A single-cell transcriptome atlas profiles early organogenesis in human embryos

Xu et al. provide a single-cell transcriptomic atlas of 4-6 week human embryos, thereby profiling early human organogenesis. The early window of human embryogenesis is largely a black box for developmental biologists. Here we probed the cellular diversity of 4-6 week human embryos when essentially all organs are just laid out. On the basis of over 180,000 single-cell transcriptomes, we generated a comprehensive atlas of 313 clusters in 18 developmental systems, which were annotated with a collection of ontology and markers from 157 publications. Together with spatial transcriptome on embryonic sections, we characterized the molecule and spatial architecture of previously unappreciated cell types. Combined with data from other vertebrates, the rich information shed light on spatial patterning of axes, systemic temporal regulation of developmental progression and potential human-specific regulation. Our study provides a compendium of early progenitor cells of human organs, which can serve as the root of lineage analysis in organogenesis.

Automated summary

Xu et al. present a comprehensive single-cell transcriptomic atlas of 4-6 week human embryos, shedding light on early human organogenesis. By profiling over 180,000 single-cell transcriptomes, they identify 313 clusters in 18 developmental systems and annotate them with ontology and markers from previous publications. Combining spatial transcriptome data, the study reveals previously unappreciated cell types and provides insights into spatial patterning, temporal regulation, and potential human-specific regulation of development.