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. Overall design: 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.

大脑新皮层（Neocortex）包含多种细胞类型，这些细胞按层排布并聚集于功能各异的区域。为探究小鼠新皮层的细胞类型多样性，我们对初级视觉皮层（primary visual cortex, VISp）的12714个细胞以及前外侧运动皮层（anterior lateral motor cortex, ALM）的9035个细胞开展了深度单细胞RNA测序（single-cell RNA-sequencing, scRNA-seq），共鉴定出116种转录组细胞类型。

这两个皮层区域属于新皮层的远端功能分区，执行截然不同的生理功能。我们定义了50种抑制性转录组细胞类型，所有这类类型在两个皮层区域中均存在。与之相对，52种兴奋性转录组细胞类型中有49种仅在VISp或ALM中被检测到，仅3种在两个区域中共存。

通过结合单细胞RNA测序与逆行标记技术，我们证实了兴奋性转录组细胞类型与其区域特异性的长程投射靶向特异性之间的对应关系。本研究建立了小鼠皮层不同功能分区的皮层细胞类型的转录组与投射组联合分类体系。

总体实验设计：对成年小鼠皮层的两个区域——前外侧运动皮层（ALM）与初级视觉皮层（VISp）的25481个单细胞进行scRNA-seq，同时设置2986个对照样本。

请注意，当前公开的记录为232组合并后的样本记录（即28706个样本被整合为232个逻辑分组），每个单个样本的完整元数据已在"complete_metadata_28706-cells.csv"文件中提供。文件"accession_table.csv"包含所有基因表达综合数据库（Gene Expression Omnibus, GEO）与序列读取档案（Sequence Read Archive, SRA）编号，以及与元数据匹配的样本名称/标题。