Transcriptomic Profiling of IFNβ-Stimulated B16 Cells

Adar1-null or control sgRNA-transfected B16 cells were
stimulated with IFNβ (1,000 U/ml, PBL) for 36 h. RNA was extracted from
cell pellets using the Qiagen RNeasy Mini kit according to the
manufacturer’s instructions. First-strand Illumina-barcoded libraries
were generated using the NEB RNA Ultra Directional kit according to the
manufacturer’s instructions, using ribosomal RNA depletion and including
a 12-cycle PCR enrichment. Libraries were sequenced on an Illumina NextSeq 500
instrument using paired-end 37-bp reads. Data were trimmed for quality using the
Trimmomatic pipeline with the following parameters: LEADING:15 TRAILING:15
SLIDINGWINDOW:4:15 MINLEN:16. Data were aligned to mouse reference genome mm10
using Bowtie2. HTSeq was used to map aligned reads to genes and to generate a
gene count matrix. Normalized counts and differential expression analysis was
performed using the DESeq2 R package (Supplementary Information Table 5).
GSEA was performed as previously described, using the Hallmark gene signature
collection^{29 (link),31 (link)}(Supplementary Information Table
6).