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Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data
- C. Ramakers, J. Ruijter, R. H. Deprez, A. Moorman
- Biology, MedicineNeuroscience Letters
- 13 March 2003
It is shown that the first approach can lead to PCR efficiencies that vary over a 0.2 range, whereas the second approach may be off by 0.26, and proposed linear regression on the Log(fluorescence) per cycle number data as an assumption-free method to calculate starting concentrations of mRNAs and PCRefficiencies for each sample.
Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data
- J. Ruijter, C. Ramakers, +4 authors A. Moorman
- Biology, MedicineNucleic acids research
- 22 February 2009
Despite the central role of quantitative PCR (qPCR) in the quantification of mRNA transcripts, most analyses of qPCR data are still delegated to the software that comes with the qPCR apparatus. This…
Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources.
- A. J. Kal, A. V. van Zonneveld, +9 authors H. Tabak
- Biology, MedicineMolecular biology of the cell
- 1 June 1999
A genome-wide characterization of mRNA transcript levels in yeast grown on the fatty acid oleate, determined using Serial Analysis of Gene Expression (SAGE) revealed the dramatic adaptive response of yeast to a change in carbon source.
Sensitivity and accuracy of quantitative real-time polymerase chain reaction using SYBR green I depends on cDNA synthesis conditions.
- R. L. Lekanne Deprez, A. C. Fijnvandraat, J. Ruijter, A. Moorman
- Chemistry, MedicineAnalytical biochemistry
- 1 August 2002
An improved two-step real-time RT-PCR procedure using SYBR green I and the LightCycler that better permits accurate quantification of mRNAs and the choice of the cDNA priming oligo can improve detection sensitivity even further.
Evaluation of qPCR curve analysis methods for reliable biomarker discovery: bias, resolution, precision, and implications.
Developing a framework for robust and unbiased assessment of curve analysis performance whereby various publicly available curve analysis methods were thoroughly compared using a previously published large clinical data set is aimed at.
Bias in the Cq value observed with hydrolysis probe based quantitative PCR can be corrected with the estimated PCR efficiency value.
Mathematical modeling shows that ignoring the cumulative nature of the data leaves the estimated PCR efficiency practically unaffected but will lead to at least one cycle underestimation of the quantification cycle (C(q) value), corresponding to a 2-fold overestimation of target quantity.
Increased tumour risk for BWS patients correlates with aberrant H19 and not KCNQ1OT1 methylation: occurrence of KCNQ1OT1 hypomethylation in familial cases of BWS.
All four familial cases of BWS showed reduced methylation of KCNQ1OT1, suggesting that in these cases the imprinting switch mechanism is disturbed.
Regionalized Sequence of Myocardial Cell Growth and Proliferation Characterizes Early Chamber Formation
- A. Soufan, G. van den Berg, J. Ruijter, P. de Boer, M. V. D. van den Hoff, A. Moorman
- Biology, MedicineCirculation research
- 1 September 2006
Increase in cell size and proliferation of myocytes are key processes in cardiac morphogenesis, yet their regionalization during development of the heart has been described only anecdotally. We have…
Factor correction as a tool to eliminate between-session variation in replicate experiments: application to molecular biology and retrovirology
- J. Ruijter, H. Thygesen, O. Schoneveld, A. Das, B. Berkhout, W. Lamers
- Medicine, BiologyRetrovirology
- 6 January 2006
Factor correction is an effective and efficient way to deal with between-session variation in multi-session experiments and results in smaller residual error than normalisation and standardisation and therefore allows the detection of smaller treatment differences.
Fluorescent-increase kinetics of different fluorescent reporters used for qPCR depend on monitoring chemistry, targeted sequence, type of DNA input and PCR efficiency
- J. Ruijter, P. Lorenz, J. M. Tuomi, M. Hecker, M. V. D. van den Hoff
- Chemistry, MedicineMicrochimica Acta
- 14 January 2014
The kinetics of the increase in fluorescence for each of the qPCR monitoring chemistries form six groups with distinct fluorescence kinetics with respect to the input of both ds-DNA and ss-cDNA are determined.