ArticleNucleic acids research2020
Scalable and cost-effective ribonuclease-based rRNA depletion for transcriptomics.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- A Universal, Cost-Effective, and Efficient rRNA Depletion Method for Bacterial mRNA Enrichment.Biochemical genetics · 2026Article
- DepStep: An Efficient One-Step rRNA Depletion Workflow for RNA Sequencing in Non-model Organisms.Bio-protocol · 2026Article
- Phenotypic heterogeneity in the human gut microbiome revealed by subspecies-resolution single-cell transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- Versatile and Selective Biomolecule Pulldown with Combinatorial DNA-Crosslinked Polymers.Angewandte Chemie (International ed. in English) · 2026Article
- Impact of expression systems on the transcriptome ofApplied and environmental microbiology · 2025Article
- Optimizing mouse metatranscriptome profiling by selective removal of redundant nucleic acid sequences.mSystems · 2025Article
- A case report of confirmed difficult pulmonary tuberculosis based on the hybrid capture-based tNGS method.BMC pulmonary medicine · 2025Article
- Identification of determinants that allow maintenance of high-level fluoroquinolone resistance inmBio · 2025Article
- Ribosomal RNA Depletion for Poly(A)-Tail-Independent Quantification of Genome Activation.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Identification of Determinants that Allow Maintenance of High-Level Fluoroquinolone Resistance inbioRxiv : the preprint server for biology · 2024Article
- A practical introduction to holo-omics.Cell reports methods · 2024Review
- A scalable and cost-efficient rRNA depletion approach to enrich RNAs for molecular biology investigations.RNA (New York, N.Y.) · 2024Article
- High-throughput transcriptomics of 409 bacteria-drug pairs reveals drivers of gut microbiota perturbation.Nature microbiology · 2024Article
- Emerging applications of single-cell profiling in precision medicine of atherosclerosis.Journal of translational medicine · 2024Review
- Targeted rRNA depletion enables efficient mRNA sequencing in diverse bacterial species and complex co-cultures.mSystems · 2023Article
- Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes.BMC microbiology · 2023Article
- Single-cell massively-parallel multiplexed microbial sequencing (M3-seq) identifies rare bacterial populations and profiles phage infection.Nature microbiology · 2023Article
- Droplet-based high-throughput single microbe RNA sequencing by smRandom-seq.Nature communications · 2023Article
- Small RNA MTS1338 Configures a Stress Resistance Signature inInternational journal of molecular sciences · 2023Article
- Blocking Abundant RNA Transcripts by High-Affinity Oligonucleotides during Transcriptome Library Preparation.Biological procedures online · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Bacterial RNA sequencing (RNA-seq) is a powerful approach for quantitatively delineating the global transcriptional profiles of microbes in order to gain deeper understanding of their physiology and function. Cost-effective bacterial RNA-seq requires efficient physical removal of ribosomal RNA (rRNA), which otherwise dominates transcriptomic reads. However, current methods to effectively deplete rRNA of diverse non-model bacterial species are lacking. Here, we describe a probe and ribonuclease based strategy for bacterial rRNA removal. We implemented the method using either chemically synthesized oligonucleotides or amplicon-based single-stranded DNA probes and validated the technique on three novel gut microbiota isolates from three distinct phyla. We further showed that different probe sets can be used on closely related species. We provide a detailed methods protocol, probe sets for >5000 common microbes from RefSeq, and an online tool to generate custom probe libraries. This approach lays the groundwork for large-scale and cost-effective bacterial transcriptomics studies.
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