Extended Data Fig. 6: Unique clonotypes are not restricted to a T_H type and do not diversify over time.

a, Quantification of flow cytometry data on cells from mouse LP at different timepoints of infection; Left: Proportion of CD4⁺ T cells within total CD45⁺; Middle: Proportion of Teff (CD44^hi Foxp3^–) within total CD4⁺ T; Right: Proportion of IFN-γ⁺ cells within total CD4 T. b, Cell numbers per scRNAseq clustering by day post infection. Treg clusters were identified as Foxp3⁺, naive cluster as Foxp3⁻ Ccr7⁺ and Teff clusters as Foxp3⁻ Cd44⁺. c, Left: UMAP as in 5a, showing two groups of cell clusters: cells taken from mice after day 10 are colored in red, and cells taken prior to day 7 are colored in blue. Right: DEG analysis on top 20 differentially expressed genes between the two cluster groups. Asterisks represent genes that overlap with genes that are higher in Teff after Salmonella infection in Fig. 3a. d, Bar graph representing proportions of cells belonging to singlet clones (clones that appear only once) or expanded clones (clones that appear more than once) in each of the clusters defined in S6b, grouped by day post infection. e, Median Euclidean distances between cells within the same clonotype across the top 10 clonotypes for each timepoint. Euclidean distance was calculated based on the top 1000 variable genes. Each color dot represents a unique clonotype, and the size of the dot signifies the number of cells within each clonotype.