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

The early window of human embryogenesis is largely a black box for developmental biologists. Here we probed the cellular diversity of 4- to 6-week human embryos when essentially all organs are just laid out. Based on over 180,000 single-cell transcriptomes, we generated a comprehensive atlas of 313 cell types that belong to 18 developmental systems, and identified hundreds of cell type specific markers. We characterized the molecule and spatial architecture of previously unappreciated cell types by integrating with spatial transcriptome. Combined with data of 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. 185140 single-cell transcriptomes of early human embryo between Carnegie Stage 12 and 16 Please note that the 'cell_annotate.txt' file has been updated on Dec 5, 2022.