title: Rna-Seq of mus musculus: tnfrsf18 knockout SMARTA TCR-tg CD4 T cells
design: Tnfrsf18 wildtype and knockout SMARTA TCR-tg CD4 T cells were adoptive transferred into C56Bl/6 host in 1:1 ratio followed by LCMV clone 13 infection. Wildtype and knockout SMARTA cells were subsequently enriched by negative T cell selection from the spleen and separated using flow cytometry sorting at day 3 post-infection. Sample was geenerated from 12 recepient mice pooled. 3 repeats were performed each generating one wildtype and knockout sample i.e. SMARTA GITR WT 1 and KO1 from repeat #1; SMARTA GITR WT 2 and KO 2 from repeat #2 etc. Each sample total RNA was selected with stranded oligo DT Poly-A enrichment and sequenced on Illumina HiSeq 2500 with 2 files/sample named R1 and R2. Wildtype and knockout samples were analyzed for differential gene expression in pairs.