Detecting Activated Cell Populations Using Single-Cell RNA-Seq
Open accessAbstract
Single-cell RNA sequencing offers a promising opportunity for probing cell types mediating specific behavioral functions and the underlying molecular programs. However, this has been hampered by a long-standing issue in transcriptional profiling of dissociated cells, specifically the transcriptional perturbations that are artificially induced during conventional whole-cell dissociation procedures. Here, we develop Act-seq, which minimizes artificially induced transcriptional perturbations and allows for faithful detection of both baseline transcriptional profiles and acute transcriptional changes elicited by behavior/experience-driven activity. Using Act-seq, we provide the first detailed molecular taxonomy of distinct cell types in the amygdala. We further show that Act-seq robustly detects seizure-induced acute gene expression changes in multiple cell types, revealing cell-type-specific activation profiles. Furthermore, we find that acute stress preferentially activates neuronal subpopulations that express the neuropeptide gene Cck. Act-seq opens the way for linking physiological stimuli with acute transcriptional dynamics in specific cell types in diverse complex tissues.
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No explicit statistical methods were used to predetermine sample sizes, but the study's sample sizes exceed those reported in previous publications.
“No explicit statistical methods were used to predetermine sample sizes but our sample sizes exceed those reported in previous publications32,34,43.”
From Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain (2022) · cites this paper as [32]
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- Authors
- Wu, Y. E., Pan, L., Zuo, Y., Li, X., & Hong, W.
- Affiliations
- University of California, Los Angeles (US)
- Corresponding author
- Hong, Weizhe
- Venue
- Neuron
- Publisher
- Elsevier BV
- Published
- 2017-10
- Volume
- 96
- Issue
- 2
- Pages
- 313-329.e6
- ISSN
- 0896-6273 (ISSN-L)
- OpenAlex
- W2762506555
- Cited by
- 438
- References
- 62
- Citations by year
- 2026: 33 · 2025: 43 · 2024: 37 · 2023: 65 · 2022: 83 · 2021: 64 · 2020: 50 · 2019: 39 · 2018: 22 · 2017: 2
- FWCI
- 12.63
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Neuron (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Whitehall Foundation
- NARSAD Young Investigator
- Searle Scholars Award
- 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 Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- single-cell RNA sequencing, seizure-induced gene expression, acute stress response, cholecystokinin, neuronal subpopulations
- MeSH terms
- Amygdala, Animals, Male, Mice, Inbred C57BL, Organ Culture Techniques, Sequence Analysis, RNA, Mice, Single-Cell Analysis
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