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. 2023 Dec 19;14:8452. doi: 10.1038/s41467-023-44184-0

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — A scVelo RNA velocity UMAP showing differentiation dynamics (A) and pseudotime inferred from RNA velocity (A”) in AEP organoids. B Slingshot trajectory analysis and pseudotime inference of AEP organoids demonstrate similar lineage relationships to RNA velocity. C–E Lineage drivers defined by CellRank for differentiation of pAEP/AEP to AT2 cells (C), AT1 cells via AT1tr (D), and Krt8 cells (E). F Heatmap showing major cell markers differentiating cell states in the alveolar epithelium. G Model of cellular relationships and AT1 differentiation inferred from alveolar organoids.