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For this subset of markers the possibility of multiplex amplification was tested, as were the variability and allele range of these markers.
Multiplex amplification was performed in two different ways.
However, the capacity of multiplex amplification was limited by interaction between primers.
Multiplex amplification was successful under such conditions, and we finally tested DNA of 44 samples from two natural populations of A. miyabei subsp. miyabei f. miyabei at Bibi and Kyouwa in Chitose city, Hokkaido, Japan (Appendix 1).
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Whilst LAMP is inexpensive to perform, primer design is complex and multiplex amplification is at present difficult.
This screening detected 16 polymorphic loci that consistently amplified (Table 1); however, only 12 with adequate sizes for multiplex amplification were selected to genotype the whole set of samples.
Multiplex amplifications were performed in mixtures containing 1.5 mM MgCl2, 0.2 mM dNTPs and 0.05 U of Taq recombinant polymerase per µl.
Multiplex amplifications were carried out in a total volume of 15 μL.
The first multiplex amplifications were carried out using equal concentration of locus specific forward and reverse primers (0.2 μM each) to screen eight individuals.
Based on the results, the minimum required quantity of target DNA for multiplex PCR amplification was 1 ng/μL and for color and absorption alteration of solution in colorimetric assay was 20 ng/μL.
Multiplex PCR amplification was performed for sjTREC, together with the CD3γ chain, in 100 µl (10 min for initial denaturation at 95°C, 30 sec at 95°C, 30 sec at 60°C, 2 min at 72°C for 22 cycles) using the 'outer' 3'/5' primer pairs.
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