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This result underscores the importance of optimizing PCRs for different primers.
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By optimizing PCR conditions, the frequency of PCR recombination can be reduced [ 24].
Additional file 6: List of primers used and optimized PCR conditions for all markers.
To optimize PCR amplification conditions, we designed primers for the ompA gene (ompA3e: 5′-CTC CAA CATTATT CGC TCT GGC-3′ and ompA4b: 5′-GCA GTT CGC CCT TGC CTT-3′) and risA gene (RisA1c: 5′-AAA ACCACCATCTCCACA TCC GC-3′ and RisA2d: 5′-ACA GGTGAGCAGCATCAGGAGG GC-3′).
To optimize PCR at various annealing temperatures, we evaluated each primer pair using a gradient PCR procedure.
Optionally to optimize PCR experiment, standard PCR conditions can be modified through the primer-parameters.
We would like to thank Hien Fuh Ng and Yan Ling Wong for helping us to design primers and optimizing the PCR for the 3 new gene markers in this project.
Although we did not optimize the long PCRs for each group, we are confident that optimization on a per group basis (e.g., increasing template volume, altering annealing temperatures, and/or long PCR profiles) and/or the use of fresh tissue for DNA extractions would improve success rates.
102 µl diluted cDNA reaction was mixed with 2x RT2 qPCR Master Mix (SA Biosciences) and H2O to reach a final volume of 2.7 ml. 25 µl of the mixture was added into each of the wells of the RT2 Profiler PCR Arrays (SA Biosciences) and PCR was carried out on the Roche480 Cycler using a cycling program optimized for PCR arrays (SA Biosciences).
The specific chemistry and quality of the reaction components play an important role in optimizing Q-PCR reactions, underlining the requirement for critical evaluation in order to overcome subjectivity inherent to the Q-PCR assay [ 6].
Furthermore, difficulties in optimizing semiquantitative PCR assays have limited the utility of these methods for MRD.
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