Relative expression was calculated between B. rapa and B. oleracea or between the reference sample (1 to 1 parent mix) and the six allopolyploid samples using PROC MIXED in SAS Version 9.1: This analysis assumed equal primer efficiencies and used Tubulin CT values to calculate baseline corrected CT values for each gene of interest [45].
We used it for calculating the distribution of the Pearson correlation coefficient between the reference sample concentrations and the 1000 cell sample concentrations for each gene (Fig. 2a).
Only one marker in a potential CNV which was detected in only one animal failed validation by showing no difference between the reference sample.
Relative quantification (RQ) values were expressed using the formula: (2Ctr − Ctt) where Ctr − Ctt represents the difference between delta Ct between the reference sample (untreated control) and tested samples (resveratrol treatment).
Additionally, we found that the level of correlation coefficient for the CNVs validation is highly dependent on the copy number differences of CNV intervals between the reference sample and the test sample, i.e., the less difference of copy number, the lower the calculation of correlation coefficient.
Four hybridizations, including the dye-swap experiment, were carried out between the target and the reference samples.
In contrast, the HNE/PI3 ratio was not statistically significant different between the controls and the reference samples (two sample t-test, P = 0.105).
For each patient long-term culture of tumorigenic GBM cells, gains and losses were assigned by comparing the peaks between the patient and the reference samples (DNA from normal human astrocytes).
To determine the contribution of individual genera to the average Bray-Curtis dissimilarity between the experimental samples and the reference samples, the similarity percentages analysis (SIMPER) was applied to nematode relative abundances.
This approach generated sufficient amount of reference samples for the microarrays, facilitated better comparison between the two regional arrays and also highlighted the variations in gene expression between the biological replicates but not the reference samples.
