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Cited by 289Single-cell and spatial transcriptomicsNeurogenesis and neuroplasticity mechanismsDevelopmental Biology and Gene Regulation

Single-cell transcriptomic analysis of mouse neocortical development

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Loo, Lipin, Simon, Jeremy M., Xing, Lei, McCoy, Eric S., Niehaus, Jesse K., Guo, Jiami, Anton, E. S., Zylka, Mark J.·2019·Nature Communications
DOI 10.1038/s41467-018-08079-9PMC PMC6329831

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Abstract

The development of the mammalian cerebral cortex depends on careful orchestration of proliferation, maturation, and migration events, ultimately giving rise to a wide variety of neuronal and non-neuronal cell types. To better understand cellular and molecular processes that unfold during late corticogenesis, we perform single-cell RNA-seq on the mouse cerebral cortex at a progenitor driven phase (embryonic day 14.5) and at birth—after neurons from all six cortical layers are born. We identify numerous classes of neurons, progenitors, and glia, their proliferative, migratory, and activation states, and their relatedness within and across age. Using the cell-type-specific expression patterns of genes mutated in neurological and psychiatric diseases, we identify putative disease subtypes that associate with clinical phenotypes. Our study reveals the cellular template of a complex neurodevelopmental process, and provides a window into the cellular origins of brain diseases.

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  • Previous studies mostly perform scRNA seq in younger mice, while single nucleus RNA sequencing is more common in adult mice.

    “Previous studies mostly perform scRNA seq in younger mice, while single nucleus RNA sequencing is more common in adult mice (Hook et al., 2018;Loo et al., 2019;Zeisel et al., 2015;Zhou et al., 2020).”

    From Single-cell resolution analysis of the crosstalk between chemogenically activated astrocytes and microglia (2020) · cites this paper as Loo et al., 2019

    The Results section, “Single-cell transcriptomics of the E14.5 and P0 cortex” (page unavailable), confirms that this study used single-cell RNA sequencing in embryonic and newborn mice. The paper does not establish that previous studies mostly used younger mice or that single-nucleus sequencing was more common in adults; its Introduction also describes single-cell RNA-seq being used to catalog adult nervous-system cells. (LLM, conf=0.84)

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Cited by

Sorted by citations

Authors
Loo, L., Simon, J. M., Xing, L., McCoy, E. S., Niehaus, J. K., Guo, J., Anton, E. S., & Zylka, M. J.
Affiliations
University of North Carolina at Chapel Hill (US)
Corresponding author
Zylka, Mark J.
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2019-01-11
Volume
10
Issue
1
Pages
134-134
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-018-08079-9
PMC
PMC6329831
OpenAlex
W2908670724
Cited by
289
References
17
Citations by year
2026: 27 · 2025: 42 · 2024: 28 · 2023: 38 · 2022: 46 · 2021: 56 · 2020: 35 · 2019: 16 · 2018: 1
FWCI
12.82
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Carolina Digital Repository (University of North Carolina at Chapel Hill) (submittedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • UNC Libraries
Funders
  • Simons Foundation (393316)
  • National Institutes of Health (NS 090029)
  • National Institute of Mental Health (R01MH060929)
  • National Institute of Neurological Disorders and Stroke (P30NS045892, F31NS105397, R01NS090029, R56NS090029, T32NS007431)
  • National Institute of Environmental Health Sciences (R56ES028236, DP1ES024088, P30ES010126)
  • National Institute of Child Health and Human Development
  • Eunice Kennedy Shriver National Institute of Child Health and Human Development (U54HD079124)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Life Sciences › Neuroscience › Developmental Neuroscience › Neurogenesis and neuroplasticity mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
Keywords
neocortex development, cortical development, cerebral cortex, neuronal cell types, glial cell types, neural progenitor cells, neuronal migration, cortical layers, single-cell transcriptomics, disease-associated genes, mouse embryo
MeSH terms
Ciliopathies, Animals, Base Sequence, Mental Disorders, Cell Line, Female, Humans, Male, Mice, Inbred C57BL, Neurons, Stem Cells, Transcription, Genetic, Sequence Analysis, RNA, Cell Lineage, Neocortex, Gene Expression Profiling, Embryonic Development, Mice, HEK293 Cells, Single-Cell Analysis, Neurodevelopmental Disorders

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