ArticleNature genetics2025
An integrated transcriptomic cell atlas of human endoderm-derived organoids.
Article in Nature genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- ArchMap is a web-based platform for reference-based analysis of single-cell datasets.Nature genetics · 2026Article
- A transcription factor regulatory atlas for activity inference and perturbation prediction.Nucleic acids research · 2026Article
- From a developmental atlas to maps of disease origin.Clinical and translational medicine · 2026Article
- Human iPSC-derived 3D cardiac models for cardiomyopathies: organoids, spheroids, and engineered heart tissues as translational platforms.Stem cells (Dayton, Ohio) · 2026Review
- Organoids in Pediatric Congenital Hepatobiliary Diseases: Current Status and Progress in Clinical Translational Research.Biomedicines · 2026Review
- Novel role of the lncRNA EPR as oncosuppressor in intestinal cancer.bioRxiv : the preprint server for biology · 2026Article
- Review
- Single-cell transcriptomic comparison of the developing human fetal stomach and pluripotent stem cell-derived gastric organoids.Development (Cambridge, England) · 2026Article
- Single-cell atlas of the transcriptome and chromatin accessibility in the human retina.Nature genetics · 2026Article
- Butyrate Regulating Inflammatory Responses in Chronic Obstructive Pulmonary Disease via the Gut-Lung Axis.International journal of chronic obstructive pulmonary disease · 2026Review
- Analyses ofHuman mutation · 2026Article
- Tissue-specific aging-a new paradigm based on transcriptional insights from select model systems and humans.Frontiers in genetics · 2026Review
- Organoid: a promising solution to current challenges in cancer immunotherapy.npj biomedical innovations · 2025Review
- A novel paradigm for single-cell annotation in stem cell research.Stem cell reports · 2025Review
- A comparative review of single-cell atlases: mapping cellular diversity across species and tissues.Cellular and molecular life sciences : CMLS · 2025Review
- Benchmarking porcine pancreatic ductal organoids for drug screening applications.EMBO molecular medicine · 2025Article
- Distinct roles of Atf3, Zfp711 and Bcl6b in early embryonic hematopoietic and endothelial lineage specification.Development (Cambridge, England) · 2025Article
- Integrating single-cell RNA-seq datasets with substantial batch effects.BMC genomics · 2025Article
- Deep learning the dynamic regulatory sequence code of cardiac organoid differentiation.bioRxiv : the preprint server for biology · 2025Article
- Fluctuation structure predicts genome-wide perturbation outcomes.Research square · 2025Article
Corrections and comments
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Authors and funding
32 authors.
Funding
Abstract
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.