Massively Parallel Single Nucleus Transcriptional Profiling Defines Spinal Cord Neurons and Their Activity during Behavior
Open accessAbstract
To understand the cellular basis of behavior, it is necessary to know the cell types that exist in the nervous system and their contributions to function. Spinal networks are essential for sensory processing and motor behavior and provide a powerful system for identifying the cellular correlates of behavior. Here, we used massively parallel single nucleus RNA sequencing (snRNA-seq) to create an atlas of the adult mouse lumbar spinal cord. We identified and molecularly characterized 43 neuronal populations. Next, we leveraged the snRNA-seq approach to provide unbiased identification of neuronal populations that were active following a sensory and a motor behavior, using a transcriptional signature of neuronal activity. This approach can be used in the future to link single nucleus gene expression data with dynamic biological responses to behavior, injury, and disease.
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hSpS cluster annotation overall matched previously annotated mouse spinal cord clusters.
“We found that, overall, cluster annotation in hSpS matched previously annotated spinal cord clusters”
From Generation of Functional Human 3D Cortico-Motor Assembloids (2020) · cites this paper as Sathyamurthy et al., 2018
The taxonomy recapitulated the known hierarchical organization of neuronal subpopulations in the spinal cord.
“Our taxonomy recapitulated the known hierarchical organization of neuronal subpopulations in the spinal cord9,12,31–33 (Extended Data Fig. 4a–g).”
From The neurons that restore walking after paralysis (2022) · cites this paper as [9]
The merged dataset contains over one hundred thousand cells and nuclei from the first six published studies of the postnatal mouse spinal cord.
“We first created a merged dataset with over one hundred thousand cells and nuclei from the first six published studies of the postnatal mouse spinal cord1–6.”
From A harmonized atlas of mouse spinal cord cell types and their spatial organization (2021) · cites this paper as [1]
The general feature of lower robustness in mid and ventral clusters is consistent with previous observations and likely reflects similar patterns of gene expression amongst mid and ventral clusters.
“This general feature was consistent with previous observations and likely reflects similar patterns of gene expression amongst mid and ventral clusters1,4.”
From A harmonized atlas of mouse spinal cord cell types and their spatial organization (2021) · cites this paper as [1]
The authors previously noted differences in the robustness of dorsal and ventral cell type clusters.
“We had previously noted differences in the robustness of dorsal and ventral cell type clusters1 and a similar trend of overlapping ventral cell types was observed in the neonatal spinal cord4.”
From A harmonized atlas of mouse spinal cord cell types and their spatial organization (2021) · cites this paper as [1]
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Spinal Interneurons as Gatekeepers to Neuroplasticity after Injury or Disease
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Neuronal diversity in the somatosensory system: bridging the gap between cell type and function
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Prioritization of cell types responsive to biological perturbations in single-cell data with Augur
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Decoding cell type diversity within the spinal cord
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Self-citationTranscriptional profile of spinal dynorphin-lineage interneurons in the developing mouse
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- Authors
- Sathyamurthy, A., Johnson, K. R., Matson, K. J. E., Dobrott, C. I., Li, L., Ryba, A. R., Bergman, T. B., Kelly, M. C., Kelley, M. W., & Levine, A. J.
- Affiliations
- National Institute of Neurological Disorders and Stroke (US)
- National Institutes of Health (US)
- Corresponding author
- Levine, Ariel J.
- ORCID
- Venue
- Cell Reports
- Publisher
- Elsevier BV
- Published
- 2018-02
- Volume
- 22
- Issue
- 8
- Pages
- 2216-2225
- ISSN
- 2211-1247 (ISSN-L)
- PMC
- PMC5849084
- OpenAlex
- W2788833165
- Cited by
- 370
- References
- 59
- Citations by year
- 2026: 15 · 2025: 36 · 2024: 42 · 2023: 52 · 2022: 54 · 2021: 71 · 2020: 58 · 2019: 30 · 2018: 11
- FWCI
- 15.21
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Cell Reports (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (acceptedVersion, cc-by-nc-nd)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- National Institutes of Health (2 U42 OD011158)
- National Institute of Neurological Disorders and Stroke (1 ZIA NS003153 02)
- National Institute on Deafness and Other Communication Disorders (1 ZIA DC000059 18)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
- Keywords
- lumbar spinal cord, neuronal cell types, single-nucleus RNA sequencing, sensory behavior, motor behavior, spinal cord transcriptome, mice
- MeSH terms
- Animals, Behavior, Animal, Cell Nucleus, Female, Gene Expression Regulation, Male, Mice, Inbred ICR, Neurons, Spinal Cord, Sequence Analysis, RNA, Gene Expression Profiling, High-Throughput Nucleotide Sequencing
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