In summary, we provide a resource and an initial analysis revealing key principles of the molecular diversity and composition of the mammalian nervous system. The atlas can be used to identify genes and gene combinations unique to specific cell types, which in turn can be used to genetically target cells for visualization, ablation, optogenetic manipulation, gene targeting, and more. The atlas will also help us understand the function of specific genes—for example, those implicated in disease (Skene et al., 2018). This can lead to actionable hypotheses on the mechanism of disease, as well as identifying the relevant cell types to generate mouse models of human disease.