Ulk1/2+/+ and Ulk1/2−/− MEFs were plated as four biological replicates and were either left untreated or were treated for 6 hours with mouse IFN-γ (2.5 × 103 IU/ml). Total RNA was isolated using the RNeasy Mini Kit (Qiagen), following the manufacturer’s instructions. Library construction and stranded mRNA sequencing were conducted at the NUSeq Core Facility of Northwestern University. Briefly, RNA quality and quantity were first determined with the Agilent Bioanalyzer 2100 and Qubit fluorometer, and all samples presented an RNA integrity number of 10. Sequencing libraries were prepared from 1 μg of high-quality RNA samples using the Illumina TruSeq Stranded mRNA Library Preparation Kit (Illumina), as per the manufacturer’s instructions. This procedure includes mRNA purification and fragmentation, complementary DNA (cDNA) synthesis, 3′ end adenylation, Illumina adapter ligation, and library PCR amplification and validation. An Illumina NextSeq 500 Sequencer was used to sequence the libraries with the production of single-end, 75-bp reads.

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