Single-Cell RNA-Seq Reveals Hypothalamic Cell Diversity
Open accessAbstract
The hypothalamus is one of the most complex brain structures involved in homeostatic regulation. Defining cell composition and identifying cell-type-specific transcriptional features of the hypothalamus is essential for understanding its functions and related disorders. Here, we report single-cell RNA sequencing results of adult mouse hypothalamus, which defines 11 non-neuronal and 34 neuronal cell clusters with distinct transcriptional signatures. Analyses of cell-type-specific transcriptomes reveal gene expression dynamics underlying oligodendrocyte differentiation and tanycyte subtypes. Additionally, data analysis provides a comprehensive view of neuropeptide expression across hypothalamic neuronal subtypes and uncover Crabp1 + and Pax6 + neuronal populations in specific hypothalamic sub-regions. Furthermore, we found food deprivation exhibited differential transcriptional effects among the different neuronal subtypes, suggesting functional specification of various neuronal subtypes. Thus, the work provides a comprehensive transcriptional perspective of adult hypothalamus, which serves as a valuable resource for dissecting cell-type-specific functions of this complex brain region.
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Neuronal cells have a higher number of mRNAs (UMI) and genes expressed than non-neuronal cells.
“Since previous studies have showed that neuronal cells have a higher number of mRNAs (UMI) and genes expressed than that of non-neuronal cells69,70, which was confirmed in our dataset (Supplementary Fig. 1b), we decided to filter cells using ≥800 genes/cell for non-neuronal cells, and ≥1,500 genes/cells for neuronal cells.”
From Cell type-specific transcriptional programs in mouse prefrontal cortex during adolescence and addiction (2019) · cites this paper as [70]
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- Authors
- Chen, R., Wu, X., Jiang, L., & Zhang, Y.
- Affiliations
- Boston Children's Hospital (US)
- Corresponding author
- Zhang, Yi
- Venue
- Cell Reports
- Publisher
- Elsevier BV
- Published
- 2017-03
- Volume
- 18
- Issue
- 13
- Pages
- 3227-3241
- ISSN
- 2211-1247 (ISSN-L)
- PMC
- PMC5782816
- OpenAlex
- W2601723752
- Cited by
- 592
- References
- 47
- Citations by year
- 2026: 36 · 2025: 57 · 2024: 65 · 2023: 84 · 2022: 76 · 2021: 80 · 2020: 71 · 2019: 60 · 2018: 49 · 2017: 13 · 2016: 1
- FWCI
- 21.68
- 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)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- NIH (U01 MH105960)
- HHMI
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Neuroscience › Endocrine and Autonomic Systems › Regulation of Appetite and Obesity
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
- Keywords
- hypothalamus, neuronal cell types, non-neuronal cells, cell type-specific transcriptome, oligodendrocyte differentiation, tanycytes, neuropeptide expression, CRABP1, Pax6, food deprivation, homeostatic regulation, mice
- MeSH terms
- Aging, Animals, Cell Differentiation, Female, Food Deprivation, Gene Expression Regulation, Hypothalamus, Male, Mice, Inbred C57BL, Neurons, Neuropeptides, Oligodendroglia, Transcription, Genetic, Sequence Analysis, RNA, Single-Cell Analysis, Transcriptome, Ependymoglial Cells
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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