ArticlePLoS genetics2021
RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics.
Article in PLoS genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 46 citations in OpenAlex.
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- Synthetic redesign of Corynebacterium glutamicum for 1,4-butanediol production via L-glutamate-derived CoA-independent pathway.Journal of biological engineering · 2025Article
- Transcriptional regulatory networks of the human gut symbiont Bacteroides thetaiotaomicron are uncovered using machine learning.Nucleic acids research · 2025Article
- Multi-omics analysis reveals the genetic basis for rapid COmSystems · 2025Article
- Determination of the transcription unit landscape and associated regulatory elements inMicrobiology spectrum · 2025Article
- Advances in ribosome profiling technologies.Biochemical Society transactions · 2025Review
- Engineered CRISPR-Cas9 for Streptomyces sp. genome editing to improve specialized metabolite production.Nature communications · 2025Article
- Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase.mSystems · 2025Article
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- Machine-Learning Analysis of Streptomyces coelicolor Transcriptomes Reveals a Transcription Regulatory Network Encompassing Biosynthetic Gene Clusters.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Diversity of Transcriptional Regulatory Adaptation in E. coli.Molecular biology and evolution · 2024Article
- Modulating bacterial function utilizing A knowledge base of transcriptional regulatory modules.Nucleic acids research · 2024Article
- CyuR is a dual regulator for L-cysteine dependent antimicrobial resistance in Escherichia coli.Communications biology · 2024Article
- Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts.Nature communications · 2024Article
- The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions.mSystems · 2024Article
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Corrections and comments
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA sequencing techniques have enabled the systematic elucidation of gene expression (RNA-Seq), transcription start sites (differential RNA-Seq), transcript 3' ends (Term-Seq), and post-transcriptional processes (ribosome profiling). The main challenge of transcriptomic studies is to remove ribosomal RNAs (rRNAs), which comprise more than 90% of the total RNA in a cell. Here, we report a low-cost and robust bacterial rRNA depletion method, RiboRid, based on the enzymatic degradation of rRNA by thermostable RNase H. This method implemented experimental considerations to minimize nonspecific degradation of mRNA and is capable of depleting pre-rRNAs that often comprise a large portion of RNA, even after rRNA depletion. We demonstrated the highly efficient removal of rRNA up to a removal efficiency of 99.99% for various transcriptome studies, including RNA-Seq, Term-Seq, and ribosome profiling, with a cost of approximately $10 per sample. This method is expected to be a robust method for large-scale high-throughput bacterial transcriptomic studies.
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