Plasmid dilution series raw data

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

Format

A list of 32 data frames.

Well
| ExptType
| Experiment | Sample + Dilution step | TypeAssay | Assay
A01
| Absolute Quantification
| ABS | gDNA + P 10^4 | Ch1Unknown | ileS
B01
| Absolute Quantification
| ABS | gDNA + P 10^4 | Ch1Unknown | ileS
C01
| Absolute Quantification
| ABS | gDNA + P 10^4 | Ch1Unknown | ileS
D01
| Absolute Quantification
| ABS | gDNA + P 10^4 | Ch1Unknown | ileS
E01
| Absolute Quantification
| ABS | gDNA + P 10^3 | Ch1Unknown | ileS
F01
| Absolute Quantification
| ABS | gDNA + P 10^3 | Ch1Unknown | ileS
G01
| Absolute Quantification
| ABS | gDNA + P 10^3 | Ch1Unknown | ileS
H01
| Absolute Quantification
| ABS | gDNA + P 10^3 | Ch1Unknown | ileS
A02
| Absolute Quantification
| ABS | gDNA + P 10^2 | Ch1Unknown | ileS
B02
| Absolute Quantification
| ABS | gDNA + P 10^2 | Ch1Unknown | ileS
C02
| Absolute Quantification
| ABS | gDNA + P 10^2 | Ch1Unknown | ileS
D02
| Absolute Quantification
| ABS | gDNA + P 10^2 | Ch1Unknown | ileS
E02
| Absolute Quantification
| ABS | gDNA + P 10^1 | Ch1Unknown | ileS
F02
| Absolute Quantification
| ABS | gDNA + P 10^1 | Ch1Unknown | ileS
G02
| Absolute Quantification
| ABS | gDNA + P 10^1 | Ch1Unknown | ileS
H02
| Absolute Quantification
| ABS | gDNA + P 10^1 | Ch1Unknown | ileS
A03
| Absolute Quantification
| ABS | gDNA + P 10^0 | Ch1Unknown | ileS
B03
| Absolute Quantification
| ABS | gDNA + P 10^0 | Ch1Unknown | ileS
C03
| Absolute Quantification
| ABS | gDNA + P 10^0 | Ch1Unknown | ileS
D03
| Absolute Quantification
| ABS | gDNA + P 10^0 | Ch1Unknown | ileS
E03
| Absolute Quantification
| ABS | gDNA + P 10^-1 | Ch1Unknown | ileS
F03
| Absolute Quantification
| ABS | gDNA + P 10^-1 | Ch1Unknown | ileS
G03
| Absolute Quantification
| ABS | gDNA + P 10^-1 | Ch1Unknown | ileS
H03
| Absolute Quantification
| ABS | gDNA + P 10^-1 | Ch1Unknown | ileS
A04
| Absolute Quantification
| ABS | gDNA | Ch1Unknown | ileS
B04
| Absolute Quantification
| ABS | gDNA | Ch1Unknown | ileS
C04
| Absolute Quantification
| ABS | gDNA | Ch1Unknown | ileS
D04
| Absolute Quantification
| ABS | gDNA | Ch1Unknown | ileS
E04
| Absolute Quantification
| ABS | B + P 10^2 | Ch1NTC | ileS
F04
| Absolute Quantification
| ABS | B + P 10^2 | Ch1NTC | ileS
G04
| Absolute Quantification
| ABS | B | Ch1NTC | ileS
H04
| Absolute Quantification
| ABS | B | Ch1NTC | ileS
A01
| Absolute Quantification
| ABS | gDNA + P 10^4 | Ch2Unknown | styA
B01
| Absolute Quantification
| ABS | gDNA + P 10^4 | Ch2Unknown | styA
C01
| Absolute Quantification
| ABS | gDNA + P 10^4 | Ch2Unknown | styA
D01
| Absolute Quantification
| ABS | gDNA + P 10^4 | Ch2Unknown | styA
E01
| Absolute Quantification
| ABS | gDNA + P 10^3 | Ch2Unknown | styA
F01
| Absolute Quantification
| ABS | gDNA + P 10^3 | Ch2Unknown | styA
G01
| Absolute Quantification
| ABS | gDNA + P 10^3 | Ch2Unknown | styA
H01
| Absolute Quantification
| ABS | gDNA + P 10^3 | Ch2Unknown | styA
A02
| Absolute Quantification
| ABS | gDNA + P 10^2 | Ch2Unknown | styA
B02
| Absolute Quantification
| ABS | gDNA + P 10^2 | Ch2Unknown | styA
C02
| Absolute Quantification
| ABS | gDNA + P 10^2 | Ch2Unknown | styA
D02
| Absolute Quantification
| ABS | gDNA + P 10^2 | Ch2Unknown | styA
E02
| Absolute Quantification
| ABS | gDNA + P 10^1 | Ch2Unknown | styA
F02
| Absolute Quantification
| ABS | gDNA + P 10^1 | Ch2Unknown | styA
G02
| Absolute Quantification
| ABS | gDNA + P 10^1 | Ch2Unknown | styA
H02
| Absolute Quantification
| ABS | gDNA + P 10^1 | Ch2Unknown | styA
A03
| Absolute Quantification
| ABS | gDNA + P 10^0 | Ch2Unknown | styA
B03
| Absolute Quantification
| ABS | gDNA + P 10^0 | Ch2Unknown | styA
C03
| Absolute Quantification
| ABS | gDNA + P 10^0 | Ch2Unknown | styA
D03
| Absolute Quantification
| ABS | gDNA + P 10^0 | Ch2Unknown | styA
E03
| Absolute Quantification
| ABS | gDNA + P 10^-1 | Ch2Unknown | styA
F03
| Absolute Quantification
| ABS | gDNA + P 10^-1 | Ch2Unknown | styA
G03
| Absolute Quantification
| ABS | gDNA + P 10^-1 | Ch2Unknown | styA
H03
| Absolute Quantification
| ABS | gDNA + P 10^-1 | Ch2Unknown | styA
A04
| Absolute Quantification
| ABS | gDNA | Ch2NTC | styA
B04
| Absolute Quantification
| ABS | gDNA | Ch2NTC | styA
C04
| Absolute Quantification
| ABS | gDNA | Ch2NTC | styA
D04
| Absolute Quantification
| ABS | gDNA | Ch2NTC | styA
E04
| Absolute Quantification
| ABS | B + P 10^2 | Ch2Unknown | styA
F04
| Absolute Quantification
| ABS | B + P 10^2 | Ch2Unknown | styA
G04
| Absolute Quantification
| ABS | B | Ch2NTC | styA
H04
| Absolute Quantification
| ABS | B | Ch2NTC | styA

Source

Michael Jahn Flow cytometry group / Environmental microbiology Helmholtz Centre for Environmental Research - UFZ Permoserstrasse 15 / 04318 Leipzig / Germany phone +49 341 235 1318 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)
#>                   Cluster.1  Cluster.2 Cluster.3   Cluster.4
#> Counts Ch. 1       11.00000    3.00000  398.0000 11552.00000
#> Counts Ch. 2       11.00000    3.00000  398.0000 11552.00000
#> Location Ch. 1    553.69556 2026.70093  995.2142   590.94425
#> Location Ch. 2   1084.54590  995.84230 3694.3724  3676.18494
#> Dispersion Ch. 1   24.43643   80.47304  182.0612    51.25585
#> Dispersion Ch. 2   84.69588   32.88620  136.8308   115.59810