Fig. 2: Enrichment of resident phenotype in global and antigen-specific T cells in BAL.

a, The t-SNE plots of concatenated PBMCs and BAL CD4⁺ (top) or CD8⁺ T cells (bottom) highlighting sample tissue origin. b, The t-SNE plots of concatenated PBMCs and BAL CD4⁺ (top) or CD8⁺ T cells (bottom) highlighting expression of CD69 and CD103. c, Example plot and percentage of CD69 expression on CD4⁺ T cells from PBMCs or BAL. d, Example plot and percentage of CD103 and CD69 expression on CD8⁺ T cells from PBMCs or BAL. e, Example plots of TNF- or IFN-γ-producing CD4⁺ T cells (top) and CD69 expression on total, TNF⁺ or IFN-γ⁺CD4⁺ T cells (bottom) using NSP12 peptide pool. f, Example plots of TNF- or IFN-γ-producing CD8⁺ T cells (top) and CD103 versus CD69 expression on total, TNF⁺ or IFN-γ⁺ CD8⁺ T cells (bottom) using NSP12 peptide pool. g, Comparison of CD4⁺CD69⁺ and CD69⁻ cells in BAL producing TNF (left) or IFN-γ (right) per peptide pool. h, Comparison of CD8⁺CD69⁺CD103⁺, CD69⁺CD103⁻ and CD69⁻ cells in BAL producing TNF (left) or IFN-γ (right) per peptide pool. a–h, Four biologically independent samples with the highest frequencies of IFN-γ production examined over one independent experiment. Bars at median (c, d, g and h); floating bars indicating the mean, minimum and maximum values within the dataset (e and f); Kruskal–Wallis one-way ANOVA test and Dunn’s multiple comparison (c–f and h); Wilcoxon’s paired test (g).

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