The paper details the creation of the Human Endoderm-derived Organoid Cell Atlas (HEOCA), a massive integrated dataset comprising nearly one million single-cell transcriptomes. Researchers synthesized data from 55 publications and nine different tissue types to harmonize cell annotations and establish a benchmark for organoid fidelity. By comparing lab-grown tissues to primary fetal and adult references, the study reveals how different stem cell sources influence the maturity and accuracy of models like the lung and intestine. The authors introduced sc2heoca, a toolkit designed to help scientists project new data onto the atlas to evaluate novel protocols and identify off-target cells. Furthermore, the sources demonstrate the utility of this atlas in modeling diseases and biological perturbations, such as viral infections or colorectal cancer. Ultimately, this centralized resource streamlines the development of high-fidelity human biosystems for translational research and drug testing.

References:

• Xu Q, Halle L, Hediyeh-Zadeh S, et al. An integrated transcriptomic cell atlas of human endoderm-derived organoids[J]. Nature genetics, 2025, 57(5): 1201-1212.