Single cell sequecing analysis of exhausted CD8 T cell subsets in LCMV-clone13 infected mice

To identify the subsets of exhausted T cells and to analyze the transcriptional-metabolic programs alongside their developmental trajectories at single-cell resolution, we isolated CD44+ PD-1hi CD8+ T cells from chronically infected wild-type (WT) mice 21 days after infection with the 'clone 13' strain of lymphocytic choriomeningitis virus (LCMV) by FACs sorting aand performed scRNA-sequencing. Overall design: C57BL/6 WT Mice were infected with 2x10^6 IU LCMV clone13 after CD4 T cell depletion at d-2 and d0 with 300µg GK1.5 anti-CD4 antibody. At the chronic infection phase (> d21), splenocytes were isolated and CD8+, CD44+, PD-1high cells were sorted using FACS AriaIII.