Supplementary Figure 2: Progenitor exhausted and terminally exhausted CD8⁺ T cell populations confirmed in multiple mouse tumor models by flow cytometry.

a, Representative flow cytometry gating strategy for progenitor and terminally exhausted cells (left) with tetramer full-minus one (FMO, right). b, Frequency of progenitor exhausted (Tcf1⁺Tim-3^–) and terminally exhausted (Tcf1^–Tim-3⁺) CD8⁺ T cells from B16-OVA tumors (top), B16.F10 tumors (middle) or D4M.3A-OVA tumors (bottom) gated on PD-1⁺CD44⁺ cells. Representative flow plot (left) and summary (right) of three independent experiments, n = 17 mice (B16-OVA), n = 5 mice (B16.F10), or one of two independent experiments, n = 5 mice (D4M.3A-OVA). c, Frequency of Tcf1⁺ cells within Slamf6⁺Tim-3^– or Slamf6^–Tim-3⁺ cells (top) or frequency of Slamf6⁺ cells within Tcf1⁺Tim-3^– or Tcf1^–Tim-3⁺ cells (bottom) from B16-OVA tumors. Representative flow plots (left) and summary (right) of one of two independent experiments, n = 9 mice. d, Scatter plot of transcript abundance (log₁₀) between replicates for all 13,012 transcripts. e, Hypergeometric overlap of gene expression profiles from progenitor exhausted or terminally exhausted gene signatures from LCMV or TILs with expression data from indicated cell states from the literature, top 150 differentially expressed transcripts used for comparison. Mean +/- s.d. (b,c), two-sided Student’s t test (b,c); two-sided hypergeometric test (e); **** p ≤ 0.0001.