Paired scRNA-seq and scTCR-seq of GP33-specific CD8 T cells in chronic LCMV infection

Chronic viral infection results in CD8 T cell exhaustion. Here, we use paired single-cell RNA sequencing (scRNA-seq) and single-cell T cell receptor sequencing (scTCR-seq) to investigate CD8 T cell phenotypic and clonal heterogeneity in multiple mice during the late stage of LCMV Clone 13 infection. Mice were infected with 2 million PFU LCMV Clone 13. On day 33 (Mouse 1, M1), 33 (M2), and 35 (M3), mice were euthanized and spleens were harvested. GP33-specific CD8 T cells were FACS sorted and the 10x Genomics pipeline was used to perform single-cell RNA and TCR library construction. Libraries were sequenced on an Illumina NextSeq 500 platform.