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A set of primer pairs was rationally designed, which amplified 6 overlapping fragments encompassing the whole genome.
From this dataset, a set of primer pairs (15) was validated by polymerase chain reaction with 86% consistent amplification, confirming the accuracy of the in silico prediction.
A set of primer pairs specific for those target genes was designed and employed in the SYBR Green-based multiplex RTi-PCR assay.
The PCR method was standardised using another set of primer, DITRYF/R, and 400 bp was amplified from blood and tissue samples of experimentally infected animals.
Finally, a set of primer pairs were designed, and a validation test showed that 58 of 220 new primers can be used in rice bean and 53 can be transferred to mung bean.
A multiplex PCR was designed for the differential diagnosis of the two parasite species by targeting the 18S rRNA gene with a set of primer combinations, amplifying DNA fragments of 1451-bp and 833-bp for P. falciparum and P. vivax, respectively.
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To begin development on our dimer prediction algorithm PrimerDimer, a set of primer-dimer artefacts were first sequenced to assess the types of primer-primer interactions that cause dimer formation (Supplementary Fig. S1).
Despite the small set of primer-taxa, each core-ortholog was extended by at least one fungal sequence.
PCR cycling conditions were as follows: 1st cycle: 94°C for 2 min; Subsequent cycles (see Table 1 for the total number of cycles using a set of primer-pair) for amplification were as follows: 94°C for 30 sec, a specific annealing temperature for the primer set (see Table 1 ) for 30 sec and 72°C for 20 sec.
Considering minimum repeat number criteria such as six for di- and tri- nucleotides and four for tetra-, penta- and hexa-nucleotides, a sub-set of primer pairs were developed for only 77 SSRs.
The identification of germline T gene duplication in familial chordomas [10] prompted us to perform quantitative real-time PCR in our set of sporadic chordomas using one set of primer/probe targeted to T and a reference control primer/probe set targeted to MCM7.
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