Extended Data Fig. 2: Single-cell transcriptome analysis of homeostatic IIO model.
From: Human organoids with an autologous tissue-resident immune compartment
a, Flow cytometry plots displaying daily CD8+ TRM IEL proportions and GzmB expression in baseline (untreated) IIO cultures after digestion, across 96 h. Plots are representative of 3 independent IIO experiments. b-d, UMAP embeddings of single-cell transcriptome data colored by cell cluster (b), condition (c) and donor origin (d). The sequenced conditions include intestinal organoids containing TRMs (IIO), organoids containing PBMCs (PBMC) and TRMs cultured in matrigel (TRM). e, Dotplot summarizing marker gene expression across different immune (left) and epithelial (right) cell clusters. f, Boxplots displaying the minimum, mean and maximum number of cells across all donors (n = 3) for clusters of epithelial cells cultured with TRMs (IIO) or PBMCs (PBMC). g, Violin plots illustrating the expression of HES1 and ID3 transcription factors in intestinal epithelial stem cells cultured with TRMs or PBMCs. h, UMAP embedding of subsetted T cells colored by condition as portrayed in Fig. 2b. i, Heatmaps representing T cell densities along the reconstructed integration index vector for each condition (rows) and donor (groups) membership. j, Stacked barplot showing the proportion of TRMs cultured with epithelium (IIO), TRMs cultured in matrigel (TRM) and PBMCs cultured with epithelium (PBMC) within 5 equidistant bins of the integration index. k, Dotplot summarizing marker gene expression of TRMs cultured in matrigel (left, bin3) and TRMs cultured with epithelium (right, bin5).
