Single-cell transcriptome atlas of human embryos after gastrulation

The comprehensive spatiotemporal atlas of gene expression during early human embryonic development is critical for insights into embryogenesis, organogenesis, and disease origins. 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. Furthermore, we characterized the allelic gene expression within specific organs at different developmental stages. This work presents a groundbreaking compilation of genome-wide gene expression profiles for each spatially defined cell population, which can be visualized as a spatial display of the embryonic transcriptional landscape. These results offer the most thorough delineation to data of the spatiotemporal transcriptomic dynamics of human organogenesis.