Pseudotemporal analysis of CD4⁺ T cell fates during L.m. infection . Related to Fig. 3. (a) Force-directed layout depicting the developmental relationship between C7 CD4⁺ naïve and effector T cells during infection with L.m.-ESAT. Cells are colored by sampling time point after infection. (b) Gene expression trends along the two branches of T effector/memory differentiation. Cells exhibiting low levels of TCR-dependent genes (“TCR-lo”) exhibit sustained expression of ISGs. (c) Unimputed log normalized expression of Il2 and Il2ra for individual C7 effectors profiled at 16 and 40 h post activation, demonstrating coexpression of these two genes. Each dot represents an individual cell colored by the time-point of sampling. Percentages of cells expressing Il2, Il2ra, or both are listed on the right. (d) Enrichment of MsigDB Hallmark pathways in “TCR-lo” (pT_CM) versus “TCR-hi” (effector) differentiation branches. (e) Histogram of IFNAR1 staining of naïve CD4⁺ T cells, T_CM and T_EM (left) and quantification (right). Representative of two independent experiments. Statistical significance determined by one-way ANOVA; ****P < 0.0001.