Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq
Open accessAbstract
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.
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Some eSPN subsets share markers that earlier work used to distinguish SPN subtypes.
“Subsets of the eSPN class share markers previously reported to distinguish SPN subtypes (Gökce et al., 2016).”
From Molecular diversity and specializations among the cells of the adult mouse brain (2018) · cites this paper as Gökce et al., 2016
Some facets of cellular identity are transient in time and space, and temporal processes may progress along trajectories, oscillate, or be influenced by spatial position.
“First, in contexts such as development and physiology, some facets of cellular identity are transient in time and space. Temporal processes may, for example, progress along one or more trajectories (e.g., differentiation); oscillate continuously between cellular states (e.g., the cell cycle98,99 or circadian rhythm100); or be influenced by the physical position and neighborhood of the cell71,93.”
From Revealing the vectors of cellular identity with single-cell genomics (2016) · cites this paper as [100]
The improved Smart-seq2 protocol has become widely used.
“and this improved Smart-seq2 protocol (Picelli et al., 2014b) has also become widely used (Gokce et al., 2016; Reinius et al., 2016; Tirosh et al., 2016).”
From Comparative Analysis of Single-Cell RNA Sequencing Methods (2017) · cites this paper as Gokce et al., 2016
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“Subsets of the eSPN class share markers previously reported to distinguish SPN subtypes (Gökce et al., 2016).”
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- Authors
- Gokce, O., Stanley, G. M., Treutlein, B., Neff, N. F., Camp, J. G., Malenka, R. C., Rothwell, P. E., Fuccillo, M. V., Südhof, T. C., & Quake, S. R.
- Affiliations
- Max Planck Institute for Evolutionary Anthropology (DE)
- Stanford University (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Südhof, Thomas C.
- Quake, Stephen R.
- ORCID
- Venue
- Cell Reports
- Publisher
- Elsevier BV
- Published
- 2016-07
- Volume
- 16
- Issue
- 4
- Pages
- 1126-1137
- ISSN
- 2211-1247 (ISSN-L)
- PMC
- PMC5004635
- OpenAlex
- W2312055187
- Cited by
- 430
- References
- 72
- Citations by year
- 2026: 30 · 2025: 40 · 2024: 45 · 2023: 30 · 2022: 41 · 2021: 69 · 2020: 45 · 2019: 49 · 2018: 46 · 2017: 32 · 2016: 3
- FWCI
- 22.51
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Cell Reports (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Open access LMU (Ludwid Maxmilian's Universitat Munchen) (submittedVersion)
- Max Planck Digital Library (submittedVersion, other-oa)
- Funders
- National Institutes of Health
- National Institute of Mental Health (R37MH052804)
- National Institute on Drug Abuse (K99DA038112, P01DA008227)
- National Institute of General Medical Sciences (T32GM008294)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- striatum, cell type classification, medium spiny neurons, neuronal cell types, marker genes, transcription factors, alternative splicing, cognitive disorders, addiction, mouse brain
- MeSH terms
- Animals, Astrocytes, Cell Differentiation, Corpus Striatum, Ependyma, Male, Neurons, Oligodendroglia, RNA, Transcription Factors, Behavior, Addictive, Mice, Transcriptome, Cognitive Dysfunction
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