chipPCR.datasets: Overview for data sets of the 'chipPCR' package

In chipPCR: Toolkit of Helper Functions to Pre-Process Amplification Data

Description

The chipPCR package contains numerous data sets from commercial and experimental technologies for the amplification of nucleic acids. The data sets include results from qPCR experiments with the 'VideoScan' 'HCU' (Roediger et al. 2013), Bio-Rad (iQ5, CFX96), capillary convective PCR (ccPCR) and Roche Light Cycler 1.5. Real-time monitored amplification reactions were performed using standard amplification methods (qPCR, based on Taq polymerase) and quantitative isothermal amplification (qIA). In selected data sets are melting curves and dilution series available. Most of the data sets have equidistant measure points. However, some datasets have none homogeneous measure points as indicated below.

capillary convective PCR (ccPCR)

capillaryPCR: The capillary convective PCR (ccPCR) is a modified device of the ccPCR system proposed by Chou et al. 2013.

standard qPCR - commercial thermo cyclers

C60.amp: qPCR Experiment for the Amplification of MLC-2v and Vimentin (as decadic dilutions) Using the Roche Light Cycler 1.5.

C60.melt: Melt Curves MLC-2v and Vimentin for the qPCR experiment C60.amp using the Roche Light Cycler 1.5

C126EG595: A quantitative PCR (qPCR) with the DNA binding dye (EvaGreen) (Mao et al. 2007) was performed in a Bio-Rad iQ5 thermo cycler. The cycle-dependent increase of the fluorescence was quantified at the elongation step (59.5 degrees Celsius).

C126EG685: A quantitative PCR (qPCR) with the DNA binding dye (EvaGreen) (Mao et al. 2007) was performed in a Bio-Rad iQ5 thermo cycler. The cycle-dependent increase of the fluorescence was quantified at the elongation step (68.5 degrees Celsius).

C127EGHP: Quantitative PCR (qPCR) with a hydrolysis probe (Cy5/BHQ2) and DNA binding dye (EvaGreen) (Mao et al. 2007) performed in the Roche Light Cycler 1.5 thermo cycler.

VIMCFX96_60: Human vimentin amplification curve data (measured during annealing phase at 60 degrees Celsius) for 96 replicate samples in a Bio-Rad CFX96 thermo cycler.

VIMCFX96_69: Human vimentin amplification curve data (measured during elongation phase at 69 degrees Celsius) for 96 replicate samples in a Bio-Rad CFX96 thermo cycler.

VIMCFX96_meltcurve: Human vimentin melting curve data for 96 replicate samples in a Bio-Rad CFX96 thermo cycler.

VIMiQ5_595: Human vimentin amplification curve data (measured during annealing phase at 59.5 degrees Celsius) for 96 replicate samples in a Bio-Rad iQ5 thermo cycler.

VIMiQ5_685: Human vimentin amplification curve data (measured during elongation phase at 68.5 degrees Celsius) for 96 replicate samples in a Bio-Rad iQ5 thermo cycler.

VIMiQ5_melt: Human vimentin melting curve data for 96 replicate samples in a Bio-Rad iQ5 thermo cycler.

standard qPCR - experimental thermo cyclers

C54: qPCR Experiment in the 'VideoScan' heating/cooling-unit for the amplification using different concentrations of MLC-2v input cDNA quantities.

CD74: Quantitative PCR with a hydrolysis probe and DNA binding dye (EvaGreen) for MLC-2v measured at 59.5 degrees Celsius (annealing temperature), 68.5 degrees Celsius (elongation temperature) and at 30 degrees Celsius.

Simulations

Eff625: Highly replicate number amplification curves with an approximate amplification efficiency of 62.5 percent at cycle number 18. The data were derived from a simulation such as the AmpSim function.

Eff750: Highly replicate number amplification curves with an approximate amplification efficiency of 75 percent at cycle number 18. The data were derived from a simulation such as the AmpSim function.

Eff875: Highly replicate number amplification curves with an approximate amplification efficiency of 87.5 percent at cycle number 18. The data were derived from a simulation such as the AmpSim function.

Eff1000: Highly replicate number amplification curves with an approximate amplification efficiency of 100 percent at cycle number 18. The data were derived from a simulation such as the AmpSim function.

Isothermal Amplification - Helicase Dependent Amplification

C67: A Helicase Dependent Amplification (HDA) of HPRT1 (Homo sapiens hypoxanthine phosphoribosyltransferase 1), performed at different input DNA quantities using the Bio-Rad iQ5 thermo cycler.

CD75: Helicase Dependent Amplification in the 'VideoScan' 'HCU' of HPRT1 (Homo sapiens hypoxanthine phosphoribosyltransferase 1) measured at at 55, 60 or 65 degrees Celsius.

C81: Helicase Dependent Amplification (HDA) of pCNG1 using the 'VideoScan' Platform (Roediger et al. (2013)). The HDA was performed at 65 degree Celsius. Two concentrations of input DNA were used.

C85: Helicase Dependent Amplification (HDA) of Vimentin (Vim) in the 'VideoScan' Platform (Roediger et al. (2013)). The HDA was performed at 65 degree Celsius with three dilutions of input DNA.

Source

Stefan Roediger

References

A Highly Versatile Microscope Imaging Technology Platform for the Multiplex Real-Time Detection of Biomolecules and Autoimmune Antibodies. S. Roediger, P. Schierack, A. Boehm, J. Nitschke, I. Berger, U. Froemmel, C. Schmidt, M. Ruhland, I. Schimke, D. Roggenbuck, W. Lehmann and C. Schroeder. Advances in Biochemical Bioengineering/Biotechnology. 133:33–74, 2013.

Examples

data(VIMiQ5_melt)

tmp <- VIMiQ5_melt

plot(NA, NA, xlim = c(55,95), ylim = c(0, 40000), 
    xlab = "Temperature (degrees Celsius)",ylab = "RFU", 
    main = "Melting curve in iQ5 (Bio-Rad)")
apply(tmp[, 2:ncol(tmp)], 2, 
      function(x) lines(tmp[1:nrow(tmp),1],x))

Fmean <- rowMeans(tmp[, 2:ncol(tmp)])
lines(tmp[1:nrow(tmp),1], Fmean, col = "red", lwd = 3)

legend(55, 4000, c("Raw", "Mean"), pch = c(19,19), col = c(1,2))

chipPCR documentation built on March 5, 2021, 9:06 a.m.