ArticleNature communications2021
High-throughput RNA sequencing of paraformaldehyde-fixed single cells.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
50 citing papers in PubMed, 71 citations in OpenAlex.
- Single-cell and spatial RNA sequencing in prostate cancer.Nature reviews. Urology · 2026Review
- A Microcapsule-Integrated smRandom-seq Platform Enables Fixation-Free Single Microbe RNA Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Single-cell fixed RNA profiling of the osteosarcoma clinical Spectrum identifies ADAMTS12 and RNASE1 as key drivers of the metastatic niche.Journal of bone oncology · 2026Article
- Single-cell fixed RNA profiling uncovers SEMA4D and LMCD1 as therapeutic targets in a liver fibrosis model.JHEP reports : innovation in hepatology · 2026Article
- Age-associated B cells (ABCs) develop from a CNS-localized progenitor pool into a pro-inflammatory phenotype after stroke.bioRxiv : the preprint server for biology · 2026Article
- Evaluating the practical aspects and performance of commercial single-cell RNA sequencing technologies.NAR genomics and bioinformatics · 2026Article
- RNA-specific local translation is patterned by condensates for multinucleate cell growth.Nature cell biology · 2026Article
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- A Field-Friendly, Non-Toxic Fixative for Integrated Morphological and Molecular Research in Non-Model Invertebrates.Ecology and evolution · 2026Article
- Characterizing epithelial-mesenchymal transition-linked heterogeneity in breast cancer circulating tumor cells at a single-cell level.Molecular oncology · 2025Article
- Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues.Nature communications · 2025Article
- Functional phenotyping of genomic variants using joint multiomic single-cell DNA-RNA sequencing.Nature methods · 2025Article
- Cell sorting based on single nucleotide variation enables characterization of mutation-dependent transcriptome and chromatin states.Nucleic acids research · 2025Article
- Advances in Single-Cell Sequencing for Infectious Diseases: Progress and Perspectives.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- The Curated Cancer Cell Atlas provides a comprehensive characterization of tumors at single-cell resolution.Nature cancer · 2025Article
- snCED-seq: high-fidelity cryogenic enzymatic dissociation of nuclei for single-nucleus RNA-seq of FFPE tissues.Nature communications · 2025Article
- Single-cell omics technologies - Fundamentals on how to create single-cell looking glasses for reproductive health.American journal of obstetrics and gynecology · 2025Review
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- Assessing the Influence of Selected Permeabilization Methods on Lymphocyte Single-Cell Multi-Omics.Antibodies (Basel, Switzerland) · 2025Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Single-cell transcriptomic studies that require intracellular protein staining, rare cell sorting, or inactivation of infectious pathogens are severely limited. This is because current high-throughput single-cell RNA sequencing methods are either incompatible with or necessitate laborious sample preprocessing for paraformaldehyde treatment, a common tissue and cell fixation and preservation technique. Here we present FD-seq (Fixed Droplet RNA sequencing), a high-throughput method for droplet-based RNA sequencing of paraformaldehyde-fixed, permeabilized and sorted single cells. We show that FD-seq preserves the RNA integrity and relative gene expression levels after fixation and permeabilization. Furthermore, FD-seq can detect a higher number of genes and transcripts than methanol fixation. We first apply FD-seq to analyze a rare subpopulation of cells supporting lytic reactivation of the human tumor virus KSHV, and identify TMEM119 as a potential host factor that mediates viral reactivation. Second, we find that infection with the human betacoronavirus OC43 leads to upregulation of pro-inflammatory pathways in cells that are exposed to the virus but fail to express high levels of viral genes. FD-seq thus enables integrating phenotypic with transcriptomic information in rare cell subpopulations, and preserving and inactivating pathogenic samples.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.