Perspectives on single-nucleus RNA sequencing in different cell types and tissues
Open accessAbstract
Single-cell RNA sequencing has become a powerful and essential tool for delineating cellular diversity in normal tissues and alterations in disease states. For certain cell types and conditions, there are difficulties in isolating intact cells for transcriptome profiling due to their fragility, large size, tight interconnections, and other factors. Single-nucleus RNA sequencing (snRNA-seq) is an alternative or complementary approach for cells that are difficult to isolate. In this review, we will provide an overview of the experimental and analysis steps of snRNA-seq to understand the methods and characteristics of general and tissue-specific snRNA-seq data. Knowing the advantages and limitations of snRNA-seq will increase its use and improve the biological interpretation of the data generated using this technique.
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Use of nuclei enables study of postmortem, frozen, or biobank tissue, including neurodegenerative conditions such as Alzheimer's disease.
“Additionally, the use of nuclei, rather than whole cells, enables the study of samples that were previously difficult to analyze via scRNA-seq, such as postmortem, frozen, or biobank tissue, including those obtained from individuals with neurodegenerative conditions such as Alzheimer’s disease (AD)[12, 16].”
From Comparative analysis of nuclei isolation methods for brain single-nucleus RNA sequencing (2026) · cites this paper as [12]
The Experimental Procedures section says archived frozen tissue is a primary target for single-nucleus RNA sequencing, and “Neurons in the brain” describes its use with postmortem human brain tissue. That section also discusses neurodegenerative disease, but the copy does not explicitly establish the claimed use of biobank tissue from individuals with Alzheimer’s disease; Alzheimer’s appears only in a cited study’s title in the References. Page numbers were not available in our copy. (LLM, conf=0.82)
Experimental — accuracy not yet measuredsnRNA-seq overcomes the need for intact cell dissociation, thereby minimizing dissociation-associated challenges and providing a more physiologically accurate representation of the brain's cellular heterogeneity.
“snRNA-seq overcomes the need for intact cell dissociation, thereby minimizing dissociation-associated challenges and providing a more physiologically accurate representation of the brain’s cellular heterogeneity[12, 14, 15].”
From Comparative analysis of nuclei isolation methods for brain single-nucleus RNA sequencing (2026) · cites this paper as [12]
The Abstract says snRNA-seq avoids enzymatic dissociation of intact cells and can reduce cellular and stress-response biases. The “Neurons in the brain” section says it improves representation of neuronal cell types, but also notes limitations in capturing non-neuronal cells and recommends combining it with scRNA-seq. The source therefore does not establish that snRNA-seq alone gives a more physiologically accurate representation of the brain’s overall cellular heterogeneity. (LLM, conf=0.86)
Experimental — accuracy not yet measuredConventional 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 [12]
The Abstract says enzymatic tissue dissociation may damage neurons, and the Experimental Procedures section describes neurons as fragile and difficult to dissociate. The paper does not attribute neuronal damage to mechanical shearing or say that dissociation induces glial activation. No page numbers were supplied for these passages. (LLM, conf=0.86)
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- Authors
- Kim, N., Kang, H., Jo, A., Yoo, S.-A., & Lee, H.-O.
- Affiliations
- Catholic University of Korea (KR)
- Corresponding author
- Kim, Nayoung
- Kang, Huiram
- Venue
- Journal of Pathology and Translational Medicine
- Published
- 2023-01-15
- Volume
- 57
- Issue
- 1
- Pages
- 52-59
- ISSN
- 1738-1843 (ISSN-L)
- 2383-7837
- 2383-7845
- PMC
- PMC9846005
- OpenAlex
- W4313892712
- Cited by
- 97
- References
- 40
- Citations by year
- 2026: 42 · 2025: 33 · 2024: 11 · 2023: 11
- FWCI
- 2.56
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Journal of Pathology and Translational Medicine (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Research Foundation of Korea (2019M3A9B6064691)
- Ministry of Science and ICT
- 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-nucleus RNA sequencing, single-cell RNA sequencing, tissue-specific transcriptomics, gene expression profiling, cellular diversity
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