Total RNA was extracted from control Luc gRNA iMACs and Irf2 gRNA2 KO iMAC lines (n = 3) using an RNeasy kit (Qiagen) with on-column deoxyribonuclease digestion. Quality control of total RNA was performed to determine sample quantity and quality. The concentration of RNA was determined using a NanoDrop 8000 (Thermo Fisher Scientific), and the integrity of the RNA was determined by Fragment Analyzer (Advanced Analytical Technologies). Total RNA (100 ng) was used as an input material for library preparation using the TruSeq Stranded Total RNA Library Prep Kit (Illumina). The sizes of the libraries were confirmed using High Sensitivity D1K screen tape (Agilent Technologies), and their concentrations were determined with a quantitative PCR–based method using a Library Quantification kit (KAPA). The libraries were multiplexed and sequenced on an Illumina HiSeq4000 (Illumina) to generate 30 million single-end, 50-bp reads. For RNA-seq analysis, the raw FASTQ reads were aligned to the mouse reference genome (GRCm38-mm10) using GSNAP (with parameters -M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna = 200000 --clip-overlap). Reads were filtered to include only the uniquely mapped reads. Differential expression analysis was performed using the voom/limma R package (38). Genes were considered to be differentially expressed if the log2 of the fold change was >1 or <−1 and the adjusted P value was <0.05. RNA-seq data generated are available under the following Gene Expression Omnibus (GEO) submission ID: GSE130195.

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