Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

Nat Neurosci. 2016 Feb;19(2):335-46. doi: 10.1038/nn.4216. Epub 2016 Jan 4.


Nervous systems are composed of various cell types, but the extent of cell type diversity is poorly understood. We constructed 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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Cell Line
  • Cerebral Cortex / cytology*
  • Classification*
  • Gene Library
  • Genetic Markers
  • Glutamic Acid / physiology
  • Interneurons
  • Male
  • Mice
  • Mice, Inbred C57BL
  • Mice, Transgenic
  • Neurons / classification
  • RNA / genetics
  • Sequence Analysis, RNA
  • Transcriptome*
  • Visual Cortex / cytology
  • gamma-Aminobutyric Acid / physiology


  • Genetic Markers
  • Glutamic Acid
  • gamma-Aminobutyric Acid
  • RNA