Fig. 4: Intestinal CD8⁺ T cells are rapidly activated early after Salmonella infection.

A UMAP plot showing cell type clusters of intestinal T cells, B cells, plasma cells and myeloid cells and their NTR at each time point post Salmonella infection. All cells from indicated time points were combined to identify cell types (left). NTR was overlaid on the UMAP plots (right). B Bubble plot showing log-normalized and scaled new RNA expression of genes. C New RNA (red) imaging of small intestine sections, co-stained with CD8a (green) and EpCAM antibodies (blue). Arrows denote new RNA signal positive CD8⁺ T cells. Scale bar, 20 μm. D GSEA analysis of new RNA in CD8⁺ T cells showing enrichment of indicated gene sets at 2 h post Salmonella infection (left) compared to 0 h (right). E Scatter plots showing fold change of new RNA (left) and total RNA (right) in CD8⁺ T cells between 2 h and 0 h. F UMAP plot showing new RNA expression of Gzma and Ccl5 at 0 h and 2 h. Cell type defining of this UMAP plot was the same as in (A). G Flow cytometry analysis of GzmA and GzmB expression in CD8⁺ T cells. H 3D imaging of GzmA⁺ T cells at different time points post infection. GzmA (red), CD8a (green) and EpCAM (cyan) antibodies were stained. GzmA positive granules per villus are provided (right). Scale bar, 100 μm. n = 5 biologically independent replicates, 30 villi of each mouse for statistics. Results are shown as mean ± SEM. p values were determined by one-way ANOVA. I 3D imaging of GzmA⁺ T cells. Imaris surface rendering model of CD8⁺ T cells was built to estimate the inside and outside states of GzmA⁺ granules. Outside GzmA⁺ granules are indicated with arrows. Scale bar, 10 μm. n = 9 biologically independent replicates, 30 villi of each mouse for statistics. Results are shown as mean ± SEM. p values were determined by two-way ANOVA. Data in (C), (G), (H) and (I) are representative of at least three independent experiments. Source data are provided as a Source Data file.