ArticleGenomics, proteomics & bioinformatics2014
PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data.
Article in Genomics, proteomics & bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed.
- Reporting quality of quantitative polymerase chain reaction (qPCR) methods in scientific publications.Research integrity and peer review · 2026Article
- PeakPrime: a peak-guided primer design pipeline for target enrichment in 3'-end RNA-seq.Bioinformatics advances · 2026Article
- Article
- IsoPrimer: a pipeline for designing isoform-aware primer pairs for comprehensive gene expression quantification.Bioinformatics advances · 2025Article
- KDM3A and KDM3B Maintain Naïve Pluripotency Through the Regulation of Alternative Splicing.bioRxiv : the preprint server for biology · 2024Article
- A Method to Quantitatively Examine Heat Stress-Induced Alternative Splicing in Plants by RNA-Seq and RT-PCR.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Article
- Unveiling the Role of Dynamic Alternative Splicing Modulation After Infestation with Sea Lice (Caligus rogercresseyi) in Atlantic Salmon.Marine biotechnology (New York, N.Y.) · 2023Article
- Imaging Inflammasome Activation in Microglia.Current protocols · 2022Article
- Genome-wide transcriptome analysis of the early developmental stages of Echinococcus granulosus protoscoleces reveals extensive alternative splicing events in the spliceosome pathway.Parasites & vectors · 2021Article
- Methods for Characterization of Alternative RNA Splicing.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Function, clinical application, and strategies of Pre-mRNA splicing in cancer.Cell death and differentiation · 2019Review
- MAJIQ-SPEL: web-tool to interrogate classical and complex splicing variations from RNA-Seq data.Bioinformatics (Oxford, England) · 2018Article
- A Genomic View of Alternative Splicing of Long Non-coding RNAs during Rice Seed Development Reveals Extensive Splicing and lncRNA Gene Families.Frontiers in plant science · 2018Article
- H3K4 demethylase KDM5B regulates global dynamics of transcription elongation and alternative splicing in embryonic stem cells.Nucleic acids research · 2017Article
- Expression level is a key determinant of E2F1-mediated cell fate.Cell death and differentiation · 2017Article
- Transcriptome sequencing of gingival biopsies from chronic periodontitis patients reveals novel gene expression and splicing patterns.Human genomics · 2016Article
- Impacts of Alternative Splicing Events on the Differentiation of Adipocytes.International journal of molecular sciences · 2015Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
The vast majority of multi-exon genes in higher eukaryotes are alternatively spliced and changes in alternative splicing (AS) can impact gene function or cause disease. High-throughput RNA sequencing (RNA-seq) has become a powerful technology for transcriptome-wide analysis of AS, but RT-PCR still remains the gold-standard approach for quantifying and validating exon splicing levels. We have developed PrimerSeq, a user-friendly software for systematic design and visualization of RT-PCR primers using RNA-seq data. PrimerSeq incorporates user-provided transcriptome profiles (i.e., RNA-seq data) in the design process, and is particularly useful for large-scale quantitative analysis of AS events discovered from RNA-seq experiments. PrimerSeq features a graphical user interface (GUI) that displays the RNA-seq data juxtaposed with the expected RT-PCR results. To enable primer design and visualization on user-provided RNA-seq data and transcript annotations, we have developed PrimerSeq as a stand-alone software that runs on local computers. PrimerSeq is freely available for Windows and Mac OS X along with source code at http://primerseq.sourceforge.net/. With the growing popularity of RNA-seq for transcriptome studies, we expect PrimerSeq to help bridge the gap between high-throughput RNA-seq discovery of AS events and molecular analysis of candidate events by RT-PCR.
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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.