Cell
Volume 184, Issue 12, 10 June 2021, Pages 3222-3241.e26
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Article
A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

https://doi.org/10.1016/j.cell.2021.04.021Get rights and content
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Highlights

  • Single-cell transcriptomics from >1.3 million cells in the mouse cortex and hippocampus

  • Many neuron types specific to associational cortex and hippocampal regions are identified

  • Parallel cell-type and laminar organization between isocortex and hippocampal formation

  • Large-scale continuous neuron-type variation in isocortex and hippocampus/subiculum

Summary

The isocortex and hippocampal formation (HPF) in the mammalian brain play critical roles in perception, cognition, emotion, and learning. We profiled ∼1.3 million cells covering the entire adult mouse isocortex and HPF and derived a transcriptomic cell-type taxonomy revealing a comprehensive repertoire of glutamatergic and GABAergic neuron types. Contrary to the traditional view of HPF as having a simpler cellular organization, we discover a complete set of glutamatergic types in HPF homologous to all major subclasses found in the six-layered isocortex, suggesting that HPF and the isocortex share a common circuit organization. We also identify large-scale continuous and graded variations of cell types along isocortical depth, across the isocortical sheet, and in multiple dimensions in hippocampus and subiculum. Overall, our study establishes a molecular architecture of the mammalian isocortex and hippocampal formation and begins to shed light on its underlying relationship with the development, evolution, connectivity, and function of these two brain structures.

Keywords

single-cell RNA sequencing
single-cell transcriptomics
cell type
cortex
hippocampus
glutamatergic
GABAergic
excitatory neuron
interneuron

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