in addition, organoids derived from primary fscs or ascs could be contaminated because of handling or the adjacency of tissues during tissue acquisition, or cell states could be different from the tissue of origin because of stem cell plasticity. therefore, it is important to develop strategies to compare organoid cells with reference counterparts. to evaluate the fidelity of cell states observed in the human endod erm - derived organoid cell atlas ( heoca ), we obtained published scrna - seq data on human endod erm - derived organs from adult ( small and large intestine, lung, liver, pancreas, prostate, salivary gland ) ( fig. 2a ) and fetal ( small and large intestine, lung, liver, pancreas, stomach, esophagus ) ( fig. 2b ) specimens. to assess on - and off - target cells in organoids, we projected organoid cells to the fetal and adult primary tissue atlases, and inferred the target tissue via label transfer ( fig. 2c ). psc - derived organoids have a lower on - target percentage in both fetal and adult primary tissues compared with fsc - and asc - derived organoids ( fig. 2c and extended data fig. 5a – d ). focusing on intestine and lung organoids, fsc - and asc - derived intestine organoids demonstrated high on - target percentages, with an average of 91. 12 % in fsc - derived organoids and 98. 14 % in asc - derived organoids ( fig. 2d ). by contrast, psc - derived organoids displayed a median on - target percentage of between 23. 28 % and 83. 63 % depending on fetal or adult reference atlas comparison; however, this is likely a low estimate because datasets from early organoid time points are difficult to assess using this reference comparison ( fig. 2c – e ). we identified major cell types from each adult and fetal tissue ( fig. 2a, b ), and compared organoid cell types and states with primary counterparts using neighborhood graph correlation. we quantified the proportion of cell types in each organoid sample and compared the similarity of each cell type with counterparts in adult and fetal tissues ( fig. 2f – h and extended data fig. 5a, b ). asc - derived organoids had the highest similarity to adult counterparts, whereas psc - derived organoids were most similar to fetal counterparts, with fsc - derived organoid cell states showing an intermediate distribution ( fig. 2i ). multiple regression analyses revealed that similarity to reference atlases was influenced by publication and stem cell source but not by scrna - seq methods, total sample counts or total sample genes ( extended data fig. 5e, f ). to explore organoid cell states of different stem cell origin, we focused on intestinal organoid models in which there is substantial coverage from psc -, fsc - and asc - derived organoid cells. this subset consisted of 98 samples from 23 different publications representing 353, 140 single - cell transcriptomes ( fig. 3a, extended data fig. 6a and supplementary table 1 ). we reintegrated all cells and defined 5 cell types at level 1, 26 cell types at level 2 and 32 cell types at level 3 in the atlas ( fig. 3b, c and extended data fig. 6b, c ). this integrated intestinal organoid atlas ( hioca ) covers epithelial states from the duodenum, ileum, colon and psc - derived organoids, and contains a large fraction of mesenchymal cells, and minor populations of neural, endothelial and immune cell types ( fig. 3b, c and extended data fig. 6d – f ). we subsetted and reintegrated stem cells and enterocytes, and found that cells from different sources or tissues clustered together and exhibited distinc t gene expression profiles ( extended data fig. 6h, i ). we used the large collection of protocols to examine factors that influence cell - type proportion ( extended data fig. 6m – o ). for instance, tumor necrosis factor ( tnf ) and interleukin - 22 ( il - 22 ) are linked to more abundant microfold ( m ) and paneth cells in asc - derived organoids, respectively, and xenografted psc - derived tissues harbor both paneth and tuft cells, which are absent in early stage psc - derived organoids. protocol evaluation suggests tailored approaches to enrich specific cell types or enhanced maturation ( extended data fig. 6o ). to assess intestinal organoid fidelity and maturation, we integrated time series scrna - seq data from duodenal development ( 59 to 132 days post fertilization ) with adult intestinal epithelium ( fig. 3e ). these data revealed distinc t fetal and adult stem cell - to - enterocyte differentiation trajectories, while other epithelial cell types, such as goblet, tuft, m and enteroendocrine cells, showed similar states across both stages ( fig. 3f, g and extended data fig. 7a – f ). comparing organoids with the primary reference revealed that psc - derived organoids resembled fetal tissue, whereas fsc - and asc - derived organoids aligned with adult tissues ( fig. 3h ), consistent with reports that fsc - derived organoids lose fetal traits during extended culture. metrics such as cell - type proportion, projection probability and similarity to fetal and adult cell types highlighted substantial variation across samples ( fig. 3i – l and extended data fig. 7g, h ). for example, psc - derived organoids increase in complexity and reference similarity over time in culture, and after xenografting into a mouse host for maturation, the organoids obtain higher cellular diversity and similarity to primary tissue differentiated enterocytes. altogether, these results reveal the diversity of cell composition and cell maturation in intestinal organoids from different sources, time points and protocols. we performed a detailed analysis of lung organoid cells, consisting of 221, 425 cells obtained from 52 samples and 13 publications, comprising psc -, fsc - and asc - derived sources ( fig. 4a ). we integrated, clustered and annotate d these data to generate a human lung organoid cell atlas ( hloca ) ( fig. 4b, c ). the uniform manifold approximation and projection ( umap ) representation showed integration of data from different publications and samples with undifferentiated stem cells positioned centrally surrounded by more differentiated cell types ( fig. 4b ). organoids from pscs displayed a higher proportion of lowly differentiated early endod erm development marker genes such as fabp1 and afp - defined progenitor cells, which were largely absent in the asc - derived organoids ( fig. 4d ). in turn, organoids obtained via asc - protocols frequently contained a relevant proportion of club cells, whereas a high incidence of goblet and neuroendocrine cells was primarily observed in samples produced using fsc protocols ( fig. 4b – d ). overall, the differences in cell - type composition suggest effects from stem cell source as well as details of the protocol, including media and growth factors. we provide a structured account of the publicly available metadata on lung organoid datasets in the atlas including information on all available protocol components, concentrations and intervals, which can be linked to the samples in the shared hloca object. to gain insights into how the lung organoid datasets correspond with primary tissue, we integrated a unified reference of primary adult and fetal lung tissues ( fig. 4e – k ). the query to reference mapping of the lung organoid data showed that psc - derived organoid cells preferentially integrated with fetal counterparts, asc - derived organoid cells integrated with adult counterparts and fsc - derived organoid cells projected to both fetal and adult references ( fig. 4h ). this finding is consistent with previous observations from intestine reference mapping analysis in which psc - derived organoids model fetal biology, asc - derived organoids model adult biology and fsc - derived organoids have intermediate or unclear mappings. metrics such as cell - type proportion, projection probability and similarity to fetal and adult cell types also highlighted substantial variation across samples ( fig. 4i – k ).