What Is a Microarray

Microarrays are densely packed arrays of DNA probes which are fixed to a solid substrate in a predetermined matrix on a small surface area. The arrays are then amenable to hybridization with RNA or DNA nucleotide samples isolated from experimental cultures. The nucleotides are labeled before hybridization and afterwards the fluorescent intensity from each probe spot can be measured. When compared to a control, the fluorescent intensity from each spot can be taken to indicate the relative level of that nucleotide present in the sample. Because the arrays contain probes for all of the open reading frames in a genome, this is achieved on a genome-wide scale with each array used.

There are two commonly used forms of microarray, the spotted array and the Affymetrix gene chip, which differ in their method of construction and use. The choice of one array type over another depends largely on cost, application, and commercial availability as well as the need to design and construct specialized arrays within the laboratory. The fundamental differences between the synthesis methods and their use and analysis mean they often show varying degrees of agreement with one another and the expression levels that they report are usually not amenable to direct comparison [10].

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