High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysis
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Abstract
BACKGROUND: High-fidelity preservation strategies for primary tissues are in great demand in the single cell RNAseq community. A reliable method would greatly expand the scope of feasible multi-site collaborations and maximize the utilization of technical expertise. When choosing a method, standardizability and fidelity are important factors to consider due to the susceptibility of single-cell RNAseq analysis to technical noise. Existing approaches such as cryopreservation and chemical fixation are less than ideal for failing to satisfy either or both of these standards. RESULTS: Here we propose a new strategy that leverages preservation schemes developed for organ transplantation. We evaluated the strategy by storing intact mouse kidneys in organ transplant preservative solution at hypothermic temperature for up to 4 days (6 h, 1, 2, 3, and 4 days), and comparing the quality of preserved and fresh samples using FACS and single cell RNAseq. We demonstrate that the strategy effectively maintained cell viability, transcriptome integrity, cell population heterogeneity, and transcriptome landscape stability for samples after up to 3 days of preservation. The strategy also facilitated the definition of the diverse spectrum of kidney resident immune cells, to our knowledge the first time at single cell resolution. CONCLUSIONS: Hypothermic storage of intact primary tissues in organ transplant preservative maintains the quality and stability of the transcriptome of cells for single cell RNAseq analysis. The strategy is readily generalizable to primary specimens from other tissue types for single cell RNAseq analysis.
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scRNA-seq methods require fresh tissues, which can be difficult to obtain and lead to logistic complexities.
“First, these methods require the use of fresh tissues, which can be difficult to obtain and thus lead to logistic complexities (Alles et al., 2017; Attar et al., 2018; Wang et al., 2018; Lafzi et al., 2018).”
From Robust single-nucleus RNA sequencing reveals depot-specific cell population dynamics in adipose tissue remodeling during obesity (2025) · cites this paper as Wang et al., 2018
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- Authors
- Wang, W., Penland, L., Gokce, O., Croote, D., & Quake, S. R.
- Affiliations
- Stanford University (US)
- Corresponding author
- Quake, Stephen R.
- Venue
- BMC Genomics
- Published
- 2018-02-13
- Volume
- 19
- Issue
- 1
- Pages
- 140-140
- ISSN
- 1471-2164 (ISSN-L)
- PMC
- PMC5811979
- OpenAlex
- W2953150185
- Cited by
- 23
- References
- 41
- Citations by year
- 2025: 1 · 2024: 5 · 2023: 4 · 2022: 2 · 2021: 3 · 2020: 2 · 2019: 4 · 2018: 1 · 2017: 1
- FWCI
- 0.89
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- BMC Genomics (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)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Open access LMU (Ludwid Maxmilian's Universitat Munchen) (submittedVersion, cc-by)
- Funders
- National Institutes of Health (5UH2AR06767603)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Molecular Biology Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- single-cell RNA sequencing, cell viability, tissue banking, mouse kidney
- MeSH terms
- Animals, Cell Survival, Kidney, Reproducibility of Results, Cryopreservation, Kidney Transplantation, Sequence Analysis, RNA, Gene Expression Profiling, Mice, Single-Cell Analysis, Transcriptome, Gene Ontology
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