ArticleBMC bioinformatics2014
A tool for design of primers for microRNA-specific quantitative RT-qPCR.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 146 papers.
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Who cites it
146 citing papers in PubMed.
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- Natural polymorphisms in the bovine leukemia virus microRNA cluster modulate miRNA expression and host regulatory pathways.Veterinary research · 2026Article
- New molecular players: siRNA expression and gene regulation in Hordeum vulgare L. ageing seeds after germination.BMC genomics · 2026Article
- Identification of stable miRNA references for qRT-PCR normalization in ovine fasciolosis.BMC genomics · 2026Article
- Sex-Specific Pathophysiological Signatures in Allometric Dosing-Controlled Bleomycin Acute Lung Injury Model.bioRxiv : the preprint server for biology · 2026Article
- Toward Understanding the Role of miRNAs in Cleft Palate Only: Observations from Patient Tissues and In Vitro Assays.International journal of molecular sciences · 2026Article
- Targetome profile of hsa-miR-93-5p is resistant to isoform formation in prostate adenocarcinoma.PeerJ · 2026Article
- MicroRNAs Let-7b-5p and miR-24-3p as Potential Therapeutic Agents Targeting Pancreatic Cancer Stem Cells.International journal of molecular sciences · 2025Article
- Comprehensive Profiling of the miRNome and Degradome Reveals Regulatory Signatures of Seed Aging and Germination.International journal of molecular sciences · 2025Article
- Exploring potent miRNA combinations for detecting early-stage breast cancer.Molecular therapy. Nucleic acids · 2025Article
- Loss of multiple micro-RNAs uncovers multi-level restructuring of gene regulation in rodents.BMC genomics · 2025Article
- MiRNA-186 as a Biomarker of Disease Exacerbation in Rheumatoid Arthritis: Insights from Clinical Data and Molecular Marker Analysis.International journal of molecular sciences · 2025Article
- Circulating microRNA profiles in early-stage osteoarthritis and rheumatoid arthritis.Scientific reports · 2025Article
- MiR-7a-Klf4 axis as a regulator and therapeutic target of neuroinflammation and ferroptosis in Alzheimer's disease.NAR molecular medicine · 2025Article
- Identification and characterisation of temporal abundance of microRNAs in synovial fluid from an experimental equine model of osteoarthritis.Equine veterinary journal · 2025Article
- Comprehensive transcriptome analysis reveals MSTRG.19853.1/ssc-miR-361-3p/NPPA axis is related to hypoxic adaptation in Tibetan pigs.BMC genomics · 2025Article
- Differential Expression of Small Non-Coding RNAs in Uterine Leiomyomas.International journal of molecular sciences · 2025Article
- Dynamic microRNA expression profiles in goat ovarian tissues before and after pregnancy.Journal of animal science · 2025Article
- Identification of stable reference genes and differential miRNA expression in Sri Lankan type 2 diabetes mellitus patients: a cross-sectional study.Frontiers in endocrinology · 2025Article
86 more citing papers are in PubMed but not listed here.
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1 author.
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Abstract
backgroundMicroRNAs are small but biologically important RNA molecules. Although different methods can be used for quantification of microRNAs, quantitative PCR is regarded as the reference that is used to validate other methods. Several commercial qPCR assays are available but they often come at a high price and the sequences of the primers are not disclosed. An alternative to commercial assays is to manually design primers but this work is tedious and, hence, not practical for the design of primers for a larger number of targets.
resultsI have developed the software miRprimer for automatic design of primers for the method miR-specific RT-qPCR, which is one of the best performing microRNA qPCR methods available. The algorithm is based on an implementation of the previously published rules for manual design of miR-specific primers with the additional feature of evaluating the propensity of formation of secondary structures and primer dimers. Testing of the primers showed that 76 out of 79 primers (96%) worked for quantification of microRNAs by miR-specific RT-qPCR of mammalian RNA samples. This success rate corresponds to the success rate of manual primer design. Furthermore, primers designed by this method have been distributed to several labs and used successfully in published studies.
conclusionsThe software miRprimer is an automatic and easy method for design of functional primers for miR-specific RT-qPCR. The application is available as stand-alone software that will work on the MS Windows platform and in a developer version written in the Ruby programming language.
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