ArticleeLife2024
An improved bacterial single-cell RNA-seq reveals biofilm heterogeneity.
Article in eLife, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed.
- Association ofPathogens (Basel, Switzerland) · 2026Article
- Siderophore sharing protects clonalApplied and environmental microbiology · 2026Article
- Unravelling bacterial complexity at high resolution with single-cell transcriptomics.Nature microbiology · 2026Review
- LncIMF1 Promotes Adipogenesis of Porcine Intramuscular Preadipocyte by Sponging miR-187.Biochemical genetics · 2026Article
- Review
- Profiling the heterogeneity of microbial populations and communities at the single-cell level.mLife · 2025Review
- Dissecting microbial communities with single-cell transcriptome analysis.Science (New York, N.Y.) · 2025Review
- Host-Associated Biofilms:Microorganisms · 2025Review
- Navigating single-cell RNA-sequencing: protocols, tools, databases, and applications.Genomics & informatics · 2025Review
- Resolving spatiotemporal dynamics in bacterial multicellular populations: approaches and challenges.Microbiology and molecular biology reviews : MMBR · 2025Review
- Single-cell RNA sequencing using split-pool barcoding reveals transcriptional heterogeneity inJournal of oral microbiology · 2025Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
In contrast to mammalian cells, bacterial cells lack mRNA polyadenylated tails, presenting a hurdle in isolating mRNA amidst the prevalent rRNA during single-cell RNA-seq. This study introduces a novel method, ribosomal RNA-derived cDNA depletion (RiboD), seamlessly integrated into the PETRI-seq technique, yielding RiboD-PETRI. This innovative approach offers a cost-effective, equipment-free, and high-throughput solution for bacterial single-cell RNA sequencing (scRNA-seq). By efficiently eliminating rRNA reads and substantially enhancing mRNA detection rates (up to 92%), our method enables precise exploration of bacterial population heterogeneity. Applying RiboD-PETRI to investigate biofilm heterogeneity, distinctive subpopulations marked by unique genes within biofilms were successfully identified. Notably, PdeI, a marker for the cell-surface attachment subpopulation, was observed to elevate cyclic diguanylate (c-di-GMP) levels, promoting persister cell formation. Thus, we address a persistent challenge in bacterial single-cell RNA-seq regarding rRNA abundance, exemplifying the utility of this method in exploring biofilm heterogeneity. Our method effectively tackles a long-standing issue in bacterial scRNA-seq: the overwhelming abundance of rRNA. This advancement significantly enhances our ability to investigate the intricate heterogeneity within biofilms at unprecedented resolution.
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What Socratic holds
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 Socratic graph.