ArticleNucleic acids research2011
Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
59 citing papers in PubMed, 120 citations in OpenAlex.
- A Universal, Cost-Effective, and Efficient rRNA Depletion Method for Bacterial mRNA Enrichment.Biochemical genetics · 2026Article
- Article
- Toxicity assessment of doxycycline-aided artificial intelligence-assisted drug design targeting candidate 16S rRNA methyltransferase gene.BMC pharmacology & toxicology · 2025Article
- Mitochondria facilitate neuronal differentiation by metabolising nuclear-encoded RNA.Cell communication and signaling : CCS · 2024Article
- Brainstem transcriptomic changes in male Wistar rats after acute stress, comparing the use of duplex specific nuclease (DSN).Scientific reports · 2024Article
- An improved bacterial mRNA enrichment strategy in dual RNA sequencing to unveil the dynamics of plant-bacterial interactions.Plant methods · 2024Article
- Improvement of duplex-specific nuclease salt tolerance by fusing DNA-binding domain of DNase from an extremely halotolerant bacterium Thioalkalivibrio sp. K90mix.Extremophiles : life under extreme conditions · 2023Article
- Blocking Abundant RNA Transcripts by High-Affinity Oligonucleotides during Transcriptome Library Preparation.Biological procedures online · 2023Article
- Pore-Forming Cardiotoxin VVA2 (Volvatoxin A2) Variant I82E/L86K Is an Atypical Duplex-Specific Nuclease.Toxins · 2022Article
- Comparison of rRNA depletion methods for efficient bacterial mRNA sequencing.Scientific reports · 2022Article
- Recent Progress in Nanomaterials Modified Electrochemical Biosensors for the Detection of MicroRNA.Micromachines · 2021Review
- Comparative analysis of RNA enrichment methods for preparation of Cryptococcus neoformans RNA sequencing libraries.G3 (Bethesda, Md.) · 2021Article
- RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics.PLoS genetics · 2021Article
- Optimized design of antisense oligomers for targeted rRNA depletion.Nucleic acids research · 2021Article
- Bias in RNA-seq Library Preparation: Current Challenges and Solutions.BioMed research international · 2021Review
- High Throughput Sequencing for the Detection and Characterization of RNA Viruses.Frontiers in microbiology · 2021Review
- Paired rRNA-depleted and polyA-selected RNA sequencing data and supporting multi-omics data from human T cells.Scientific data · 2020Article
- Improved bacterial RNA-seq by Cas9-based depletion of ribosomal RNA reads.RNA (New York, N.Y.) · 2020Article
- A smart polymer for sequence-selective binding, pulldown, and release of DNA targets.Communications biology · 2020Article
- Scalable and cost-effective ribonuclease-based rRNA depletion for transcriptomics.Nucleic acids research · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing has great potential for application in bacterial transcriptomics. However, unlike eukaryotes, bacteria have no clear mechanism to select mRNAs over rRNAs; therefore, rRNA removal is a critical step in sequencing-based transcriptomics. Duplex-specific nuclease (DSN) is an enzyme that, at high temperatures, degrades duplex DNA in preference to single-stranded DNA. DSN treatment has been successfully used to normalize the relative transcript abundance in mRNA-enriched cDNA libraries from eukaryotic organisms. In this study, we demonstrate the utility of this method to remove rRNA from prokaryotic total RNA. We evaluated the efficacy of DSN to remove rRNA by comparing it with the conventional subtractive hybridization (Hyb) method. Illumina deep sequencing was performed to obtain transcriptomes from Escherichia coli grown under four growth conditions. The results clearly showed that our DSN treatment was more efficient at removing rRNA than the Hyb method was, while preserving the original relative abundance of mRNA species in bacterial cells. Therefore, we propose that, for bacterial mRNA-seq experiments, DSN treatment should be preferred to Hyb-based methods.
Indexed as
Identifiers
What OpenQuestion holds
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.