Fig. 5: T cell subtypes preferentially reside into different MEs, correlating with their functionality.
A All T cells in our dataset were mapped to a tumor-infiltrating lymphocyte dataset. The T cells were mapped to six known cell populations - helper T cells (CD4T), cytotoxic T cells (CD8T Eff_mem), naive and exhausted CD8 (CD8_Naive, CD8_exhauseted), and regulatory T cells (Treg). The violin plot shows marker gene expression for each of the T cell subtypes in our data. B Fraction of T cells of each subtype in AKI enriched MEs (5, 15, 16) for n = 3 AKI mice. Each dot represents one mouse. The fraction is the total fraction of each subtype out of all T cells within the specified ME. The boxplot middle line represents the median value, and box boundaries show the 25th and 75th percentiles. Source data are provided as a Source Data file. C Average expression of three M1 (blue) and four M2(red) markers within Macrophages in the AKI enriched MEs. D Fractions of Mrc + (left) and Ccr7 + (right) Macrophages within the AKI enriched MEs boxplots showing the distribution for n = 3 AKI mice as in (B). Dots represent individual mice. The boxplot middle line represents the median value, and box boundaries show the 25th and 75th percentiles. Source data are provided as a Source Data file. E Spatial distribution of the same genes as in (D). Left - ME-15 is indicated and Mrc+ cells are colored in red. Right - ME-16 is indicated and Ccr7+ cells are colored in blue. F. Spatial locations of the T cell subtypes within one AKI sample. ME-16 is depicted in color. G Vcam1 antibody staining, as well as the markers Cd4, Cd8, and the DC marker Clec9a, are detected with RNAscope on a control sample. The image is of one representative control sample out of two. A larger kidney area from this experiment is presented in Supplementary Fig. 15. H Same as in G for an AKI sample. The image is of one representative AKI sample out of three. A larger kidney area from this experiment is presented in Supplementary Fig. 15.
