ArticleGenome research2010
Strand-specific deep sequencing of the transcriptome.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 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
49 citing papers in PubMed, 83 citations in OpenAlex.
- Detection of mRNA Transcript Variants.Genes · 2025Review
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- Methodologies for bacterial ribonuclease characterization using RNA-seq.FEMS microbiology reviews · 2023Review
- Alternative σ Factors Regulate Overlapping as Well as Distinct Stress Response and Metabolic Functions inPathogens (Basel, Switzerland) · 2021Article
- Comparative Transcriptome Analysis ofAntibiotics (Basel, Switzerland) · 2019Article
- Capturing the 'ome': the expanding molecular toolbox for RNA and DNA library construction.Nucleic acids research · 2018Review
- TheFrontiers in microbiology · 2018Article
- Hidden Gems in the Transcriptome Maps of Competent Streptococci.Frontiers in molecular biosciences · 2018Article
- UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq.Scientific reports · 2017Article
- Home Alone: Elimination of All but One Alternative Sigma Factor inFrontiers in microbiology · 2017Article
- Article
- On the study of microbial transcriptomes using second- and third-generation sequencing technologies.Journal of microbiology (Seoul, Korea) · 2016Review
- Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances.Nucleic acids research · 2016Article
- Transcriptome profiling of a spirodiclofen susceptible and resistant strain of the European red mite Panonychus ulmi using strand-specific RNA-seq.BMC genomics · 2015Article
- Spatio-temporal regulation of circular RNA expression during porcine embryonic brain development.Genome biology · 2015Article
- External guide sequence technology: a path to development of novel antimicrobial therapeutics.Annals of the New York Academy of Sciences · 2015Review
- Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host.Nucleic acids research · 2015Article
- Identification of protein coding regions in RNA transcripts.Nucleic acids research · 2015Article
- RNA Sequencing and Analysis.Cold Spring Harbor protocols · 2015Article
- Evaluation and application of the strand-specific protocol for next-generation sequencing.BioMed research international · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Several studies support that antisense-mediated regulation may affect a large proportion of genes. Using the Illumina next-generation sequencing platform, we developed DSSS (direct strand specific sequencing), a strand-specific protocol for transcriptome sequencing. We tested DSSS with RNA from two samples, prokaryotic (Mycoplasma pneumoniae) as well as eukaryotic (Mus musculus), and obtained data containing strand-specific information, using single-read and paired-end sequencing. We validated our results by comparison with a strand-specific tiling array data set for strain M129 of the simple prokaryote M. pneumoniae, and by quantitative PCR (qPCR). The results of DSSS were very well supported by the results from tiling arrays and qPCR. Moreover, DSSS provided higher dynamic range and single-base resolution, thus enabling efficient antisense detection and the precise mapping of transcription start sites and untranslated regions. DSSS data for mouse confirmed strand specificity of the protocol and the general applicability of the approach to studying eukaryotic transcription. We propose DSSS as a simple and efficient strategy for strand-specific transcriptome sequencing and as a tool for genome annotation exploiting the increased read lengths that next-generation sequencing technology now is capable to deliver.
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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.