Adult Mouse Cortical Cell Taxonomy Revealed by Single Cell Transcriptomics

Nervous systems are composed of various cell types, but the extent of cell type diversity is poorly understood. We construct a cellular taxonomy of one cortical region, primary visual cortex, in adult mice on the basis of single-cell RNA sequencing. We identified 49 transcriptomic cell types, including 23 GABAergic, 19 glutamatergic and 7 non-neuronal types. We also analyzed cell type–specific mRNA processing and characterized genetic access to these transcriptomic types by many transgenic Cre lines. Finally, we found that some of our transcriptomic cell types displayed specific and differential electrophysiological and axon projection properties, thereby confirming that the single-cell transcriptomic signatures can be associated with specific cellular properties. INTRODUCTION The mammalian brain is likely the most complex animal organ, given the variety and scope of functions it controls, the diversity of cells it comprises, and the number of genes it expresses. In the mammalian brain, the neocortex is essential for sensory, motor and cognitive behaviors. Although different cortical areas have dedicated roles in information processing, they exhibit a similar layered structure, with each layer harboring distinct neuronal populations. In the adult cortex, many types of neurons have been identified through characterization of their molecular, morphological, connectional, physiological and functional properties. Despite much effort, objective classification on the basis of quantitative features has been challenging, and our understanding of the extent of cell-type diversity remains incomplete. Cell types can be preferentially associated with molecular markers that underlie their unique structural, physiological and functional properties, and these markers have been used for cell classification. Transcriptomic profiling of small cell populations from fine dissections on the basis of cell surface or transgenic markers has been informative; however, any populationlevel profiling obscures potential heterogeneity in collected cells. Recently, robust and scalable transcriptomic single cell profiling has emerged as a powerful approach to characterization and classification of single cells, including neurons. We used single-cell RNA-seq to characterize and classify more than 1,600 cells from the primary visual cortex in adult male mice. The