ArticleG3 (Bethesda, Md.)2013
FlyPrimerBank: an online database for Drosophila melanogaster gene expression analysis and knockdown evaluation of RNAi reagents.
Article in G3 (Bethesda, Md.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.
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Who cites it
101 citing papers in PubMed, 154 citations in OpenAlex.
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- Natural SEL1L variants rescue a model of NGLY1 deficiency and modify ERAD function and proteasome sensitivity.PLoS genetics · 2025Article
- Chondroitin sulfate regulates proliferation of Drosophila intestinal stem cells.PLoS genetics · 2025Article
- FlyRNAi.org 2025 update-expanded resources for new technologies and species.Nucleic acids research · 2025Article
- Genome-Wide Expression Profiling and Phenotypic Analysis of Downstream Targets Identify the Fox Transcription Factor Jumeau as a Master Regulator of Cardiac Progenitor Cell Division.International journal of molecular sciences · 2024Article
- Evolutionary rate covariation is pervasive between glycosylation pathways and points to potential disease modifiers.PLoS genetics · 2024Article
- Egg multivesicular bodies elicit an LC3-associated phagocytosis-like pathway to degrade paternal mitochondria after fertilization.Nature communications · 2024Article
- Article
- Berberis vulgaris L. extract supplementation exerts regulatory effects on the lifespan and healthspan of Drosophila through its antioxidant activity depending on the sex.Biogerontology · 2024Article
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- Mating-induced increase of kynurenine in Drosophila ovary enhances starvation resistance of progeny.The Journal of biological chemistry · 2024Article
- A single amino acid polymorphism in natural Metchnikowin alleles of Drosophila results in systemic immunity and life history tradeoffs.PLoS genetics · 2024Article
- A Drosophila screen identifies a role for histone methylation in ER stress preconditioning.G3 (Bethesda, Md.) · 2024Article
- Protein retention in the endoplasmic reticulum rescues Aβ toxicity in Drosophila.Neurobiology of aging · 2023Article
41 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
Abstract
The evaluation of specific endogenous transcript levels is important for understanding transcriptional regulation. More specifically, it is useful for independent confirmation of results obtained by the use of microarray analysis or RNA-seq and for evaluating RNA interference (RNAi)-mediated gene knockdown. Designing specific and effective primers for high-quality, moderate-throughput evaluation of transcript levels, i.e., quantitative, real-time PCR (qPCR), is nontrivial. To meet community needs, predefined qPCR primer pairs for mammalian genes have been designed and sequences made available, e.g., via PrimerBank. In this work, we adapted and refined the algorithms used for the mammalian PrimerBank to design 45,417 primer pairs for 13,860 Drosophila melanogaster genes, with three or more primer pairs per gene. We experimentally validated primer pairs for ~300 randomly selected genes expressed in early Drosophila embryos, using SYBR Green-based qPCR and sequence analysis of products derived from conventional PCR. All relevant information, including primer sequences, isoform specificity, spatial transcript targeting, and any available validation results and/or user feedback, is available from an online database (www.flyrnai.org/flyprimerbank). At FlyPrimerBank, researchers can retrieve primer information for fly genes either one gene at a time or in batch mode. Importantly, we included the overlap of each predicted amplified sequence with RNAi reagents from several public resources, making it possible for researchers to choose primers suitable for knockdown evaluation of RNAi reagents (i.e., to avoid amplification of the RNAi reagent itself). We demonstrate the utility of this resource for validation of RNAi reagents in vivo.
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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.