A single-cell transcriptome atlas of human early embryogenesis

In order to systematically define the early organ-specific progenitor cells in human development, we conducted single-cell RNA-seq on embryos between Carnegie Stage 12 and 16, when the neural tube finishes closure, the limbs emerge, and essentially all organs are laid out. Based on 103,264 single-cell transcriptomes, we identified 333 cell types in 19 tissue types. We characterized expression patterns of five major signaling pathways that are extensively involved in vertebrate embryonic patterning. We further reconstructed spatial axes in neural progenitors and demonstrated the conservation between human and mouse neural cell types. We defined precise domains for limb mesenchymal cells and provided a thorough characterization of dynamic gene expression during limb patterning. Finally, we revealed the differentiation process of retina development when combined with published data on later human development. Our study provides a compendium of early progenitor cells of human organs, which can serve as basis of lineage analysis in organogenesis as well as benchmarks for iPS and ESC-based in vitro induction systems. Overall design: 103264 single-cell transcriptomes of early human embryo between Carnegie Stage 12 and 16