pds_raw: Plasmid dilution series raw data

In michbur/dpcR: Digital PCR Analysis

Plasmid dilution series raw data

Description

Subset of raw data from the pds_raw data set as measured by the Bio-Rad QX100 Droplet Digital PCR System.

Format

A list of 3 data frames.

Well

| ExptType

| Experiment | Sample + Dilution step | TypeAssay | Assay

D01

| Absolute Quantification

| ABS | gDNA + P 10^4 | Ch1Unknown | ileS

D02

| Absolute Quantification

| ABS | gDNA + P 10^2 | Ch1Unknown | ileS

C04

| Absolute Quantification

| ABS | gDNA | Ch1Unknown | ileS

Details

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

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

Setup: Duplex assay with a 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).

#' Setup: Duplex assay with a 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 full data are located at https://github.com/michbur/dpcR_data as QX100_rawdata.zip.

Author(s)

Michael Jahn, Stefan Roediger, Michal Burdukiewcz

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

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[["D02"]], main = "Well D02", pch = 19)

michbur/dpcR documentation built on Nov. 17, 2022, 5:02 a.m.