Fig. 2: Mapping organoid cell types to a primary tissue reference atlas to assess organoid fidelity.

a,b, UMAP representations of an integrated object comprising primary adult (a) and fetal (b) cell types and tissues are shown in the top right, as presented in the original publication. c, Bar plots showing the tissue proportion of the most similar adult (top) and fetal (bottom) tissue, sorted by organoid tissue and stem cell source. The upper annotation bar indicates the organoid tissue and stem cell source, with tissue colors matching Fig. 1e and stem cell source colors matching Fig. 1i. Matching tissue and organoid indicate on-target, whereas mismatched tissue and organoid indicate off-target. Scaled color bars at the bottom of the bar plots represent the mean confidence of on-target and off-target cells. Missing reference samples are depicted as a gray bar with a black line. d, Box plots reveal the percentage of on-target cells in intestine and lung organoid samples for adult (top) and fetal (bottom) cells. e, Similar to c, a subset of all intestine organoid epithelium cells projected to adult tissue is split by the source of stem cells. On- and off-target confidence is shown at the bottom of each bar plot, with three marker gene expressions in corresponding cell types shown at the top. f, Box plots illustrate the highest similarity of all cell types in the corresponding primary adult and fetal tissues for each organoid sample, sorted as shown in c. g, UMAPs for primary adult (left) and fetal (right) tissues demonstrate the maximum similarity of all organoids in the comprehensive cross-tissue organoid atlas. h, Box plots show the maximum similarity of each adult (left) and fetal (right) cell type in different tissues. i, Box plots present the median similarity to primary adult (left) and fetal (right) cell types among different sources of stem cell organoids. For plots in d, f, h and i, P values are from two-tailed Mann–Whitney U-tests. In box plots, the center represents the median; bounds show the 25% and 75% percentiles; and whiskers indicate values within 1.5× the interquartile range. EEC, enteroendocrine cell; NK, natural killer; PP, pancreatic polypeptide; TA, transit-amplifying.