Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq

Ozgun Gokce, Geoffrey M. Stanley, Barbara Treutlein, Norma F. Neff, J. Gray Camp, Robert C. Malenka, Patrick E. Rothwell, Marc V. Fuccillo, Thomas C. Südhof, Stephen R. Quake

Research output: Contribution to journalArticlepeer-review

268 Scopus citations


The striatum contributes to many cognitive processes and disorders, but its cell types are incompletely characterized. We show that microfluidic and FACS-based single-cell RNA sequencing of mouse striatum provides a well-resolved classification of striatal cell type diversity. Transcriptome analysis revealed ten differentiated, distinct cell types, including neurons, astrocytes, oligodendrocytes, ependymal, immune, and vascular cells, and enabled the discovery of numerous marker genes. Furthermore, we identified two discrete subtypes of medium spiny neurons (MSNs) that have specific markers and that overexpress genes linked to cognitive disorders and addiction. We also describe continuous cellular identities, which increase heterogeneity within discrete cell types. Finally, we identified cell type-specific transcription and splicing factors that shape cellular identities by regulating splicing and expression patterns. Our findings suggest that functional diversity within a complex tissue arises from a small number of discrete cell types, which can exist in a continuous spectrum of functional states.

Original languageEnglish
Pages (from-to)1126-1137
Number of pages12
JournalCell Reports
Issue number4
StatePublished - 26 Jul 2016
Externally publishedYes


Dive into the research topics of 'Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq'. Together they form a unique fingerprint.

Cite this