Fig. 1: CD8⁺ T cells in the gut LP and epithelial layer have remodeled the transcription of mitochondria-encoded genes.

a Schematic representation of the gut-specific CD8⁺ T cell response and strategy designed to investigate it. Image created with Biorender.com. b Uniform Manifold Approximation and Projection (UMAP) of the single cell RNA and ADT sequencing data obtained from the experiments designed as in (a). Upon clustering analysis, 10 RNA-based clusters (0–9) were identified, using a resolution of 0.2. 49,111 cells obtained from 4 tissues and 3 biological replicates were analyzed. Color-coding is indicated in the legend. c UMAP of the single cell RNA and ADT sequencing data. Color-coding is according to the tissue of origin as outlined in the legend. The labeling in quotation marks refers to the data in (b). d Bar graph of the distribution of the clusters identified in (b) across different tissues of origin. Within every tissue, cell numbers are normalized to 100% and the fractional contribution of every cluster is indicated. Color-coding resembles the one used in (b). e UMAP of the single cell RNA and ADT sequencing data showing the ratio of mitochondrial transcripts over the total transcriptome, across different clusters. The labeling in quotation marks refers to the data in (b). Violin plots show the fraction of mitochondria-derived transcripts over the total transcriptome, across different clusters. The black dashed line indicates the median value identified for cluster 6. f Plots representing the expression of selected genes as a function of pseudotime, as identified in the data shown in Supplementary Fig. 2a. On the x axis, the interquartile range of every cluster is indicated, to facilitate the correlation between gene expression and progression of cells through pseudotime. Color-coding is indicated in the legend.