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Although many miRNAs were aberrantly expressed after RDX exposure, almost all detected miRNAs, either in control or in treated mice but not in both, gave low microarray signals, suggesting these miRNAs were expressed at low levels.
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Most of the remaining cDNAs corresponded to spots of low-intensity signal, suggesting that microarray hybridization failed to reach the sensitivity of the SSH procedure to detect low-abundance transcripts.
The microarray signals were analyzed using the Affymetrix RMA algorithm.
Microarray signals were determined using Affymetrix Microarray Suite 5.1.
To compare qPCR-array and microarray assays, the log2 of microarray signals was used.
We found that 18 of the top 26 candidates (69%) show high microarray signal or POLII gene body occupancy, suggesting that they are actively transcribed during 3T3-L1 differentiation.
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.
These findings suggest that technical factors, such as a slightly non-linear dynamic range among the lower microarray signal intensities, may be causing the slightly skewed distributions.
The microarray signal was extracted using GenePix.
The presence of miRNA was determined based on a corresponding microarray signal of greater than [mean + 2 × standard deviation] of the negative control signals, from which the most and least intense signals were removed.
After fully correcting the subtype from the result of microarray signal intensity, the microarray output method combined with bioinformatics tools, identified and monitored genetic variations of H5N1.
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