human endoderm organoid cell atlas
Summary
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 (HEOCA). 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 HEOCA makes diverse datasets centrally available, and will be valuable to assess fidelity, characterize perturbed and diseased states, and streamline protocol development.
Metadata
- Dataset Type
- Integrated. The file includes an integrated collection of datasets.
- Total Cells
- 806,646
- organism
- Homo sapiens
- tissue
- intestine (174,036 cells)alveolar sac (116,946 cells)lung (100,892 cells)pancreas (90,618 cells)duodenum (72,077 cells)liver (63,319 cells)ileum (53,810 cells)colon (53,217 cells)salivary gland epithelium (15,796 cells)intrahepatic bile duct (10,580 cells)gallbladder (10,031 cells)common bile duct (8,898 cells)biliary system (6,848 cells)corpus (5,955 cells)prostate gland (5,375 cells)stomach (4,903 cells)bronchus (4,073 cells)nasopharynx (3,576 cells)thyroid gland (2,999 cells)pyloric antrum (2,697 cells)
- assay
- 10x 3' v3 (424,097 cells)10x 3' v2 (210,560 cells)10x 5' v1 (92,407 cells)10x multiome (65,825 cells)SORT-seq (5,820 cells)Seq-Well S3 (4,261 cells)CEL-seq2 (3,504 cells)Smart-seq (172 cells)
- disease
- normal