A DNA Microarray Experiment

1. Prepare your DNA chip using your chosen target DNAs. 3. Incubate your hybridization mixture containing fluorescently labeled cDNAs with your DNA chip. 4. Detect bound cDNA using laser technology and store data in a computer. 5. Analyze data using computational methods. 2. Generate a hybridization solution containing a mixture of fluorescently labeled cDNAs.

After this hybridization step is complete, a researcher will place the microarray in a "reader" or "scanner" that consists of some lasers, a special microscope, and a camera. The fluorescent tags are excited by the laser, and the microscope and camera work together to create a digital image of the array. These data are then stored in a computer, and a special program is used either to calculate the red-to-green fluorescence ratio or to subtract out background data for each microarray spot by analyzing the digital image of the array. If calculating ratios, the program then creates a table that contains the ratios of the intensity of red-to-green fluorescence for every spot on the array. For example, using the scenario outlined above, the computer may conclude that both cell types express gene A at the same level, that cell 1 expresses more of gene B, that cell 2 expresses more of gene C, and that neither cell expresses gene D. But remember, this is a simple example used to demonstrate key points in experimental design. Some microarray experiments can contain up to 30,000 target spots. Therefore, the data generated from a single array can mount up quickly

http://www.ncbi.nlm.nih.gov/About/primer/microarrays.html