Figure 1.

Effector memory CD4⁺ T cell heterogeneity during acute bacterial infection. (a) Strategy to isolate wild-type gp66:I-A^b+ CD4⁺ T cells for scRNA-seq, 7 days after infection with L.m.-gp66. (b) UMAP of 2964 gp66:I-A^b-specific CD4⁺ T cells colored by Phenograph clusters and annotated by inferred CD4⁺ T cell effector/memory lineage. (c) UMAP overlaid with imputed expression of canonical T_FH, T_H1, or T_CM genes. (d) Imputed, log-normalized expression of top 20 DEGs (log₂FC > 0.5, FDR < 0.01) for each phenograph cluster shown in Fig. 1 b. Colored bar at the top of the heatmap indicates cluster assignments. (e) Diffusion map of gp66:I-A^b-specific CD4⁺ T cells using the first two DCs reflecting distinct CD4⁺ T cell fates. Cells are colored by cluster as in Fig. 1 b.