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When the Tm reached to 60°C, distinct bands indicated the lowest concentration of mixed template was 10 viral particles/ml for multiplex DPO PCR.
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The mixed templates are composed of CTAB and glucose with a molar ratio of 1/1.
The three samples with the addition of different amounts of the above-mixed templates were prepared to study the effects of dosage.
To test the ability to detect two different NDV variants in a single sample, a series of mixed template PCRs was prepared.
Briefly, 2 μl of cDNA template was mixed with 12.5 μl SYBR Green master mix containing Taq and dNTPs (Qiagen), 8.5 μl DNase-free water and 1 μl each of forward and reverse primers.
For a 20 μl PCR reaction, cDNA template was mixed with TaKaRa Ex Taq (TaKaTa) plus the appropriate primers to a final concentration of 200 nM each.
Briefly, 2 μl of cDNA template was mixed with 1.25 μl of specific primers and probes labeled with FAM-reporter dye.
Briefly, 0.1 ng template was mixed with 0.2 mM each dNTP, 0.2 μM each primer, 1X Mutazyme II Buffer, and 2.5 U Mutazyme II in 50 μL.
The control template was mixed with genomic DNA that had undergone digestion and random ligation so that PCR efficiency was not affected by the total amount of DNA present (similar to the 300 ng/reaction for the real 3C samples) (16).
In all, 20 ng of the reversed-transcribed cDNA template was mixed with SYBR Green PCR Master Mix Applied BiosystemsStockholm, Swedenden) and amplified using a 7500 Real-Time PCR System (Applied Biosystems), with the following program: 40 cycles, with each cycle consisting of a denaturation step at 95 °C for 15 s and an annealing/extension step at 60 °C for 1 min.
The template was a mixed DNA from 111 prostate cancer patients to generate DNA fragments with heterozygous alleles.
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