Figure 3.

scRNA-seq reveals intertissue and intratissue heterogeneity. T_RM cells within a single tissue display varying expression of genes associated with effector and memory potential, showing that distinct subsets of T_RM cells exist. Scales for each gene are consistent across tissues to allow for comparison within and among tissues. Data from (a) Crowl et al. 2022 (scRNA-seq of murine IV⁻ CD8⁺ P14 T cells from IEL, kidney, SG, and liver at day 32 post infection with LCMV Armstrong) and (b) Poon et al., 2023 (scRNA-seq of human CD3⁺ T cells of two donors). Donor D551: Jejunum and Lung; Donor D492: Skin.

For visualizing the intra-tissue heterogeneity, each tissue dataset (downloaded from GEO GSE182275 and GSE206507) was normalized separately using sctransform with method = “glmGamPoi” in Seurat¹⁰². Dimensional reduction was performed using the RunPCA function in Seurat following by RunUMAP using the first 20 PCAs. In addition, data imputation was performed using MAGIC¹⁰³ using the default settings and the exact solver. Manually selected genes to highlight inter- and intratissue heterogeneity were plotted. Color scale was limited to the 98^th expression percentile.