Oligonucleotides are designed based on these sequences. Photolithography is then used to synthesize these oligos in place on the glass chip. The goal of both of these approaches is to simultaneously examine the levels of expression of as many genes as possible in a single experiment. Often cDNAs from experimental and reference samples are labeled with fluors that fluoresce at different wavelengths. Next, labeled cDNA is hybridized to the array or chip.
Hybridization is detected.
Typically, using scanning laser confocal microscopy. Hybidization can be quantified based on the level of fluorescence relative to a control or reference. This comparison is improved when the two cDNAs were hybridized in a single experiment since this controls the variability that could be introduced by comparing data from separate experiments. Next, comes the challenge of organizing the large amount of data in a way that allows the researcher to extract the biologically important information. Bioinformatics approaches to accomplish this are being developed.