Panel A shows dot plots of top marker gene expression across C D 4 T cell clusters ordered by log 2 fold change. Panel B shows bar plots of U M A P cluster proportions comparing nasal tissue and lungs across all cells analyzed. Panel C shows U M A P plots split by tissue and infection status, highlighting the distribution of clustered C D 4 T R M populations. Panel D shows U M A P plots split by tissue and antigen specificity, comparing N P and H A specific C D 4 T R M distributions. Panel E shows volcano plots of differentially expressed genes comparing nasal tissue and lungs across multiple C D 4 T cell clusters.
scRNA-seq of CD4 TRM in the NT versus lungs. (A) Dot plot representing mean expression of top five marker genes for each T cell cluster, identified by the FindAllMarker function and ordered according to log2 fold change. Color intensity from blue to red indicates average expression of genes, and size of the dot depicts percentage of cells expressing the gene within the clusters. (B) Bar graph showing proportion of each UMAP cluster divided by organ. All cells from all mice were included in the analysis. (C) UMAP plot split by tissue (lung or NT) and infection status (IAV infected or naïve) and colored according to identified clusters. (D) UMAP plot split by tissue (lung or NT) and antigen specificity (I-Ab NP306–322 tetramer or I-Ab HA91–107 tetramer) and colored according to identified clusters. Grey dots indicate cells that were not specific for the selected antigen within the specific organ. Contour lines indicate the density of the cells. (E) Volcano plot showing differentially expressed genes upregulated in the NT versus lungs among different cell clusters. Areas shaded in red indicate genes upregulated in NT, while areas shaded in grey genes upregulated in lungs. The dotted lines indicate P value and log2 fold change cutoffs. A list of differentially expressed genes is reported in Table S1.