Array Examples

This Affymetrix GeneChip contains oligomer probes for more than 12,000 mouse genes arrayed on a surface of about one square centimeter. Each gene is represented as a set of up to 20 independent oligomers, synthesized by photolithography at 20 different locations or “features” throughout the array. Every probe is accompanied by a mismatch oligomer to detect background or cross-hybridization, synthesized in a feature adjacent to the perfect match probe. An estimate of the total number of features in this image, therefore, is 12,000 genes X 40 paired probes, or 480,000 features not counting control genes and markers.
This view of a portion of the Affymetrix Mouse GeneChip is centered on a grid of 16x16 features. Each feature is 24 micrometers across, about one-fourth the width of a human hair. The grid is surrounded by probe pairs for mouse genes; note that the upper perfect match probe usually gives much greater hybridization signal than its mismatch counterpart directly beneath.
A composite image of a probe microarray printed on a glass microscope slide. PCR fragments were deposited in 1 nl aliquots, producing features about 120 microns in diameter. These probes were used for competitive hybridization of two samples, one labeled with the dye Cy3 and the other Cy5. The ratio of labeled target hybridizing to each probe is reflected by its color: more green means higher amounts of the targeted RNA in sample 1, more red for greater abundance in sample 2, and yellow for equivalent amounts in both samples.
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Last Updated on 9/3/03


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