ArticleRNA (New York, N.Y.)2011
The rocks and shallows of deep RNA sequencing: Examples in the Vibrio cholerae RNome.
Article in RNA (New York, N.Y.), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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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.
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
21 citing papers in PubMed, 37 citations in OpenAlex.
- Chemical capping improves template switching and enhances sequencing of small RNAs.Nucleic acids research · 2022Article
- Do small RNAs unlock the below ground microbiome-plant interaction mystery?Frontiers in molecular biosciences · 2022Review
- Quantification of purified endogenous miRNAs with high sensitivity and specificity.Nature communications · 2020Article
- The Vc2 Cyclic di-GMP-Dependent Riboswitch of Vibrio cholerae Regulates Expression of an Upstream Putative Small RNA by Controlling RNA Stability.Journal of bacteriology · 2019Article
- Utilization of Small RNA Genes to DistinguishThe American journal of tropical medicine and hygiene · 2019Article
- Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation.BMC genomics · 2018Article
- Capturing the 'ome': the expanding molecular toolbox for RNA and DNA library construction.Nucleic acids research · 2018Review
- Detecting RNA modifications in the epitranscriptome: predict and validate.Nature reviews. Genetics · 2017Review
- Article
- Count ratio model reveals bias affecting NGS fold changes.Nucleic acids research · 2015Article
- A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence.PLoS pathogens · 2015Article
- Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm formation.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Non-protein coding RNA genes as the novel diagnostic markers for the discrimination of Salmonella species using PCR.PloS one · 2015Article
- Transcriptional profile of Salmonella enterica subsp. enterica serovar Weltevreden during alfalfa sprout colonization.Microbial biotechnology · 2014Article
- Biases in small RNA deep sequencing data.Nucleic acids research · 2014Review
- PARma: identification of microRNA target sites in AGO-PAR-CLIP data.Genome biology · 2013Article
- Transcriptomic profiling of the oyster pathogen Vibrio splendidus opens a window on the evolutionary dynamics of the small RNA repertoire in the Vibrio genus.RNA (New York, N.Y.) · 2012Article
- Comparative genomics and transcriptomics of trait-gene association.BMC genomics · 2012Article
- RNA processing in the minimal organism Nanoarchaeum equitans.Genome biology · 2012Article
- Expression Profiling of a Heterogeneous Population of ncRNAs Employing a Mixed DNA/LNA Microarray.Journal of nucleic acids · 2012Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
New deep RNA sequencing methodologies in transcriptome analyses identified a wealth of novel nonprotein-coding RNAs (npcRNAs). Recently, deep sequencing was used to delineate the small npcRNA transcriptome of the human pathogen Vibrio cholerae and 627 novel npcRNA candidates were identified. Here, we report the detection of 223 npcRNA candidates in V. cholerae by different cDNA library construction and conventional sequencing methods. Remarkably, only 39 of the candidates were common to both surveys. We therefore examined possible biasing influences in the transcriptome analyses. Key steps, including tailing and adapter ligations for generating cDNA, contribute qualitatively and quantitatively to the discrepancies between data sets. In addition, the state of 5'-end phosphorylation influences the efficiency of adapter ligation and C-tailing at the 3'-end of the RNA. Finally, our data indicate that the inclusion of sample-specific molecular identifier sequences during ligation steps also leads to biases in cDNA representation. In summary, even deep sequencing is unlikely to identify all RNA species, and caution should be used for meta-analyses among alternatively generated data sets.
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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.