Single-cell transcriptome atlas of human embryos after gastrulation

Leveraging Stereo-seq technology, we generated spatial transcriptomic profiles across 77 sagittal sections of 13 whole human embryos ranging from Carnegie stage 12 to 23, integrated with single-nucleus RNA-seq to elucidate gene expression patterns within defined cellular contexts, revealing the cellular heterogeneity that drives organ-specific differentiation.

Our study has established a regulatory profile for the development of 50 organs and 198 substructures, and identified potential tissue-identity regulators. Notably, it uncovered previously uncharacterized gene functions in cardiac and brain development. The atlas not only substantiates and refines current understanding of human organ development but also highlights key organs susceptible to viral infections and genetic disorders.