Single cell transcriptome atlases of the developing mouse and human spinal cord [mouse dataset]

The spinal cord receives input from peripheral sensory neurons and controls motor output by regulating muscle innervating motor neurons. These functions are carried out by neural circuits comprising molecularly and physiologically distinct neuronal subtypes that are generated in a characteristic spatial-temporal arrangement from progenitors in the embryonic neural tube. The systematic mapping of gene expression in mouse embryos has provided insight into the diversity and complexity of cells in the neural tube. For human embryos, however, less information has been available. To address this, we used single cell mRNA sequencing to profile cervical and thoracic regions in four human embryos of Carnegie Stages (CS) CS12, CS14, CS17 and CS19 from Gestational Weeks (W) 4-7. In total we recovered the transcriptomes of 71,219 cells. Analysis of progenitor and neuronal populations from the neural tube, as well as cells of the peripheral nervous system, in dorsal root ganglia adjacent to the neural tube, identified dozens of distinct cell types and facilitated the reconstruction of the differentiation pathways of specific neuronal subtypes. Comparison with existing mouse datasets revealed the overall similarity of mouse and human neural tube development while highlighting specific features that differed between species. These data provide a catalogue of gene expression and cell type identity in the developing neural tube that will support future studies of sensory and motor control systems. Three independent mouse embryos were dissected and processed together to obtain a concentration of cells similar to the other mouse datasets. These were separated into two biological replicates from which scRNA-seq libraries were prepared.脊髓接收外周感觉神经元的输入，并通过调控支配肌肉的运动神经元来控制运动输出。上述功能由分子与生理特性各异的神经元亚型构成的神经环路执行，这些神经元亚型由胚胎神经管的祖细胞以特定的时空模式产生。对小鼠胚胎基因表达的系统性图谱绘制，已为解析神经管内细胞的多样性与复杂性提供了关键见解。然而，针对人类胚胎的相关研究信息却相对匮乏。为填补这一研究空白，我们采用单细胞mRNA测序（single cell mRNA sequencing）技术，对4例妊娠4-7周（Gestational Weeks, W）、对应卡内基分期（Carnegie Stages, CS）CS12、CS14、CS17及CS19的人类胚胎的颈段与胸段区域开展转录组表征分析。最终我们共获取了71219个细胞的转录组数据。通过对神经管来源的祖细胞与神经元群体，以及紧邻神经管的背根神经节（dorsal root ganglia）内的外周神经系统细胞的分析，我们鉴定出数十种不同的细胞类型，并重构了特定神经元亚型的分化通路。与已公开的小鼠数据集进行比对后，我们发现小鼠与人类神经管发育整体上具有高度相似性，同时也揭示了二者间存在的物种特异性特征。本数据集提供了发育中神经管内基因表达与细胞类型特征的参考目录，将为后续感觉与运动控制系统的研究提供有力支持。我们还对3只独立的小鼠胚胎进行了解剖与联合处理，以获取与其他小鼠数据集相近的细胞浓度，并将其分为两个生物学重复样本，用于制备单细胞RNA测序（single-cell RNA sequencing, scRNA-seq）文库。