Fig. 3: CD4⁺ T cells in the intraepithelial compartment are differentially distributed between Ccr9^+/+ and Ccr9^−/− mice.

Droplet-based single-cell RNA sequencing (scRNA-seq) was performed using the Chromium 10X platform. CD4⁺ T cells from the spleen, mesenteric lymph nodes (MLNs), LPLs and IELs were sorted from Ccr9^+/+ and Ccr9^−/− mice for scRNA-seq. CD4⁺ T cells from spleen and MLNs were collected from one Ccr9^+/+ and Ccr9^−/− mice, and LPLs and IELs were collected from three Ccr9^+/+ and three Ccr9^−/− mice. Sorted IELs and LPLs were pooled in a 2:1 ratio, and cells of each tissue were pooled in a 1:1 ratio between Ccr9^+/+ and Ccr9^−/− mice. a Cells were positioned by gene expression similarities, and 17 clusters were identified based on their top differentially expressed genes (DEGs), as visualized by uniform manifold approximation and projection (UMAP). b UMAP representation of all sequenced cells, color-coded by cluster and separated by tissue of origin. c Heatmap of the top DEGs in each cluster. d UMAP representation of all sequenced cells and separated by tissue of origin. Cell distribution in each tissue from Ccr9^+/+ mice (middle), Ccr9^−/− mice (bottom), and both (top) is shown. e Bar graph shows the proportion of cells in each cluster originating from the spleen, MLN, LPLs, and IELs of Ccr9^+/+ and Ccr9^−/− mice. f Expression of Cd8a, Runx3, Tbx21 and Gzma in sequenced cells are shown via UMAP. Source data are provided as a Source data file.