Elucidating the cellular architecture of the human cerebral cortex is central to understanding our cognitive abilities and susceptibility to disease. Here we applied single nucleus RNA-sequencing to perform a comprehensive analysis of cell types in the middle temporal gyrus of human cortex. We identified a highly diverse set of excitatory and inhibitory neuronal types that are mostly sparse, with excitatory types being less layer-restricted than expected. Comparison to similar mouse cortex single cell RNA-sequencing datasets revealed a surprisingly well-conserved cellular architecture that enables matching of homologous types and predictions of human cell type properties. Despite this general conservation, we also find extensive differences between homologous human and mouse cell types, including dramatic alterations in proportions, laminar distributions, gene expression, and morphology. These species-specific features emphasize the importance of directly studying human brain.

18Neocortex contains a multitude of cell types segregated into layers and functionally distinct regions. To 19investigate the diversity of cell types across the mouse neocortex, we analyzed 12,714 cells from the 20 primary visual cortex (VISp), and 9,035 cells from the anterior lateral motor cortex (ALM) by deep single-21cell RNA-sequencing (scRNA-seq), identifying 116 transcriptomic cell types. These two regions represent 22 distant poles of the neocortex and perform distinct functions. We define 50 inhibitory transcriptomic cell 23 types, all of which are shared across both cortical regions. In contrast, 49 of 52 excitatory transcriptomic 24 types were found in either VISp or ALM, with only three present in both. By combining single cell RNA-25 seq and retrograde labeling, we demonstrate correspondence between excitatory transcriptomic types and 26 their region-specific long-range target specificity. This study establishes a combined transcriptomic and 27projectional taxonomy of cortical cell types from functionally distinct regions of the mouse cortex. 28 29 1

SUMMARY Modern genetic approaches are powerful in providing access to diverse cell types in the brain and facilitating the study of their function. Here we report a large set of driver and reporter transgenic mouse lines, including 23 new driver lines targeting a variety of cortical and subcortical cell populations and 26 new reporter lines expressing an array of molecular tools. In particular, we describe the TIGRE2.0 transgenic platform and introduce Cre-dependent reporter lines that enable optical physiology, optogenetics, and sparse labeling of genetically-defined cell populations. TIGRE2.0 reporters broke the barrier in transgene expression level of single-copy targeted-insertion transgenesis in a wide range of neuronal types, along with additional advantage of a simplified breeding strategy compared to our first-generation TIGRE lines. These novel transgenic lines greatly expand the repertoire of high-precision genetic tools available to effectively identify, monitor, and manipulate distinct cell types in the mouse brain.