Shared and distinct transcriptomic cell types across neocortical areas

Neocortex contains a multitude of cell types segregated into layers and functionally distinct regions. To investigate the diversity of cell types across the mouse neocortex, we analyzed 12,714 cells from the primary visual cortex (VISp), and 9,035 cells from the anterior lateral motor cortex (ALM) by deep single-cell RNA-sequencing (scRNA-seq), identifying 116 transcriptomic cell types. These two regions represent distant poles of the neocortex and perform distinct functions. We define 50 inhibitory transcriptomic cell types, all of which are shared across both cortical regions. In contrast, 49 of 52 excitatory transcriptomic types were found in either VISp or ALM, with only three present in both. By combining single cell RNA-seq and retrograde labeling, we demonstrate correspondence between excitatory transcriptomic types and their region-specific long-range target specificity. This study establishes a combined transcriptomic and projectional taxonomy of cortical cell types from functionally distinct regions of the mouse cortex. scRNA-seq of 25,481 single cells from two regions of adult Mouse cortex: anterior lateral motor cortex (ALM) and primary visual cortex (VISp) and 2,986 control samples Please note that the current records represent 232-grouped sample records (i.e. 28706-samples collaped into 232-logical groups) and the complete metadata for each single sample is provided as 'complete_metadata_28706-cells.csv'. The file 'accession_table.csv' provides all of the GEO and SRA IDs along with the sample_name/title that matches the metadata.