Extended Data Fig. 2: Duodenal ALI organoids contain diverse immune populations, related to Fig. 1.

a, Integrated UMAP plot of CD45⁺-sorted cells from scRNA-seq, revealing diverse immune populations in small intestine ALI organoids at day 14, n = 6 CeD patients. b, Violin plots showing expression of genes used to identify the immune populations shown in (a). c, UMAP plots of overlap between tissue and organoid CD45⁺ immune populations as in (a, b). d, scRNA-seq Jaccard index of TCR overlap between fresh small intestine tissue (n = 1 CeD patient) and ALI organoids (n = 4 CeD patients). e, Integrated UMAP from scRNA-seq of active CeD organoid T cells (n = 6 patients). Cells expressing KIR3DL1 or KIR2DL3 are rendered in red. f, Plot of CD8⁺ T cells from (e). g, Integrated UMAP from scRNA-seq of active CeD organoid T cells (top left) (n = 6 patients). Cells in red exhibit expression of KIR3DL1 or KIR2DL3 (top right), NKG2C (bottom left) and NKG2D (bottom right). h, Pie bar graph showing organoid-derived TCR counts in which each segment represents a unique clonotype, n = 5 patients. Expanded clonotypes (TCR counts ≥ 2) are indicated in red.