Among the 32 studies that we identified, only three concluded that microarray platforms do not correlate well (<10%).
Overall the two microarray platforms did not reveal a clear correlation between differential CpG methylation and differential mRNA expression in long-term culture or aging (Fig. 4B,C).
Although microarray platforms do not enable direct comparison of intensities between genes, that limitation does not affect our approach since gene-to-gene variations in intensity are included in the β ij s.
An investigation of the probe sequences of the most highly expressed genes in the microarray platforms did not reveal noticeable differences in the number of possible sequence matches between those found in MPSS and those not found in MPSS.
In contrast to the conventional miRNA microarrays, our platform does not require RNA extraction, labeling and target amplification, thus significantly reducing both the sample preparation steps as well as the total assay duration.
Third, the Illumina microarray platform, strikingly, did not trend well with the sample titration as the absolute fold-change values that followed the sample titrations were observed in only 5-75-7%f genes.
Cytochrome c-1 (CYC1), present in the microarray platform and did not show differences in expression between tissue samples of the transgenic and non-transgenic fish, was used as a reference gene.
To identify house-keeping gene controls, we selected 8 genes from our microarray platform that did not show significant differences between the treatments and whose ratios of expression were not significantly different from one (single t-test, α = 0.05).
Profiling on the individual microarray platforms was done according to manufacturer's specifications.
Mapping across microarray platforms was done using the "Cleanex" database [ 14] to retrieve corresponding gene symbols and Affymetrix probe sets.
