Cited by 465Single-cell and spatial transcriptomicsGenomics and Phylogenetic StudiesRNA Research and Splicing

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Detecting Activated Cell Populations Using Single-Cell RNA-Seq

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Wu, Ye Emily, Pan, Lin, Zuo, Yanning, Li, Xinmin, Hong, Weizhe·2017·Neuron

DOI 10.1016/j.neuron.2017.09.026

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Abstract

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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Additional file 12 of Transcriptomic analysis of paternal behaviors in prairie voles
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Additional file 26 of Transcriptomic analysis of paternal behaviors in prairie voles
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Additional file 3 of Transcriptomic analysis of paternal behaviors in prairie voles
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Additional file 15 of Transcriptomic analysis of paternal behaviors in prairie voles
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Additional file 27 of Transcriptomic analysis of paternal behaviors in prairie voles
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Additional file 17 of Transcriptomic analysis of paternal behaviors in prairie voles
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Additional file 3 of Immune stimulation recruits a subset of pro-regenerative macrophages to the retina that promotes axonal regrowth of injured neurons
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Additional file 4 of Immune stimulation recruits a subset of pro-regenerative macrophages to the retina that promotes axonal regrowth of injured neurons
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Additional file 18 of Transcriptomic analysis of paternal behaviors in prairie voles
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Additional file 13 of Transcriptomic analysis of paternal behaviors in prairie voles
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Additional file 7 of Immune stimulation recruits a subset of pro-regenerative macrophages to the retina that promotes axonal regrowth of injured neurons
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Additional file 6 of Transcriptomic analysis of paternal behaviors in prairie voles
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Additional file 19 of Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits
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Additional file 20 of Transcriptomic analysis of paternal behaviors in prairie voles
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Additional file 19 of Transcriptomic analysis of paternal behaviors in prairie voles
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Additional file 28 of Transcriptomic analysis of paternal behaviors in prairie voles
Duclot, F., Liu, Y., Saland, S. K., Wang, Z., & Kabbaj, M. (2022) · Figshare · doi:10.6084/m9.figshare.21258996
Additional file 25 of Transcriptomic analysis of paternal behaviors in prairie voles
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Additional file 4 of Transcriptomic analysis of paternal behaviors in prairie voles
Duclot, F., Liu, Y., Saland, S. K., Wang, Z., & Kabbaj, M. (2022) · Figshare · doi:10.6084/m9.figshare.21259005
Additional file 5 of Immune stimulation recruits a subset of pro-regenerative macrophages to the retina that promotes axonal regrowth of injured neurons
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Additional file 5 of Transcriptomic analysis of paternal behaviors in prairie voles
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Additional file 24 of Transcriptomic analysis of paternal behaviors in prairie voles
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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
ORCID: Wu, Ye Emily
Pan, Lin
Zuo, Yanning
Li, Xinmin
Hong, Weizhe
Venue: Neuron
Publisher: Elsevier BV
Published: 2017-10
Volume: 96
Issue: 2
Pages: 313-329.e6
ISSN: 0896-6273 (ISSN-L)
DOI: 10.1016/j.neuron.2017.09.026
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: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 375 d)
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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Detecting Activated Cell Populations Using Single-Cell RNA-Seq

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