dpcR (version 0.1.4.0)

pds_raw: Plasmid dilution series raw data

Description

These are the raw data from the pds_raw data set as measured by the BioRad QX100 Droplet Digital PCR System.

source

Michael Jahn Flow cytometry group / Environmental microbiology Helmholtz Centre for Environmental Research - UFZ Permoserstrasse 15 / 04318 Leipzig / Germany phone [phone] michael.jahn [at] ufz.de / www.ufz.de

Details

The results can be as calculated by the BioRad QX100 Droplet Digital PCR System are to be found in pds.

Setup: Duplex assay with constant amount of genomic DNA and six 10-fold dilutions of plasmid DNA with 4 replicates, ranging theoretically from ~ 10^4 to 10^-1 copies/ micro L plus 4 replicates without plasmid DNA. Included are No-gDNA-control and No-template-control, 2 replicates each.

Annotation: FX.Y (X = dilution number, Y = replicate number). Hardware: Bio-Rad QX100 Droplet digital PCR system Details: Genomic DNA isolated from Pseudomonas putida KT2440. Plasmid is pCOM10-StyA::EGFP StyB [Jahn et al., 2013, Curr Opin Biotechnol, Vol. 24 (1): 79-87]. Template DNA was heat treated at 95 degree Celsius for 5 min prior to PCR. Channel 1, primers for genomic DNA marker ileS, Taqman probes (FAM labelled). Channel 2, primers for plasmid DNA marker styA, Taqman probes (HEX labelled).

The results can be as calculated by the BioRad QX100 Droplet Digital PCR System are to be found in pds.

Setup: Duplex assay with constant amount of genomic DNA and six 10-fold dilutions of plasmid DNA with 4 replicates, ranging theoretically from ~ 10^4 to 10^-1 copies/ micro L plus 4 replicates without plasmid DNA. Included are No-gDNA-control and No-template-control, 2 replicates each.

Annotation: FX.Y (X = dilution number, Y = replicate number). Hardware: Bio-Rad QX100 Droplet digital PCR system Details: Genomic DNA isolated from Pseudomonas putida KT2440. Plasmid is pCOM10-StyA::EGFP StyB [Jahn et al., 2013, Curr Opin Biotechnol, Vol. 24 (1): 79-87]. Template DNA was heat treated at 95 degree Celsius for 5 min prior to PCR. Channel 1, primers for genomic DNA marker ileS, Taqman probes (FAM labelled). Channel 2, primers for plasmid DNA marker styA, Taqman probes (HEX labelled).

References

Jahn et al., 2013, Curr Opin Biotechnol, Vol. 24 (1): 79-87

Jahn M, Vorpahl C, Tuerkowsky D, Lindmeyer M, Buehler B, Harms H, et al. Accurate Determination of Plasmid Copy Number of Flow-Sorted Cells using Droplet Digital PCR. Anal Chem 2014; 86:5969--76. doi:10.1021/ac501118v.

Examples

#str(pds_raw)
bioamp(data = pds_raw[["A01"]], main = "Well A01", pch = 19)