Single-cell transcriptomics can provide quantitative molecular signatures for large, unbiased samples of the diverse cell types in the brain^1,2,3. With the proliferation of multi-omics datasets, a major challenge is to validate and integrate results into a biological understanding of cell-type organization. Here we generated transcriptomes and epigenomes from more than 500,000 individual cells in the mouse primary motor cortex, a structure that has an evolutionarily conserved role in locomotion. We developed computational and statistical methods to integrate multimodal data and quantitatively validate cell-type reproducibility. The resulting reference atlas—containing over 56 neuronal cell types that are highly replicable across analysis methods, sequencing technologies and modalities—is a comprehensive molecular and genomic account of the diverse neuronal and non-neuronal cell types in the mouse primary motor cortex. The atlas includes a population of excitatory neurons that resemble pyramidal cells in layer 4 in other cortical regions⁴. We further discovered thousands of concordant marker genes and gene regulatory elements for these cell types. Our results highlight the complex molecular regulation of cell types in the brain and will directly enable the design of reagents to target specific cell types in the mouse primary motor cortex for functional analysis.

单细胞转录组学可以为大脑中不同细胞类型的大量无偏样本提供定量分子特征^1,2,3. 随着多组学数据集的激增，一个主要挑战是验证结果并将其整合到对细胞类型组织的生物学理解中。在这里，我们从小鼠初级运动皮层中超过 500,000 个单个细胞生成了转录组和表观基因组，这是一种在运动中具有进化保守作用的结构。我们开发了计算和统计方法来整合多模式数据并定量验证细胞类型的可重复性。由此产生的参考图谱——包含超过 56 种神经元细胞类型，可跨分析方法、测序技术和模式高度复制——是对小鼠初级运动皮层中不同神经元和非神经元细胞类型的全面分子和基因组描述。⁴ . 我们进一步发现了这些细胞类型的数千个一致的标记基因和基因调控元件。我们的结果突出了大脑中细胞类型的复杂分子调节，并将直接使试剂的设计能够针对小鼠初级运动皮层中的特定细胞类型进行功能分析。