ArticleNucleic acids research2021
Optimized design of antisense oligomers for targeted rRNA depletion.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 17 papers.
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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.
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Who cites it
17 citing papers in PubMed, 23 citations in OpenAlex.
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- 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
- NAP-seq for full-length noncapped RNA sequencing.Nature protocols · 2026Review
- Pre-marking chromatin with H3K4 methylation is required for accurate zygotic genome activation and development.Nature communications · 2025Article
- Egg-laying ChickenGTEx resource deciphers context-specific regulatory effects on fertility traits.Nature communications · 2025Article
- A ribodepletion and tagging protocol to multiplex samples for RNA-seq based virus detection: application to the cassava virome.Virology journal · 2025Article
- Ribosomal RNA Depletion for Poly(A)-Tail-Independent Quantification of Genome Activation.Methods in molecular biology (Clifton, N.J.) · 2025Article
- The human mitochondrial mRNA structurome reveals mechanisms of gene expression.Science (New York, N.Y.) · 2024Article
- Mechanisms of extracellular electron transfer in anaerobic methanotrophic archaea.Nature communications · 2024Article
- RIP-PEN-seq identifies a class of kink-turn RNAs as splicing regulators.Nature biotechnology · 2024Article
- Article
- Parallels and contrasts between the cnidarian and bilaterian maternal-to-zygotic transition are revealed in Hydractinia embryos.PLoS genetics · 2023Article
- Extracellular RNA profiles in non-small cell lung cancer plasma.Journal of thoracic disease · 2023Article
- Parallels and contrasts between the cnidarian and bilaterian maternal-to-zygotic transition are revealed inbioRxiv : the preprint server for biology · 2023Article
- Article
- Article
- Correction to 'Optimized design of antisense oligomers for targeted rRNA depletion'.Nucleic acids research · 2021Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
RNA sequencing (RNA-seq) is extensively used to quantify gene expression transcriptome-wide. Although often paired with polyadenylate (poly(A)) selection to enrich for messenger RNA (mRNA), many applications require alternate approaches to counteract the high proportion of ribosomal RNA (rRNA) in total RNA. Recently, digestion using RNaseH and antisense DNA oligomers tiling target rRNAs has emerged as an alternative to commercial rRNA depletion kits. Here, we present a streamlined, more economical RNaseH-mediated rRNA depletion with substantially lower up-front costs, using shorter antisense oligos only sparsely tiled along the target RNA in a 5-min digestion reaction. We introduce a novel Web tool, Oligo-ASST, that simplifies oligo design to target regions with optimal thermodynamic properties, and additionally can generate compact, common oligo pools that simultaneously target divergent RNAs, e.g. across different species. We demonstrate the efficacy of these strategies by generating rRNA-depletion oligos for Xenopus laevis and for zebrafish, which expresses two distinct versions of rRNAs during embryogenesis. The resulting RNA-seq libraries reduce rRNA to <5% of aligned reads, on par with poly(A) selection, and also reveal expression of many non-adenylated RNA species. Oligo-ASST is freely available at https://mtleelab.pitt.edu/oligo to design antisense oligos for any taxon or to target any abundant RNA for depletion.
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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 OpenQuestion graph.