title: RNAseq of MHV-JHM N1347A mutant virus-infected IFNgamma knock out mice
design: Library preparation was performed315 by the University of Kansas Genome Sequencing core facility, using the NEB Next RNA Library316 kit (NEB) with indexing. RNA-seq was performed using an Illumina NextSeq2000 high-output317 system with a paired-end reads of 50bp each. Raw reads were processed with the nf-core RNA318 seq pipeline v. 3.12.0 with Nextflow v. 23.04.3 [10.5281/zenodo.7998767]. Reads were trimmed319 of adapter sequences with TrimGalore v. 0.6.7 [10.5281/zenodo.5127898], assessed for batch320 effects and aligned to the C57BL6 mouse genome assembly version GRC m39 Mus321 musculus genome assembly (GCF_000001635.27) with the Ensembl version 81 annotation using322 STAR v 2.7.10a