Microarrays:

The microarrays that we use are small DNA spots placed in a grid format on specially coated slides, so the DNA sticks to it.  Each DNA spot represents the insert DNA of a cDNA clone.  The insert DNA was amplified by the polymerase chain reaction (PCR) to provide many copies for each printed spot.

The inserts are amplified from cDNA clones that are stored in microtiter dishes.  Each clone has a unique address, such as A01or B12, so it can be retrieved later.  After PCR amplification, DNA from each clone is robotically printed on a chemically treated glass slide.  The DNA spots on the slide are screened with two fluorescence-labeled probes, usually one represents the untreated control tissue and the other represents the tissue after treatement. The messenger RNA (mRNA) is isolated from each of the two tissues and independently labeled.  mRNA is the product of genes in the tissue that are being transcribe, ie. represents genes expressed at the time of tissue harvest.

Fig.1.

The microarray is scanned with a laser beam, first at one wavelength to collect fluorescence data representing one probe (tissue), then is scanned at a second wavelength to collect data representing the second probe and tissue.  A computer compares the amount of fluorescence at each spot on the microarray for each probe.  Through the use of computer software, the ratio of fluorescence is obtained and correlated with the clone address so the investigator knows which gene (spot on the slide) was expressed more in treated tissue as compared to control tissue.