bioconductor, Berkeley, CA, USA). GSEA was performed on the Board Institute Platform^{34 (link), 35} and statistical significance (false discovery rate) was set at 0.25. Microarray data are available from Gene Expression Omnibus (National Center for Biotechnology Information, Bethesda, MD, USA) under the accession number GSE45232.