ArticleBMC biology2017
Cell fixation and preservation for droplet-based single-cell transcriptomics.
Article in BMC biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 135 papers.
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Who cites it
135 citing papers in PubMed.
- RNA-aware tissue preservation workflows for high-quality spatial transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- Spatial mapping of RNA turnover kinetics in the mouse brain.Nature neuroscience · 2026Article
- A Field-Friendly, Non-Toxic Fixative for Integrated Morphological and Molecular Research in Non-Model Invertebrates.Ecology and evolution · 2026Article
- Spatial mapping of RNA turnover kinetics and regulatory landscapes of mRNA stability in the mammalian brain.bioRxiv : the preprint server for biology · 2026Article
- Multisite Assessment of Methods for Cell Preservation Upstream of Single-Cell RNA Sequencing.Journal of biomolecular techniques : JBT · 2026Article
- Single-cell transcriptomics of granulocytes in asthma and atopic diseases.Frontiers in molecular biosciences · 2026Review
- Methodologies for Sample Multiplexing and Computational Deconvolution in Single-Cell Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Characterizing epithelial-mesenchymal transition-linked heterogeneity in breast cancer circulating tumor cells at a single-cell level.Molecular oncology · 2025Article
- An Integrated Single-Cell Atlas of the Mouse Ileum Links Nutrient Metabolism with Epithelial and Immune Crosstalk.The Journal of nutrition · 2025Article
- USPPAR is a cost-effective, scalable, and highly sensitive single-cell RNA sequencing workflow compatible with diverse specimens.PLoS biology · 2025Article
- Recent advancements in tissue dissociation techniques for cell manufacturing single-cell analysis and downstream processing.Stem cells translational medicine · 2025Review
- Multi-site Assessment of Methods for Cell Preservation Upstream of Single Cell RNA Sequencing.bioRxiv : the preprint server for biology · 2025Article
- Droplet-based single-cell RNA sequencing: decoding cellular heterogeneity for breakthroughs in cancer, reproduction, and beyond.Journal of translational medicine · 2025Review
- Review
- Target sequence of single cells captured by a polymeric microfluidic device.Scientific reports · 2025Article
- scCOSMIX: A Mixed-Effects Framework for Differential Coexpression and Transcriptional Interactions Modeling in Single-Cell RNA-Seq.Statistics in medicine · 2025Article
- Highly sensitive and scalable time-resolved RNA sequencing in single cells with scNT-seq2.bioRxiv : the preprint server for biology · 2025Article
- snCED-seq: high-fidelity cryogenic enzymatic dissociation of nuclei for single-nucleus RNA-seq of FFPE tissues.Nature communications · 2025Article
- Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single-cell transcriptomics.The New phytologist · 2025Article
- Performance of cellulose-based card for direct genetic testing of spinal muscular atrophy.BMC biotechnology · 2025Article
75 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRecent developments in droplet-based microfluidics allow the transcriptional profiling of thousands of individual cells in a quantitative, highly parallel and cost-effective way. A critical, often limiting step is the preparation of cells in an unperturbed state, not altered by stress or ageing. Other challenges are rare cells that need to be collected over several days or samples prepared at different times or locations.
methodsHere, we used chemical fixation to address these problems. Methanol fixation allowed us to stabilise and preserve dissociated cells for weeks without compromising single-cell RNA sequencing data.
resultsBy using mixtures of fixed, cultured human and mouse cells, we first showed that individual transcriptomes could be confidently assigned to one of the two species. Single-cell gene expression from live and fixed samples correlated well with bulk mRNA-seq data. We then applied methanol fixation to transcriptionally profile primary cells from dissociated, complex tissues. Low RNA content cells from Drosophila embryos, as well as mouse hindbrain and cerebellum cells prepared by fluorescence-activated cell sorting, were successfully analysed after fixation, storage and single-cell droplet RNA-seq. We were able to identify diverse cell populations, including neuronal subtypes. As an additional resource, we provide 'dropbead', an R package for exploratory data analysis, visualization and filtering of Drop-seq data.
conclusionsWe expect that the availability of a simple cell fixation method will open up many new opportunities in diverse biological contexts to analyse transcriptional dynamics at single-cell resolution.
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