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Interestingly, a gap exists between the two amplification frequency bands in the range 4 5.5 Hz, implying for two types of soils with different elastic properties.
Conventional TaqMan detection chemistry requires that the probe is complementary to the region within the amplified portion of the template between the two amplification primers.
This low level of variability was also evident when comparing results between the two amplification methods (REPLI-g and GenomiPhi), suggesting comparable results irrespective of the manufacturer's protocol.
The results of these statistical tests strongly indicate, as expected, a high agreement within the same amplification method but a very low agreement between the two amplification methods.
Unsupervised clustering of the 12 individual datasets showed the same chronological clusters as found with PCA, that is, the largest difference was between tumor and bronchus and the second difference was between the two amplification procedures (data not shown).
Using the criteria for statistical significance described in methods, 309 ESTs (14%) showed different expression levels between the two amplification methods with 131 ESTs in the S' group and 178 ESTs in the M' group.
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When we observed a discrepancy between the consensus sequences from each of the two amplifications we performed a third amplification and used the consensus sequence from all three amplifications (see Additional File 1).
The R2 value of 0.72 is indicative of significant correlation between these two amplification methods for the subset of transcripts that are detected in both, an outcome similar to that seen in previous comparisons of WT-Pico vs IVT [ 20, 24].
After normalization of signals [ 22], several genes gave rise to significant signal differences between these two amplification times.
In contrast, the correlation between the two different amplification methods for both technical repeats was considerably lower, R2 = 0.52,, indicating bias in one or both amplification techniques.
Furthermore, PCR with an internal primer designed to include an allele-specific SNP at the 3′ end (site 443) showed differentiation between the two variants, 100%and4.2%2% amplification in green and red variants, respectively.
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