Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations
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Emerging results from other tissues and cell types have begun to characterize dissociation artifacts following enzymatic digestion.
“However, emerging results from other tissues/cell types have begun to characterize dissociation artifacts following enzymatic digestion43–45,65,66.”
From Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain (2022) · cites this paper as [44]
Typical enzymatic digestion of mouse brain tissue induced a host of transcriptional alterations.
“Consistent with the reports from other tissues in mice, we found that typical enzymatic digestion of mouse brain tissue induced a host of transcriptional alterations34,43,44,65.”
From Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain (2022) · cites this paper as [44]
Conventional cell dissociation protocols often compromise neuronal integrity through mechanical shearing or induce glial activation.
“For example, conventional cell dissociation protocols often compromise the integrity of neurons through mechanical shearing or induce the activation of glia[6, 8–12].”
From Comparative analysis of nuclei isolation methods for brain single-nucleus RNA sequencing (2026) · cites this paper as [9]
Many cell types, such as microglia, are especially sensitive to dissociation-induced activation.
“Many cell types, such as microglia, are especially sensitive to dissociation-induced activation, which is a known challenge in single-cell studies[9, 10].”
From Comparative analysis of nuclei isolation methods for brain single-nucleus RNA sequencing (2026) · cites this paper as [9]
One drawback of an ice-cold dissociation is the decrease in efficiency of dissociation with certain tissues such as the brain.
“However, one drawback of an ice-cold dissociation is the decrease in efficiency of dissociation with certain tissues such as the brain (Adam et al., 2017;Denisenko et al., 2019;van den Brink et al., 2017).”
From Single-cell resolution analysis of the crosstalk between chemogenically activated astrocytes and microglia (2020) · cites this paper as van den Brink et al., 2017
Cluster 3 was enriched in genes recently shown to be induced by cellular stress in other human cells; thus this cluster could represent a subset of distressed cells.
“Cluster 3 was enriched in genes that have recently been shown to be induced by cellular stress in other human cells19 (Supplementary Fig. 7); thus this cluster could represent a subset of distressed cells.”
From Single cell RNA sequencing of human microglia uncovers a subset associated with Alzheimer’s disease (2020) · cites this paper as [19]
Topic 19 may reflect a response to tissue dissociation.
“and may reflect a response to tissue dissociation (van den Brink et al., 2017)”
From A cellular and spatial map of the choroid plexus across brain ventricles and ages (2021) · cites this paper as van den Brink et al., 2017
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“However, one drawback of an ice-cold dissociation is the decrease in efficiency of dissociation with certain tissues such as the brain (Adam et al., 2017; Denisenko et al., 2019; van den Brink et al., 2017).”
Background
- Authors
- van den Brink, S. C., Sage, F., Vértesy, Á., Spanjaard, B., Peterson-Maduro, J., Baron, C. S., Robin, C., & van Oudenaarden, A.
- Affiliations
- University Medical Center Utrecht (NL)
- Max Delbrück Center (DE)
- ORCID
- Venue
- Nature Methods
- Published
- 2017-09-29
- Volume
- 14
- Issue
- 10
- Pages
- 935-936
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2759615793
- Cited by
- 1,072
- References
- 8
- Citations by year
- 2026: 138 · 2025: 104 · 2024: 154 · 2023: 113 · 2022: 127 · 2021: 145 · 2020: 163 · 2019: 75 · 2018: 48 · 2017: 4
- FWCI
- 33.52
- Type
- journal article
- Language
- en
- Open access
- green
- dspace.library.uu.nl
- Licence
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- KNAW research portal (Royal Academy of Art and Sciences (KNAW)) (publishedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (submittedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- single-cell transcriptomics, bulk transcriptomics, cell-cell interactions, skeletal muscle regeneration
- MeSH terms
- Organ Specificity, Stem Cells, Gene Expression, In Situ Hybridization, Fluorescence, Sequence Analysis, RNA, Muscle Fibers, Skeletal, Computational Biology, Gene Expression Profiling, Single-Cell Analysis
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