ArticleScientific reports2019
Efficient and specific oligo-based depletion of rRNA.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 64 citations in OpenAlex.
- 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
- Optimization of Metagenomic Library Construction for Influenza A Virus and SARS-CoV-2: Systematic Comparison of rRNA Depletion Strategies and Fragmentation Orders.Diagnostics (Basel, Switzerland) · 2026Article
- Empowering One Health with metagenomics.One health outlook · 2026Review
- An rRNA-depleted full-length transcriptome strategy using nanopore sequencing for identification of novel lncRNA isoforms.Communications biology · 2026Article
- Article
- A comparative analysis of mRNA enrichment strategies and guidance for improving their efficiency.Scientific reports · 2025Article
- SLAM-seq reveals independent contributions of RNA processing and stability to gene expression in African trypanosomes.Nucleic acids research · 2025Article
- Assessment of mRNA Decay and Calculation of Codon Occurrence to mRNA Stability Correlation Coefficients after 5-EU Metabolic Labeling.Methods in molecular biology (Clifton, N.J.) · 2025Article
- EFFICIENT RIBOSOMAL RNA DEPLETION FROMWellcome open research · 2025Article
- Ribosomal RNA Depletion for Poly(A)-Tail-Independent Quantification of Genome Activation.Methods in molecular biology (Clifton, N.J.) · 2025Article
- RNA profiles differ between small and large extracellular vesicle subsets isolated from porcine seminal plasma.BMC genomics · 2024Article
- A prion-like domain is required for phase separation and chloroplast RNA processing during cold acclimation in Arabidopsis.The Plant cell · 2024Article
- Recommendations for detection, validation, and evaluation of RNA editing events in cardiovascular and neurological/neurodegenerative diseases.Molecular therapy. Nucleic acids · 2024Review
- lncRNA Profiling of Exosomes and Its Communication Role in Regulating Silica-Stimulated Macrophage Apoptosis and Fibroblast Activation.Biomolecules · 2024Article
- Targeted rRNA depletion enables efficient mRNA sequencing in diverse bacterial species and complex co-cultures.mSystems · 2023Article
- A new osteogenic protein isolated fromBioactive materials · 2023Article
- Towards a post-pandemic future for global pathogen genome sequencing.PLoS biology · 2023Article
- An Introduction to Nanopore Sequencing: Past, Present, and Future Considerations.Micromachines · 2023Review
- Chemoproteomic discovery of a human RNA ligase.Nature communications · 2023Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In most organisms, ribosomal RNA (rRNA) contributes to >85% of total RNA. Thus, to obtain useful information from RNA-sequencing (RNA-seq) analyses at reasonable sequencing depth, typically, mature polyadenylated transcripts are enriched or rRNA molecules are depleted. Targeted depletion of rRNA is particularly useful when studying transcripts lacking a poly(A) tail, such as some non-coding RNAs (ncRNAs), most bacterial RNAs and partially degraded or immature transcripts. While several commercially available kits allow effective rRNA depletion, their efficiency relies on a high degree of sequence homology between oligonucleotide probes and the target RNA. This restricts the use of such kits to a limited number of organisms with conserved rRNA sequences. In this study we describe the use of biotinylated oligos and streptavidin-coated paramagnetic beads for the efficient and specific depletion of trypanosomal rRNA. Our approach reduces the levels of the most abundant rRNA transcripts to less than 5% with minimal off-target effects. By adjusting the sequence of the oligonucleotide probes, our approach can be used to deplete rRNAs or other abundant transcripts independent of species. Thus, our protocol provides a useful alternative for rRNA removal where enrichment of polyadenylated transcripts is not an option and commercial kits for rRNA are not available.
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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 Socratic graph.