ArticlemBio2023
Improved Bacterial Single-Cell RNA-Seq through Automated MATQ-Seq and Cas9-Based Removal of rRNA Reads.
Article in mBio, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 63 citations in OpenAlex.
- Single-bacterium RNA-seq protocol to uncover heterogeneous expression of coding and noncoding genes in Bacteroides thetaiotaomicron.STAR protocols · 2026Article
- Elucidation of ACAT1's role in hepatic ischemia-reperfusion injury: TFEB-mediated mitophagy and ferroptosis modulation as therapeutic targets.Journal of pharmaceutical analysis · 2026Article
- Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.Nature microbiology · 2026Article
- Unravelling bacterial complexity at high resolution with single-cell transcriptomics.Nature microbiology · 2026Review
- Single microorganism RNA sequencing of microbiomes using smRandom-Seq.Nature protocols · 2026Review
- Decoding the spatiotemporal heterogeneity of bacterial virulence gene expression using single-cell approaches.Frontiers in microbiology · 2026Review
- Clinical application of single-cell RNA sequencing in disease and therapy.Clinical and translational medicine · 2025Review
- Transcriptomic profiling of individual bacteria by MATQ-seq.Nature protocols · 2025Review
- Review
- Profiling the heterogeneity of microbial populations and communities at the single-cell level.mLife · 2025Review
- Bacterial Systematic Genetics and Integrated Multi-Omics: Beyond Static Genomics Toward Predictive Models.International journal of molecular sciences · 2025Review
- Article
- Dissecting microbial communities with single-cell transcriptome analysis.Science (New York, N.Y.) · 2025Review
- Advances in Single-Cell Sequencing for Infectious Diseases: Progress and Perspectives.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- Applications and techniques of single-cell RNA sequencing across diverse species.Briefings in bioinformatics · 2025Review
- Advances and applications in single-cell and spatial genomics.Science China. Life sciences · 2025Review
- Resolving spatiotemporal dynamics in bacterial multicellular populations: approaches and challenges.Microbiology and molecular biology reviews : MMBR · 2025Review
- Highly multiplexed spatial transcriptomics in bacteria.Science (New York, N.Y.) · 2025Article
- Blood microbiome signatures in systemic diseases: current insights, methodological pitfalls, and future horizons.Frontiers in cellular and infection microbiology · 2025Review
- Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bulk RNA sequencing technologies have provided invaluable insights into host and bacterial gene expression and associated regulatory networks. Nevertheless, the majority of these approaches report average expression across cell populations, hiding the true underlying expression patterns that are often heterogeneous in nature. Due to technical advances, single-cell transcriptomics in bacteria has recently become reality, allowing exploration of these heterogeneous populations, which are often the result of environmental changes and stressors. In this work, we have improved our previously published bacterial single-cell RNA sequencing (scRNA-seq) protocol that is based on multiple annealing and deoxycytidine (dC) tailing-based quantitative scRNA-seq (MATQ-seq), achieving a higher throughput through the integration of automation. We also selected a more efficient reverse transcriptase, which led to reduced cell loss and higher workflow robustness. Moreover, we successfully implemented a Cas9-based rRNA depletion protocol into the MATQ-seq workflow. Applying our improved protocol on a large set of single Salmonella cells sampled over different growth conditions revealed improved gene coverage and a higher gene detection limit compared to our original protocol and allowed us to detect the expression of small regulatory RNAs, such as GcvB or CsrB at a single-cell level. In addition, we confirmed previously described phenotypic heterogeneity in Salmonella in regard to expression of pathogenicity-associated genes. Overall, the low percentage of cell loss and high gene detection limit makes the improved MATQ-seq protocol particularly well suited for studies with limited input material, such as analysis of small bacterial populations in host niches or intracellular bacteria.
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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.