Single-cell RNA-seq of sorted CD8+ T cells from B16 melanoma tumors

CD8 T cells are the main effectors of the adaptive immune response against intracellular pathogens and cancer. Chronic antigen stimulation and inflammation lead to CD8 T cell differentiation and function that differ from those generated during acute infections. A comprehensive definition of the heterogeneity existing within both tumor-specific and total CD8 tumor-infiltrating T cells remains to be clearly established. To investigate this heterogeneity at the transcriptomic level, we performed paired single-cell RNA and TCR sequencing of >3500 CD8 T cells infiltrating B16 murine melanoma tumors, including cells of known tumor-specificity. Tumor-infiltrating CD8 T cells from B16.F10 melanoma tumor bearing C57BL/6 (CD45.1 locally bred, n=4) and PMEL (n=3) (Jackson Laboratory, Cat#005023) mice were sorted by flow cytometry 15 days post-tumor engraftment. Paired transciptomic profiles and TCR sequences were obtained at single-cell resolution using 10X Genomics Chromium technology.