title: Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq.
abstract: 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.
authors.affiliation: Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians-Universität LMU, 81377 Munich, Germany.
authors.forename: Ozgun
authors.initials: O
authors.lastname: Gokce
authors.affiliation: Biophysics Program, Stanford University, Stanford, CA 94305, USA; Departments of Bioengineering and Applied Physics, Stanford University, Stanford, CA 94305, USA.
authors.forename: Geoffrey M
authors.initials: GM
authors.lastname: Stanley
authors.affiliation: Departments of Bioengineering and Applied Physics, Stanford University, Stanford, CA 94305, USA; Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
authors.forename: Barbara
authors.initials: B
authors.lastname: Treutlein
authors.affiliation: Departments of Bioengineering and Applied Physics, Stanford University, Stanford, CA 94305, USA.
authors.forename: Norma F
authors.initials: NF
authors.lastname: Neff
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
authors.forename: J Gray
authors.initials: JG
authors.lastname: Camp
authors.affiliation: Nancy Pritzker Laboratory, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA.
authors.forename: Robert C
authors.initials: RC
authors.lastname: Malenka
authors.affiliation: Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Nancy Pritzker Laboratory, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA.
authors.forename: Patrick E
authors.initials: PE
authors.lastname: Rothwell
authors.affiliation: Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Nancy Pritzker Laboratory, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA.
authors.forename: Marc V
authors.initials: MV
authors.lastname: Fuccillo
authors.affiliation: Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA. Electronic address: tcs1@stanford.edu.
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Südhof
authors.affiliation: Departments of Bioengineering and Applied Physics, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA. Electronic address: quake@stanford.edu.
authors.forename: Stephen R
authors.initials: SR
authors.lastname: Quake
mesh_terms: D000818:Animals; D001253:Astrocytes / Q000378:metabolism / Q000502:physiology; D016739:Behavior, Addictive / Q000378:metabolism / Q000503:physiopathology; D002454:Cell Differentiation / Q000502:physiology; D060825:Cognitive Dysfunction / Q000378:metabolism / Q000503:physiopathology; D003342:Corpus Striatum / Q000378:metabolism / Q000502:physiology*; D004805:Ependyma / Q000378:metabolism / Q000502:physiology; D008297:Male; D051379:Mice; D009474:Neurons / Q000378:metabolism / Q000502:physiology; D009836:Oligodendroglia / Q000378:metabolism / Q000502:physiology; D012313:RNA / Q000235:genetics*; D014157:Transcription Factors / Q000378:metabolism; D059467:Transcriptome / Q000502:physiology
chemical_list: D014157:Transcription Factors; D012313:RNA