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.

人类胚胎发生的早期窗口在很大程度上是发育生物学家的黑匣子。在这里，我们探讨了 4-6 周人类胚胎的细胞多样性，此时基本上所有器官都刚刚布置好。基于超过 180,000 个单细胞转录组，我们生成了 18 个发育系统中 313 个簇的综合图谱，并用来自 157 篇出版物的本体论和标记集进行了注释。连同胚胎切片的空间转录组，我们描述了以前未被重视的细胞类型的分子和空间结构。结合来自其他脊椎动物的数据，丰富的信息揭示了轴的空间模式、发育进程的系统时间调节和潜在的人类特异性调节。我们的研究提供了人体器官早期祖细胞的纲要，