Analysis of CD4 ⁺ T cell responses to systemic L.m. infection . Related to Fig. 1. (a) UMAP overlaid with log normalized counts of canonical T_FH, T_H1, or T_CM genes for comparison with imputed expression Fig. 1 c. (b) UMAP overlaid with imputed (left) and log normalized (right) expression of T_FH, T_H1, or T_CM genes. (c) Heatmap showing imputed, log-normalized expression of all DEGs (log₂FC > 0.5, FDR < 0.01) identified for each T_FH cluster (cluster 6 or cluster 1). The 177 differentially expressed T_FH genes shown include the union of DEGs identified in each replicate in one vs. rest comparisons for each T_FH cluster. The colored bar at the top of the heatmap shows the assignment of cells to these clusters. (d) UMAP of single-cell transcriptomes from gp66:I-A^b+ CD4⁺ T cells colored by imputed (left) and log-normalized (right) expression of canonical germinal center T_FH genes. (e) UMAP overlaid with the mean expression of genes from the indicated KEGG pathway geneset. (f) Heatmap showing pT_CM-specific gene expression. Heatmap shows imputed, log-normalized expression of all DEGs (log₂FC > 0.5, FDR < 0.01) in pT_CM versus T_FH or pT_CM versus T_H1 comparisons. pT_CM, T_FH, and T_H1 clusters were merged prior to differential gene expression calculation. (g) Diffusion distances between pair-wise comparisons of T_FH, T_H1, and T_CM cells.