Correlation of qRT-PCR to RNA-seq Data

We used TaqMan Gene Expression primer/probe sets (ThermoFisher Scientific) with TaqMan master mix to measure expression of 6 genes from the 14 gene classifier signature per the manufacturer’s protocol. First-strand cDNA was generated from 50 ng RNA from each sample using the SuperScript III reverse transcription kit (ThermoFisher Scientific) according to the manufacturer’s protocol. All qRT-PCR reactions were performed in duplicate. We used the following FAM/MGB-labeled assays: ANKRD22 (Mm04208511_g1), IL1R2 (Mm00439622_m1), OAS2 (Mm00460961_m1), MX1 (Mm00487796_m1), MX2 (Mm00488995_m1), and FPR2 (Mm00484464_s1) multiplexed with a VIC/TAMRA-labeled 18S rRNA endogenous control assay (catalog #4310893E). All qRT-PCR assays were performed on a Bio-Rad CFX Touch Real-Tme PCR Detection System. Quantitation was performed relative to control (mock) samples and 18S expression using the 2^−ΔΔCt method.