Application of novel surface markers CD61 and CD55 to track the reversible transition of T _PEX to T _SCM cells. Related to Figs. 3 and 4. (A–D) Sequencing analysis of P14 cells as described and clustered in Fig. 3 A. (A) Anchor genes and reference list used to define T_SCM, T_PEX, and T_EX cell states. (B) Module scores of T_SCM, T_PEX, and T_EX cell genes within each defined cluster. Prominent clusters in each experimental setting are indicated with arrows. Clusters without arrows indicate clusters comprised of mixed conditions (as in Fig. 3 B). (C) Normalized mean expression heat map of key marker genes in selected clusters. (D) Pearson’s correlation analysis of all genes expressed in pseudobulk samples from indicated clusters and conditions. Each row/column is an independent biological replicate. (E) Surface protein sequencing analysis of P14 cells as described in Fig. 3. Surface expression of CD62L and CXCR6 on UMAPs of CD8⁺ T cells. (F–J) Analysis of CD61 and CD55 markers on the surface of antigen-specific CD8⁺ T cells from d8 to d14 of acute LCMV with or without d0–1 IFNAR block, and chronic LCMV infection. Data are representative of three independent experiments with three mice per infection setting per time point. Each dot in G–K represents a single mouse. Data are the mean ± SEM. Statistical differences were analyzed using a one-way ANOVA test. (F) Gating strategy to identify TCF-1⁺SLAMF6⁺CXCR6⁻CD62L⁺CD61⁺CD55⁻ T_PEX cells and TCF-1⁺SLAMF6⁺CXCR6⁻CD62L⁺CD61⁻CD55⁺ T_SCM cells. Pre-gated on P14 cells. (G and H) Graphs summarizing frequencies of (G) CD61⁺ T_PEX and (H) CD55⁺ T_SCM cells throughout infection. (I and J) Graphs summarizing the cell numbers of (I) CD61⁺ T_PEX and (J) CD55⁺ T_SCM cells throughout infection. (K and L) Surface protein expression frequency (left panels) and gMFI (right panels) on CD61⁺ T_PEX and CD55⁺ T_SCM cells. Data are the mean ± SEM. Data are representative of three independent experiments with three mice per group. Statistics was determined by unpaired t tests. (K) Frequency and gMFI of PD-1 and TIM-3 on CD61⁺ T_PEX cells. (L) Frequency and gMFI of PD-1 and TIM-3 on CD55⁺ T_SCM cells. Data are the mean ± SEM. Data are representative of three independent experiments with three to four mice per group. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001.