qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data

By Jan Hellemans, Geert Mortier, A. De Paepe, Frank Speleman, Jo Vandesompele. Genome Biology, 2007

4,067 citations recorded by the source corpus.

Although quantitative PCR (qPCR) is becoming the method of choice for expression profiling of selected genes, accurate and straightforward processing of the raw measurements remains a major hurdle. Here we outline advanced and universally applicable models for relative quantification and inter-run calibration with proper error propagation along the entire calculation track. These models and algorithms are implemented in qBase, a free program for the management and automated analysis of qPCR data.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/374e237039728cda59a7f9209ea884273c5aa699

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Citations in the corpus

Non-invasive imaging of human embryos before embryonic genome activation predicts development to the blastocyst stage (2010, background): “These were the most stable among the ten housekeeping genes that we tested and well within range of a typical heterogeneous sample se”
The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. (2009, background): “Clinical Chemistry 55:4 (2009) 7 parisontobeaccurate.Themostpopularmethodisnot necessarily the most appropriate, however, and alternative, more generalized quantitative models have been developed to correct for differences in amplification efficiency (62) and to allow the use of multiple reference g”
Reference Gene Selection for Real-Time Quantitative Polymerase Chain Reaction of mRNA Transcript Levels in Chinese Cabbage (Brassica rapa L. ssp. pekinensis) (2010, methodology): “Several statistical approaches have been proposed for evaluating reference genes such as geNorm (Hellemans et al. 2007; Huggett et al. 2005; Vandesompele et al. 2002), Normfinder (Andersen et al. 2004), and BestKeeper (Pfaffl 2001).”
5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming. (2011, methodology): “Dissociation curves were performed to confirm specificity of the PCR products and relative expression was calculated with qBase softwar”
A practical approach to RT-qPCR-Publishing data that conform to the MIQE guidelines. (2010, methodology): “Use the geNorm method (Hellemans et al. 2007) to calculate the target stability between the different conditions (available at https://genorm.cmgg.be or automatically calculated with CFX Manager Software).”
A novel and universal method for microRNA RT-qPCR data normalization (2009, methodology): “All reactions were performed on the 7900 HT (Applied Biosystems) using the gene maximization strategy [41].”
Evaluation of coffee reference genes for relative expression studies by quantitative real-time RT-PCR (2009, methodology): “3.5 (Hellemans et al. 2007) into nonnormalized relative quantities (Q), corrected by PCR efficiency, using the formula Q = EDCT, where E is the efficiency of the gene amplification and DCT is the sample with the lowest expression in the datasetT a b le 1 C o ff ee ca n d id at e re fe re n ce g en…”
How good is a PCR efficiency estimate: Recommendations for precise and robust qPCR efficiency assessments (2015, neutral): “Essentially, any of the PCR reagents can be rate and performance limiting [22] including PCR protocol; and (4) competing reactions.”
Plant-mediated facilitation between a leaf-feeding and a phloem-feeding insect in a brassicaceous plant: from insect performance to gene transcription (2012, positive): “(2002) and Hellemans et al. (2007). Primary plant compounds were analysed as described by Troelstra et al.”