Bimodal melting curve experiment on the surface of microbeads.

Description

A melting curve experiment with six microbead populations and short oligonucleotide probes (direct hybridization). Detection probes for human VIM (vimentin), MLC-2v (myosin regulatory light chain 2, ventricular/cardiac muscle isoform), SERCA2 (Atp2a2 - ATPase, Calcium-transporting ATPase sarcoplasmic reticulum type, slow twitch skeletal muscle isoform), HRPT1 (hyperparathyroidism 1) and the artificial sequences Poly(dA)20 (20 nt of dA) and aCS (artificial Control Sequence).

Format

A data frame with the melting curves of six different capture and detection probe pairs on six microbeads populations for VIM, MLC-2v, SERCA2, Poly(dA)20, aCS and HPRT1. First column contains the temperature (in degree Celsius, 1 degree Celsius per step) followed by melting curves of VIM, MLC-2v, SERCA2, Poly(dA)20, aCS and HPRT1 with bimodal melting pattern. The dyes and quencher used were Atto 647N and BHQ2.

T

a numeric vector, Temperature in degree Celsius.

VIM.no.Q

a numeric vector, VIM without quencher and without Poly(dT)20 region.

MLC2v.w.Q.w.dT20

a numeric vector, MLC-2v with quencher-labeled detection probe and fluorescent Poly(dA)20 detection probe.

SERCA2.no.Q.w.dT20

a numeric vector, SERCA2 without quencher-labeled detection probe and Poly(dA)20 detection probe.

PolydA20.w.Q

a numeric vector, Poly(dT)20 with fluorescent Poly(dA)20 detection probe (quencher labeled).

aCS.w.Q.w.dT20

a numeric vector, artificial Control Sequence without quencher-labeled detection probe and fluorescent Poly(dA)20 detection probe.

HPRT1.no.Q.w.dT20

a numeric vector, HPRT1 without quencher-labeled detection probe and fluorescent Poly(dA)20 detection probe.

Source

Data were measured with the VideoScan platform:

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. 133:35–74, 2013. http://www.ncbi.nlm.nih.gov/pubmed/22437246

Surface Melting Curve Analysis with R. S. Roediger, A. Boehm and I. Schimke. The R Journal. 5(2):37–52, 2013. http://journal.r-project.org/

See Also

MFIerror, mcaSmoother, diffQ, diffQ, MultiMelt, DualHyb

Examples

data(DMP)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MBmca)
Loading required package: robustbase
Loading required package: chipPCR
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MBmca/DMP.Rd_%03d_medium.png", width=480, height=480)
> ### Name: DMP
> ### Title: Bimodal melting curve experiment on the surface of microbeads.
> ### Aliases: DMP
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(DMP)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>