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The flexibility of the DNP instrument centered around the QO MW bridge will provide an efficient means to collect DNP data that is crucial for understanding the relationship between experimental and sample conditions, and the DNP performance.
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Transcript levels were assayed 3 times in each sample, and the fold-change ratios between experimental and control samples were calculated.
Each transcript in each sample was assayed three times and the fold-change ratios between experimental and control samples were calculated relative to β-actin.
The statistical significance (P value) between experimental and control samples was determined using the Student's t-test.
Changes were measured for each gene as ratios of signal between experimental and control samples.
Differences between experimental and control samples with P<0.05 were considered to be statistically significant.
Fold changes were then calculated between experimental and control samples: fold change = 2^ ΔC texperimental − ΔC tcontrol).
Half of the hybridizations were done with the Cy3 and Cy-5 dyes swapped between experimental and control samples.
At 24 h post-infection, a small fraction of transcript fragments differed in intensity between experimental and control samples.
Both fold change and l o g2 fold change of expression profiles (as RPKM) were computed between experimental and uninoculated samples.
Differential gene expression between experimental and control samples was determined by using linear modeling as implemented in the R/Bioconductor package "limma".
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