A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

The mammalian brain consists of millions to billions of cells that are organized into numerous cell types with specific spatial distribution patterns and structural and functional properties. An essential step towards understanding brain function is to obtain a parts list, i.e., a catalog of cell types, of the brain. Here, we report a comprehensive and high-resolution transcriptomic and spatial cell type atlas for the whole adult mouse brain. The cell type atlas was created based on the combination of two single-cell-level, whole-brain-scale datasets: a single-cell RNA-sequencing (scRNA-seq) dataset of ~7 million cells profiled (~4.0 million cells passing quality control), and a spatially resolved transcriptomic dataset of ~4.3 million cells using MERFISH. The atlas is hierarchically organized into four nested levels of classification: 34 classes, 338 subclasses, 1,201 supertypes and 5,322 clusters. We present a newly developed online platform, Allen Brain Cell (ABC) Atlas, to visualize the mouse whole brain cell type taxonomy and atlas along with the scRNA-seq and MERFISH data and metadata sets. We systematically analyzed the neuronal, non-neuronal, and immature neuronal cell types across the brain and identified a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type. The results reveal unique features of cell type organization in different brain regions, in particular, a dichotomy between the dorsal and ventral parts of the brain: the dorsal part contains relatively fewer yet highly divergent neuronal types, whereas the ventral part contains more numerous neuronal types that are more closely related to each other. We also systematically characterized cell-type specific expression of neurotransmitters, neuropeptides, and transcription factors. The study uncovered extraordinary diversity and heterogeneity in neurotransmitter and neuropeptide expression and co-expression patterns in different cell types across the brain, suggesting they mediate myriad modes of intercellular communications. Finally, we found that transcription factors are major determinants of cell type classification in the adult mouse brain and identified a combinatorial transcription factor code that defines cell types across all parts of the brain. The whole-mouse-brain transcriptomic and spatial cell type atlas establishes a benchmark reference atlas and a foundational resource for deep and integrative investigations of cellular and circuit function, development, and evolution of the mammalian brain. Single cell RNA-seq using the 10x genomics v2 and v3 methods. Cells were isolated from whole mouse brain and each library represents a small dissection area. The dataset includes 299 10x genomics v2 libraries containing ~2.5 million cells and 482 10x genomics v3 libaries containing ~4.4 million cells.哺乳动物大脑包含数百万至数十亿个细胞，这些细胞按照特定的空间分布模式、结构与功能特性，被划分为众多细胞类型。解析大脑功能的核心步骤之一，是获取大脑的组分清单，即细胞类型目录。本研究报道了一套针对成年小鼠全脑的全面系统且高分辨率的转录组空间细胞类型图谱。 该细胞类型图谱基于两套单细胞级、全脑尺度的数据集整合构建：其一为对约700万个细胞进行检测的单细胞RNA测序（single-cell RNA-sequencing, scRNA-seq）数据集（其中约400万个细胞通过质量控制）；其二为采用多重误差稳健荧光原位杂交（Multiplexed Error-Robust Fluorescence In Situ Hybridization, MERFISH）技术获取的约430万个细胞的空间分辨转录组数据集。 该图谱采用四级嵌套分类体系进行层级组织，涵盖34个大类、338个亚类、1201个超类型以及5322个聚类簇。 我们开发了全新的在线平台——艾伦脑细胞（Allen Brain Cell, ABC）图谱，用于可视化展示小鼠全脑细胞类型分类体系与图谱，同时配套提供scRNA-seq、MERFISH数据及元数据集。 我们系统分析了全脑内的神经元、非神经元及未成熟神经元细胞类型，并发现每种细胞类型的转录组特征与其空间特异性高度契合。 研究结果揭示了不同脑区细胞类型组织的独特特征，尤其体现为大脑背侧与腹侧的二分性：背侧区域的神经元类型相对较少但分化程度极高，而腹侧区域的神经元类型数量更多且彼此亲缘关系更为紧密。 我们还系统表征了神经递质、神经肽及转录因子的细胞类型特异性表达模式。本研究揭示了全脑不同细胞类型中神经递质与神经肽的表达及共表达模式存在极高的多样性与异质性，表明这些分子介导了极为丰富的细胞间通讯方式。 最后，我们发现转录因子是成年小鼠大脑细胞类型分类的核心决定因素，并鉴定出一套组合式转录因子编码体系，可用于定义全脑各处的细胞类型。 这套小鼠全脑转录组空间细胞类型图谱，为哺乳动物大脑的细胞与环路功能、发育及进化的深度整合研究提供了基准参考图谱与基础资源。 本研究采用10x Genomics V2及V3试剂盒开展单细胞RNA测序。细胞从小鼠全脑中分离得到，每个文库对应一小块解剖区域。本数据集包含299个10x Genomics V2文库（对应约250万个细胞）及482个10x Genomics V3文库（对应约440万个细胞）。