Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain

Arpiar Saunders, Evan Z. Macosko, Alec Wysoker, Melissa Goldman, Fenna M. Krienen, Heather de Rivera, Elizabeth Bien, Matthew Baum, Laura Bortolin, Shuyu Wang, Aleksandrina Goeva, James Nemesh, Nolan Kamitaki, Sara Brumbaugh, David Kulp, Steven A. McCarroll

Research output: Contribution to journalArticlepeer-review

886 Scopus citations


The mammalian brain is composed of diverse, specialized cell populations. To systematically ascertain and learn from these cellular specializations, we used Drop-seq to profile RNA expression in 690,000 individual cells sampled from 9 regions of the adult mouse brain. We identified 565 transcriptionally distinct groups of cells using computational approaches developed to distinguish biological from technical signals. Cross-region analysis of these 565 cell populations revealed features of brain organization, including a gene-expression module for synthesizing axonal and presynaptic components, patterns in the co-deployment of voltage-gated ion channels, functional distinctions among the cells of the vasculature and specialization of glutamatergic neurons across cortical regions. Systematic neuronal classifications for two complex basal ganglia nuclei and the striatum revealed a rare population of spiny projection neurons. This adult mouse brain cell atlas, accessible through interactive online software (DropViz), serves as a reference for development, disease, and evolution. Sampling across multiple brain regions identifies hundreds of transcriptionally distinct groups of cells and reveals large-scale features of brain organization and neuronal diversity.

Original languageEnglish (US)
Pages (from-to)1015-1030.e16
Issue number4
StatePublished - Aug 9 2018
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • General Biochemistry, Genetics and Molecular Biology


  • basal ganglia
  • brain
  • single-cell
  • striatum
  • transcriptional programs


Dive into the research topics of 'Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain'. Together they form a unique fingerprint.

Cite this