With the completion of the Human Genome Project, the microarray technology has evolved into a sophisticated platform by which complex diseases such as cancer, can be studied at the genome, transcriptome, and proteome levels. Here, various microarray platforms, namely comparative genomic hybridization, cDNA, oligonucleotide, and protein-based microarrays are exploited to study genomic copy-number changes in a human cancer cell line and correlate these genomic aberrations with their expression at mRNA and protein levels. The protocols described therein can be assimilated for the study of other human tissues including cancerous ones.

The use of oligonucleotides as a capture platform for microarray-based experiments is gaining popularity. Oligonucleotide-based microarrays involving various probe preparations have been compared by a number of researchers. Limited data are available, however, regarding the concordances and efficacies of various probe preparations on long oligonucleotide-based microarrays. Accordingly, the current investigation assesses two labeling methods, namely Atlas PowerScript fluorescent cDNA (random priming) and T7 in vitro transcription cRNA [poly(T) priming] labeling kits. Our data revealed that a high degree of reproducibility among the examined genes for each assay used with correlation coefficients of 0.93 and 0.94 for random priming and poly(T) priming, respectively. It is worthy of note, however, that when the two assaying methods were compared, the data showed a poor correlation coefficient. A confirmatory step involving real-time reverse transcription PCR (RT-PCR) of 18 selected genes favors the superiority of the cDNA fluorescent labeling over the T7 labeling method. Overall, the microarray results generated by the poly(T) priming methodology should be viewed cautiously even when high reproducibility is evident.