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Xu, Q.* ; Halle, L. ; Hediyeh-Zadeh, S. ; Kuijs, M. ; Riedweg, R.* ; Kilik, U.* ; Recaldin, T.* ; Yu, Q.* ; Rall, I.* ; Frum, T.* ; Adam, L.* ; Parikh, S. ; Kfuri-Rubens, R. ; Gander, M. ; Klein, D. ; Curion, F. ; He, Z.* ; Fleck, J.S.* ; Oost, K.* ; Kahnwald, M.* ; Barbiero, S.* ; Mitrofanova, O.* ; Maciag, G.J.* ; Jensen, K.B.* ; Lutolf, M.* ; Liberali, P.* ; Spence, J.R.* ; Gjorevski, N.* ; Beumer, J.* ; Treutlein, B.* ; Theis, F.J. ; Camp, J.G.*

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Nat. Genet. 57, 1201–1212 (2025)
Publ. Version/Full Text Research data DOI PMC
Open Access Gold (Paid Option)
Creative Commons Lizenzvertrag
Human pluripotent stem cells and tissue-resident fetal and adult stem cells can generate epithelial tissues of endodermal origin in vitro that recapitulate aspects of developing and adult human physiology. Here, we integrate single-cell transcriptomes from 218 samples covering organoids and other models of diverse endoderm-derived tissues to establish an initial version of a human endoderm-derived organoid cell atlas. The integration includes nearly one million cells across diverse conditions, data sources and protocols. We compare cell types and states between organoid models and harmonize cell annotations through mapping to primary tissue counterparts. Focusing on the intestine and lung, we provide examples of mapping data from new protocols and show how the atlas can be used as a diverse cohort to assess perturbations and disease models. The human endoderm-derived organoid cell atlas makes diverse datasets centrally available and will be valuable to assess fidelity, characterize perturbed and diseased states, and streamline protocol development.
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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords Stem-cell; In-vitro
ISSN (print) / ISBN 1061-4036
e-ISSN 1546-1718
Journal Nature Genetics
Quellenangaben Volume: 57, Issue: , Pages: 1201–1212 Article Number: , Supplement: ,
Publisher Nature Publishing Group
Publishing Place New York, NY
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Institute of Computational Biology (ICB)
Grants
Novo Nordisk Foundation
European Research Council
European Union
Chan Zuckerberg Foundation
Swiss National Science Foundation (SNSF)
EU
Ecole Polytechnique Federale de Lausanne (EPFL)
Chan Zuckerberg Initiative Foundation (CZIF)
Chan Zuckerberg Initiative DAF, an advised fund of the Silicon Valley Community Foundation