ArticleNature methods2010
Validation of two ribosomal RNA removal methods for microbial metatranscriptomics.
Article in Nature methods, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers, 1 of them a synthesis that pooled it.
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Who cites it
100 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Stool metatranscriptomics: A technical guideline for mRNA stabilisation and isolation.BMC genomics · 2015Guideline
- A Universal, Cost-Effective, and Efficient rRNA Depletion Method for Bacterial mRNA Enrichment.Biochemical genetics · 2026Article
- From dividing to dormant: embracing the full activity spectrum for environmental microorganisms.Microbiology and molecular biology reviews : MMBR · 2026Review
- Microbial Signals in Cancer: Dissecting Host-Microbiota-Tumor Interactions and Potential Therapeutic Strategy.MedComm · 2026Review
- 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
- Unleashing the potential of mRNA-seq to uncover the microbiome structure and their crosstalk with host cells: the vulvar ecosystem.Microbiome · 2026Article
- Primary transcript enrichment reveals a density-dependentFrontiers in microbiology · 2026Article
- Optimization of Mapping Tools and Investigation of Ribosomal RNA Influence for Data-Driven Gene Expression Analysis in Complex Microbiomes.Microorganisms · 2025Article
- Metatranscriptomics for Understanding the Microbiome in Food and Nutrition Science.Metabolites · 2025Review
- The application status of sequencing technology in global respiratory infectious disease diagnosis.Infection · 2024Review
- Diversity and composition of active and total bacteria in rhizospheric soil in response to continuous cropping years of Panax notoginseng.Folia microbiologica · 2024Article
- An improved bacterial mRNA enrichment strategy in dual RNA sequencing to unveil the dynamics of plant-bacterial interactions.Plant methods · 2024Article
- Dual RNA-seq in filarial nematodes andFrontiers in microbiology · 2024Article
- Targeted rRNA depletion enables efficient mRNA sequencing in diverse bacterial species and complex co-cultures.mSystems · 2023Article
- Comparative Analysis of rRNA Removal Methods for RNA-Seq Differential Expression in Halophilic Archaea.Biomolecules · 2022Article
- Comparison of rRNA depletion methods for efficient bacterial mRNA sequencing.Scientific reports · 2022Article
- Gut Microbiome Activity Contributes to Prediction of Individual Variation in Glycemic Response in Adults.Diabetes therapy : research, treatment and education of diabetes and related disorders · 2022Article
- Mining the Microbiome and Microbiota-Derived Molecules in Inflammatory Bowel Disease.International journal of molecular sciences · 2021Review
- Epigenetic mechanisms regulating COVID-19 infection.Epigenetics · 2021Review
- Microbial single-cell RNA sequencing by split-pool barcoding.Science (New York, N.Y.) · 2021Article
40 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The predominance of rRNAs in the transcriptome is a major technical challenge in sequence-based analysis of cDNAs from microbial isolates and communities. Several approaches have been applied to deplete rRNAs from (meta)transcriptomes, but no systematic investigation of potential biases introduced by any of these approaches has been reported. Here we validated the effectiveness and fidelity of the two most commonly used approaches, subtractive hybridization and exonuclease digestion, as well as combinations of these treatments, on two synthetic five-microorganism metatranscriptomes using massively parallel sequencing. We found that the effectiveness of rRNA removal was a function of community composition and RNA integrity for these treatments. Subtractive hybridization alone introduced the least bias in relative transcript abundance, whereas exonuclease and in particular combined treatments greatly compromised mRNA abundance fidelity. Illumina sequencing itself also can compromise quantitative data analysis by introducing a G+C bias between runs.
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20852648What 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.