Comparison of two probe preparation methods using long oligonucleotide microarrays

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(TM) PowerScrip(TM) fluorescent cDNA (random printing) 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 printing and poly(T) printing, 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) printing methodologly should be viewed cautiously even when high reproducibility is evident.