Expression and transcriptome analysis console software

RNA samples were isolated from age-matched mice of different genotypes. Fluorescently-labeled cDNA probes were prepared from extracted RNA samples and hybridized to Affymetrix Mouse Gene ST 2.0 arrays. Array hybridization, washing, and scanning were carried out per the manufacturer's instructions. Data processing and analysis were performed with Affymetrix Expression and Transcriptome Analysis Console software.

RNA from Procr^WT monocytes stimulated for 3 hours with IgG control, HL7G, R848, CpG B, or Poly I:C was processed with GeneChip™ WT PLUS Reagent Kit and hybridized on a GeneChip™ Mouse Gene 2.0 ST Array (Affymetrix). Data normalization by Robust Multi-array Average (RMA) and analysis of differentially expressed probe sets by Tukey’s Bi-weight average algorithm and Analysis of Variance (ANOVA) used the Affymetrix Expression and Transcriptome Analysis Console Software. Statistical analysis for differential expression by limma linear modeling (56 (link)) and empirical Bayes statistics used a false discovery rate <0.05. Hierarchical clustering of relative expression with complete linkage also used R version 3.6.3.