title: GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR.
abstract: The vast majority of genes in humans and other organisms undergo alternative splicing, yet the biological function of splice variants is still very poorly understood in large part because of the lack of simple tools that can map the expression profiles and patterns of these variants with high sensitivity. High-throughput quantitative real-time polymerase chain reaction (qPCR) is an ideal technique to accurately quantify nucleic acid sequences including splice variants. However, currently available primer design programs do not distinguish between splice variants and also differ substantially in overall quality, functionality or throughput mode. Here, we present GETPrime, a primer database supported by a novel platform that uniquely combines and automates several features critical for optimal qPCR primer design. These include the consideration of all gene splice variants to enable either gene-specific (covering the majority of splice variants) or transcript-specific (covering one splice variant) expression profiling, primer specificity validation, automated best primer pair selection according to strict criteria and graphical visualization of the latter primer pairs within their genomic context. GETPrime primers have been extensively validated experimentally, demonstrating high transcript specificity in complex samples. Thus, the free-access, user-friendly GETPrime database allows fast primer retrieval and visualization for genes or groups of genes of most common model organisms, and is available at http://updepla1srv1.epfl.ch/getprime/. Database URL: http://deplanckelab.epfl.ch.
authors.affiliation: Institute of Bio-engineering, School of Life Sciences, Laboratory of Systems Biology and Genetics, Lausanne, Switzerland.
authors.forename: Carine
authors.initials: C
authors.lastname: Gubelmann
authors.forename: Alexandre
authors.initials: A
authors.lastname: Gattiker
authors.forename: Andreas
authors.initials: A
authors.lastname: Massouras
authors.forename: Korneel
authors.initials: K
authors.lastname: Hens
authors.forename: Fabrice
authors.initials: F
authors.lastname: David
authors.forename: Frederik
authors.initials: F
authors.lastname: Decouttere
authors.forename: Jacques
authors.initials: J
authors.lastname: Rougemont
authors.forename: Bart
authors.initials: B
authors.lastname: Deplancke
mesh_terms: D016475:3T3 Cells; D000818:Animals; D017931:DNA Primers; D003628:Database Management Systems; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D023281:Genomics / Q000379:methods*; D006801:Humans; D051379:Mice; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results
chemical_list: D017931:DNA Primers