ArticleRNA (New York, N.Y.)2020
Nuclease-mediated depletion biases in ribosome footprint profiling libraries.
Article in RNA (New York, N.Y.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
28 citing papers in PubMed.
- Ribo-seq rRNA reads reveal co-predicted signatures of ribosome heterogeneity and collisions.Briefings in bioinformatics · 2026Article
- Data-driven design of LNA-blockers for efficient contaminant removal in Ribo-Seq libraries.Scientific reports · 2026Article
- Versatile and Selective Biomolecule Pulldown with Combinatorial DNA-Crosslinked Polymers.Angewandte Chemie (International ed. in English) · 2026Article
- Optimised Ribosome Profiling Reveals New Insights Into Translational Regulation in Synchronised Chlamydomonas reinhardtii Cultures.Plant, cell & environment · 2025Article
- Advances in ribosome profiling technologies.Biochemical Society transactions · 2025Review
- Detecting ribosome collisions with differential rRNA fragment analysis in ribosome profiling data.NAR genomics and bioinformatics · 2025Article
- Regulation of translation elongation and integrated stress response in heat-shocked neurons.Cell reports · 2025Article
- A comparative analysis of mRNA enrichment strategies and guidance for improving their efficiency.Scientific reports · 2025Article
- Optimization of ribosome profiling in plants including structural analysis of rRNA fragments.Plant methods · 2024Article
- Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts.Nature communications · 2024Article
- Comprehensive translational profiling and STE AI uncover rapid control of protein biosynthesis during cell stress.Nucleic acids research · 2024Article
- RIP-PEN-seq identifies a class of kink-turn RNAs as splicing regulators.Nature biotechnology · 2024Article
- Principles, challenges, and advances in ribosome profiling: from bulk to low-input and single-cell analysis.Advanced biotechnology · 2023Review
- A rapid protocol for ribosome profiling of low input samples.Nucleic acids research · 2023Article
- Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA.Nucleic acids research · 2023Article
- Article
- A custom library construction method for super-resolution ribosome profiling in Arabidopsis.Plant methods · 2022Article
- Selective footprinting of 40S and 80S ribosome subpopulations (Sel-TCP-seq) to study translation and its control.Nature protocols · 2022Review
- Identifying ribosome heterogeneity using ribosome profiling.Nucleic acids research · 2022Article
- Short open reading frame genes in innate immunity: from discovery to characterization.Trends in immunology · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Ribosome footprint profiling is a high-throughput sequencing-based technique that provides detailed and global views of translation in living cells. An essential part of this technology is removal of unwanted, normally very abundant, ribosomal RNA sequences that dominate libraries and increase sequencing costs. The most effective commercial solution (Ribo-Zero) has been discontinued as a standalone product and a number of new, experimentally distinct commercial applications have emerged on the market. Here we evaluated several commercially available alternatives designed for RNA-seq of human samples and find them generally unsuitable for ribosome footprint profiling. We instead recommend the use of custom-designed biotinylated oligos, which were widely used in early ribosome profiling studies. Importantly, we warn that depletion solutions based on targeted nuclease cleavage significantly perturb the high-resolution information that can be derived from the data, and thus do not recommend their use for any applications that require precise determination of the ends of RNA fragments.
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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.