License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
The following protocol describes the resuspension, dilution, and qPCR of gBlocks gene fragments. gBlocks gene fragments are synthesised double stranded DNA oligos, which can be used for standardisation.
In this protocol, the standard curves generated by the gBlocks in a triplex qPCR are used to determine a Ct cut-off value for the S.Typhi gene targets (ttr, tviB, staG) and the HF183 bacteroides rRNA gene.
qPCR DNA Extraction and Inhibition Control CY5-QXL670EurogentecCatalog #RT-SPCC-Q02
g-blocks details
g-blocks details
gBlocks gene fragments are synthesised double stranded DNA fragments which contain the sequence for the amplicon of interest, in this case for ttr, staG and tviB in S.Typhi, and HF183 bacteroides.
Once resuspended, check the concentration via Qubit or Nanodrop.
If the concentration is not 10ng/ul, carry out your first dilution in step4 to make it 1ng/ul
Create serial dilutions of your stock solution adding 2uL of stock into 18uL of nuclease free water. We recommend carrying out 12 dilutions to create a series of 12 concentrations. We recommend at least 10 replicates split over at least two days.
For example, performing four replicates of 12 dilutions three times on three separate days. This would be two plates each day to include all targets.
qPCR and generating a standard curve
qPCR and generating a standard curve
Prepare the triplex qPCR mastermix described below (or singleplex for HF183)
A
B
Reagent
Volume per reaction (uL)
ttr_F (20uM)
0.25
ttr_R (20uM)
0.25
ttr_P (5uM)
0.5
tviB_F (20uM)
0.5
tviB_R (20uM)
0.5
tviB_P (5uM)
1
staG_F (20uM)
0.5
staG_R (20uM)
0.5
staG_P (5uM)
1
2x Mastermix with ROX
12.5
Nuclease free water
2.5
Table2: Mastermix composition for triplex S.Typhi qPCR. Primer and probe sequences are provided in the qPCR protocol in the TyphoidES workspace.
A
B
Reagent
Volume per reaction (uL)
HF183_F
0.5
HF183_R
0.5
HF183_P
1
10x Control Mix (Eurogentec)
2.5
2xMastermix with ROX
12.5
Nuclease free water
3
Table3: Mastermix composition for the singleplex HF183 reaction. Primer and probe sequences are provided in the qPCR protocol in the TyphoidES workspace.
Aliquot 20uL of master mix for each reaction in a 96-well plate. Add 5uL of gBlock dilution to each reaction.
Ensure that although the reaction is designed as a triplex, you only put one target gBlock in each reaction.
Seal the plate carefully then spin down briefly to gather all reagents at the bottom of the wells and remove bubbles.
Load the plate into the real-time PCR machine after setting it up appropriately and carry out cycling using the following conditions:
A
B
C
Cycle
Temperature (C)
Duration
1
50
2 minutes
1
95
2 minutes
40
95
15 seconds
60
30 seconds
72
30 seconds
Table4: Cycling conditions for all qPCR reactions.
Analysis - determining Ct cut-off
Analysis - determining Ct cut-off
The limit of detection (LOD_95) is the genome copy number/uL and associated Ct value at which a qPCR amplification would be observed 95% of the time. This can be calculated from the results of the dilution series using PROBIT analysis.
We have provided an Excel file to calculate the LOD_95 for you from your data (resource: LOD calculation update 250124.xlsm35KB ). Make sure you allow macros to be run. You will also need to enable the Microsoft Solver add-in. Instructions for doing so are here.
Alternatively you can use the statistical programming language R to fit the PROBIT curve. Example code:
To calculate the GC/uL from the qPCR Ct values of actual samples you can use the equation:
log GC/uL = (Ct – intercept) / slope
where slope and intercept are from the linear regression of the Ct value on log GC/uL generated from the standard curves (e.g. as given in the Excel spreadsheet or from the linear model (lm) fit in R).