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Approximately equal fluorescence per spot on the array between channels on one slide indicated presence in both strains of the same phenotype, unequal fluorescence indicated presence only in one strain of the same virulence phenotype, and fluorescence not significantly different from the background indicated absence in both strains of the same virulence phenotype.
GenePix Pro software was used to determine the total fluorescence signal from each spot on the array.
We calculated the standard deviation of the log2 ratio of these intensities amongst the nine times (0, 15, 30, 45, 60, 75, 90, 105, and 120 minutes) at which expression was determined for each spot on the array.
Single-stranded labeled amplified products were hybridised to the arrays and a signal intensity value was determined for each spot on the array by calculating the quantitative staining value using IconoClust software (version 2; CLONDIAG).
With primers within and telomeric (FA and RX groups, Table 2) to the genomic fragment, we performed PAMP and array hybridization, and identified a single spot on the array (shown as a single peak in Figure 6A).
Transcript abundance is assessed by the relative intensity of signal from each spot on the array.
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The intensity of each spot on the arrays was quantified with a densitometer.
The resulting data were then expressed as the log(2) ratios of the signal in the two dye channels for each spot on the arrays.
Thereafter, two deliveries of 1 μl saturated sinapinic acid (Ciphergen Biosystems Inc ., diluted in 50% acetonitrile and 0.5% trifluoroacetic acid, were added to each spot on the arrays.
Only 16,252 transcripts out of 16,399 were left for further analyses after processing the intensity values of each spot on the arrays and after normalization.
Each spot on the arrays in the terminal study was also subjected to two laser conditions (high laser and low laser).
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