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The correlations between variations in gene expression and methylation should ideally be performed with expression data generated from the same individuals used to perform the methylation analysis.
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In order to obtain secretion efficiency data, different expressed signal peptides were analysed and time course studies were performed with expression constructs containing different promoters.
Nuclear co-transformation of P. tricornutum was performed with expression vector nuPsb28-C-EYFP and resistance vector pFCPFp-Sh ble, as previously described [18].
For their research, a total of 8 time-course experiments were performed with expression data collected at 18 to 22 times on 15-minute intervals.
A rapid analysis was performed with Expression Console (Affymetrix, MAS 5 normalisation).
Signal intensities for all ESTs on the array were then filtered (see below) and Quality control was performed with Expression Console™ 1.0.2467.39138 (Affymetrix) on RMA normalized data.
Comparisons of MET expression with clinical parameters including survival of the patients were performed with MET expression as a dichotomised variable classified as high or low.
First experiments were performed with the expression vector, pHR98/3, under the control of a constitutive and high-level expression promoter.
Subsequent data processing was performed with Nexus Expression 3.0 (BioDiscovery; El Segundo, CA, USA) as described elsewhere [22].
An ANOVA test was performed with the expression data of each spot.
Univariate cox analyses were performed with gene expression data as a predictor and overall survival in months as the response.
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