Phenotype microarray analysis measures the reduction of tetrazolium dye (see experimental section).
Microarray analysis measures the level of mRNA, however, protein expression may be a more accurate measure of cellular function, and does not always mirror mRNA expression.
First, standard methods of microarray analysis measure mRNA abundance, not mRNA synthesis or mRNA decay, and, therefore, do not provide any information regarding the mechanisms regulating transcript levels.
To independently test the validity of the differential expression signatures determined by microarray analysis, we measured the expression patterns of some of the putative biomarkers.
Relative expression of the miRNAs identified from microarray analysis was measured by real-time PCR.
Variable results include those results found to have no significant change by microarray analysis as measured by t-test.
The quality of RNA used for microarray analysis was measured using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), according to the manufacturer's instructions.
In addition, expression of several genes thought to be potential candidate genes, based on their roles in carcinogenesis but not found to be differentially expressed by microarray analysis, were measured by qRT-PCR.
For example, a decreased expression of Trp53 in microarray analysis was measured only in two probe sets that recognise multiple alternative transcripts from the same gene each, whereas a third definite probe set did not recognise any modulation of expression.
Using microarray analysis we measured the mRNA levels from each of these four cell lines specifically identifying the expression levels of GPCRs and over a hundred of GPCR-related gene products and report them here.
