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These differences, which occurred among independent PCRs using different primer pairs, among individuals and among tissues of individuals, challenge our ability to correctly characterize organellar mtDNA sequences in this taxon.
If there was a shared IS6100 element, a 0.9-kb DNA fragment containing IS6100 could be amplified by PCR using different primer pairs.
Thus, for a multi-gene PCR assay, more steps using different primer pairs are needed to generate an ideal product for genotyping.
We tested samples from all patients positive for T. whipplei twice by RTq PCR using different primer pairs and probes.
Despite several attempts using different primer pairs we could not obtain a reproducible expression pattern of the AsCBF2 gene.
In a few cases, PCR attempts using different primer pairs and cloning methods failed to produce sequence data (see Additional file 6).
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Further extensive PCR using different primer pair combinations (of those shown in Fig. 2C) confirmed that no full-length transcript of AHK5 was present in the mutant lines (Data S1).
To confirm this result, three additional PCR experiments were performed for each putative gene boundary which would be found in a coexistence scenario using different primers (pairs 17 22 on page 2 of Additional file 1).
However, because the decrease of RBCS1 gene expression was confirmed by qPCR experiments using different primer sets, including one pair designed to the RBCS-coding sequence that should be extremely conserved within the coffee RBCS gene family, this hypothesis seems unlikely.
The level of CYBB mRNA was quantified using two different primer pairs, compared with the level of the endogenous control, β-Actin (Eurogentec), and expressed as relative quantities compared with the WT cell line using the ΔΔCT method [21].
All samples were screened for the presence of mammalian, bird and lizard DNA using twelve different primer pairs (Text S1).
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