Exact(4)
RNA extraction was performed in triplicate for each cell line, and each qPCR reaction (each sample, each gene) was repeated thrice.
For an experiment that examines two hybridizations that involve the same RNA sample, each gene is matched with two intensities, S1 and S2.
This procedure resulted in a matrix where each of the 40 clusters is a sample, each gene is a variable, and each elements in the matrix have the value 0 or 1.
Using the cnaGENE function of SWITCHdna, the segment output file was converted into an indicator matrix, where for each sample, each gene's copy state was represented as −1 = loss, 0 = no change, 1 = gain.
Similar(56)
For individual samples, each gene was tested in triplicates and the mean of the 3 cycle threshold values was used to calculate relative expression levels.
Using the remaining 90% of samples, each gene was scored for its association with the mutation status in the training procedure (table 1).
The average depth of coverage for each sample for each gene per library at quality score cut-off from 10to2525 was 76.01 (average depth of coverage for each sample for each gene across libraries = the total depth of coverage/(the number of genes × number of libraries × number of samples)).
The threshold cycle (Ct) value for each amplified sample and each gene of interest was measured by using the MxPro QPCR software (Stratagene), and values were normalized to GAPDH expression by using the 2-ΔΔCt method (Frisch et al. 2016).
At least five replicates were performed on each sample for each gene.
For each sample and each gene, PCR runs were performed in triplicates.
For each sample and each gene, PCR runs were performed in duplicates.
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