Extended Data Fig. 2: Characterization of Tex^int and Tex^KLR subsets and organ-specific exhaustion signatures.

(a) Ingenuity pathway analyses of the differentially expressed genes identifying enriched biological pathways between the two subsets (Tex^int versus Tex^KLR). Top 6 hits are shown. (b) Representative flow cytometry plots that quantify CXCR6 expression in Tex^term, Tex^int and Tex^prog. Barplots summarize the quantification across three biological replicates. Significant changes were determined by two tailed, unpaired t-test at p < 0.05 (n = 3). Shown are means with SDs. (c) Representative flow cytometry plots show the MKI67⁺ fractions of the indicated Tex subsets. Boxplot depicts the quantification of MKI67⁺ Tex subsets. Significant changes were determined by two tailed, unpaired t-test at p < 0.05 (n = 5 biologically independent animals). Box center line, mean; limits, upper and lower quartiles; whiskers, minimum and maximum values. (d) Volcano plots of differentially expressed genes comparing Tex^term populations from different organs (log₂ FC > 0.25, Bonferroni adjusted p-value < 0.05, p-values determined by two-sided Wilcoxon Rank Sum test). Ingenuity pathway analysis results on the differentially expressed gene groups (bottom). Top 3 hits are shown. (e) Violin plots of the Cell Cycle score of the indicated T cell populations across organs (n = number of scRNA-seq profiles, box center line, median; box limits, upper and lower quartiles; box whiskers, 1.5× interquartile range). P-values determined by two-sided Wilcoxon Rank Sum test relative to overall distribution of single cells from the indicated Tex subsets across all organs. (f) Representative flow cytometry of the MKI67⁺ fraction of Tex^term subsets in the indicated organs. Bar plot summarizes MKI67⁺ fractions across organs. Significant changes were determined by two tailed, unpaired t-test at p < 0.05 (n = 3 biologically independent animals). Shown are means with SDs.

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