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Since this observation was true for five independent TERT qPCR assays spanning different exon junctions (Figure S5 A-D), it suggests that the microarray signal for this gene is artificially high in these cells, or that the amplification of the transcript is somehow prevented.
Due to the negative relationship between Ct and expression level, an improved method of the previous report [37] was used to compare the results of qRT-PCR and microarray by plotting the -ΔCt values of qRT-PCR versus the log2 of the microarray signal for each miRNA.
However apart from F9801A, no other strain gave a microarray signal for these probes, including C. botulinum strain 213B.
Using a cut-off value of 0.30 (because of very high signals), only one strain, F9801A, gave a positive microarray signal for all 19 CDSs.
The results of both assays were compared by plotting the ΔCt values of qPCR-array versus the log2 of the microarray signal for each miRNA.
cel7a/cbh1, the major cellobiohydrolase, is co-regulated with cel6a/cbh2, but due to saturation of the microarray signal for this transcript, we were not able to use the transcript pattern of cel7a/cbh1 to evaluate coregulated genes of cellulases.
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It might then be possible to normalize solid-state RNA (and DNA) microarray signals for the same target by inducing duplex formation in target sequences adjacent to the probe binding site using a similar strategy.
The distribution of microarray signals for the gold standard genes is not significantly different from the dataset as a whole, so they provide a fair representation of the entire dataset, and do not just represent the most well-measured genes in the dataset.
This resulted in alignment-mapped microarray signals for between-species comparisons.
Figure 2 shows that the CN provides significant improvement of the separation of the paired microarray signals for all discussed gene markers of lung AC.
Moreover, the important task of correcting microarray signals for RNA degradation effects remained unsolved at least in single chip applications to our best knowledge.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com