Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data.

By C. Ramakers, Jan Ruijter, R. H. Deprez, A. Moorman. Neuroscience Letters, 2003

3,774 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/66858dbe86b64cb027f665d948fc7c621749ae8c

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

Quantitative real-time RT-PCR data analysis: current concepts and the novel “gene expression’s CT difference” formula (2006, methodology): “In this linear range, a trendline including 3–6 data points, with the highest possible slope and with the highest correlation coefficient (also known as Pearson correlation coefficient R(2)) must be defined [9] (see Fig.”
Comprehensive Algorithm for Quantitative Real-Time Polymerase Chain Reaction (2005, methodology): “, 2002), the interactive window-of-linearity algorithm (Ramakers et al., 2003), the mid-value point regression (Peirson et al.”
PHO2, MicroRNA399, and PHR1 Define a Phosphate-Signaling Pathway in Plants1[W][OA] (2006, methodology): “PCR primer efficiencies (E) were determined using the LinRegPCR program (Ramakers et al., 2003), did not change significantly between different cDNA samples, and were always higher than (1 1 E) 5 1.84.”
Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, positive): “PCR efficiency (E) was estimated using absolute fluorescence data captured during the exponential phase of amplification of each reaction with the equation (1+E)1⁄410(–1/) (Ramakers et al., 2003).”
Comparison of reference genes for quantitative real-time polymerase chain reaction analysis of gene expression in sugarcane (2007, methodology): “The transcript abundance ratio of target gene to reference gene was determined by the following equation: relative expression = (Eref)Ctref/(Etarget)Cttarget ( Pfaffl, 2001; Czechowski et al., 2004), where Eref and Etarget are the efficiencies of the primers for the reference and target gene, respe”
Validation of Zebrafish (Danio rerio) Reference Genes for Quantitative Real-time RT-PCR Normalization (2007, methodology): “Following the removal of outliers, raw fluorescence data were exported to the programme LinReg to determine the PCR amplification efficiency [12] .”
Downregulation of Cinnamyl Alcohol Dehydrogenase (CAD) Leads to Improved Saccharification Efficiency in Switchgrass (2011, methodology): “The raw real-time RT-PCR data of each individual sample was collected and analyzed by the software of SDS 2.2.2 for 7900HT (Applied Biosystems, Foster City, CA) and the individual PCR efficiencies were checked by the LinRegPCR 7.0 software [ 31 ].”
TRPA1 contributes to cold, mechanical, and chemical nociception but is not essential for hair-cell transduction. (2006, positive): “Linear regression to determine the PCR efficiency for the Trpa1 primers was determined, and relative amounts of transcripts were calculated as described by Ramakers et al. (2003).”
LEA (Late Embryogenesis Abundant) proteins and their encoding genes in Arabidopsis thaliana (2008, methodology): “The mean PCR efficiency (E) for every primer pair was calculated using the linregPCR software [ 119 ].”
Developmental Control of Lignification in Stems of Lowland Switchgrass Variety Alamo and the Effects on Saccharification Efficiency (2009, methodology): “The raw real-time PCR data of each individual sample was collected and exported by the software of SDS 2.2.2 for 7900HT (Applied Biosystems, Foster City, CA), and the PCR efficiencies and ct values for each sample were checked by the LinRegPCR 7.0 software [ 39 ].”
Validation of Candidate Reference Genes for the Accurate Normalization of Real-Time Quantitative RT-PCR Data in Rice During Seed Development (2010, methodology): “PCR efficiency was calculated with the LinRegPCR program (Ramakers et al. 2003) from the raw fluorescence data.”
A Pseudo-Response Regulator is misexpressed in the photoperiod insensitive Ppd-D1a mutant of wheat (Triticum aestivum L.) (2007, methodology): “E values were determined by calculating the average rate of Xuorescence increase during the exponential phase across all samples in the plate showing exponential ampliWcation (Ramakers et al. 2003).”
Production and fitness of Fusarium pseudograminearum inoculum at elevated carbon dioxide in FACE (2010, methodology): “5 (Ramakers et al., 2003) and Ct is the crossing threshold.”
QuantPrime – a flexible tool for reliable high-throughput primer design for quantitative PCR (2008, methodology): “Real-time PCR amplification efficiencies were calculated using the LinRegPCR tool [21], using the best-fit method for 4 to 6 points.”