An integrated transcriptomic cell atlas of human endoderm-derived organoids

Area of Science:

• Stem cell biology
• Developmental biology
• Bioinformatics

Background:

• Human stem cells can generate endoderm-derived tissues in vitro.
• These organoid models mimic aspects of human physiology.
• A comprehensive cell atlas is needed for these models.

Purpose of the Study:

• To establish an initial version of a human endoderm-derived organoid cell atlas.
• To integrate single-cell transcriptomes from diverse organoid models.
• To provide a resource for assessing organoid fidelity and disease modeling.

Main Methods:

• Integration of single-cell transcriptomes from 218 samples.
• Analysis of nearly one million cells across various conditions and protocols.
• Harmonization of cell annotations by mapping to primary tissue counterparts.

Main Results:

• Creation of a human endoderm-derived organoid cell atlas.
• Comparison of cell types and states between organoid models.
• Demonstration of atlas utility for assessing perturbations and disease models in intestine and lung organoids.

Conclusions:

• The human endoderm-derived organoid cell atlas centralizes diverse datasets.
• The atlas is valuable for assessing organoid fidelity and characterizing diseased states.
• This resource will streamline organoid protocol development.