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Array Analysis: The Basics

transcription, probes for glass arrays are labeled with two distinct fluorescently labeled nucleotides and both probes are hybridized to the same array. Typically, one sample RNA is labeled with Cyanine 3-dNTP (Cy3) and the other with Cyanine 5-dNTP (Cy5). Each dye produces different color fluorescence. The two labeled RNA populations are hybridized to one glass slide and scanned using a fluorescent imager.


GeneChip
Affymetrix's GeneChips are glass slide arrays manufactured using special photolithographic methods and combinatorial chemistry, which allow the oligonucleotide spots to be synthesized directly onto the array substrate. The analysis procedure specifies that the RNA samples are converted to biotin-labeled cDNA, and each sample is hybridized to a separate GeneChip. The hybridized cDNA is then stained with a streptavidin-phycoerythrin conjugate and visualized with an array scanner.


Data Analysis
Where once the bottleneck in gene expression analysis was the benchwork, with array analysis, it is the computer work. Because a single array experiment can generate thousands of data points, the primary challenge of the technique is making sense of the data. Many commercial companies provide image analysis software, including BioDiscovery (ImaGene) and Imaging Research (ArrayVision). Furthermore, many array manufacturers offer software specifically for the analysis of their arrays and offer the analy
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