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A gene chip is used in microarray experiments where a specific probe is assayed to the plate to see where it hybridizes. You can pick out which genes are up or down regulated based on the standard you compare to (the chip) which the researcher knows the exact location of each gene.
Presently, there are a variety of ways to use this assay. Scientists can employ this assay to evaluate the expression of a gene, SNPs(single nucleotide polymorphisms) within the genome, and whole genome genotyping. All of the above techiniques, can be done using bead array technology with gene chips.
Bead array technology uses silica beads that are conjugated to oligonucleotides. These beads sit in tiny wells that have been etched on a glass/fiberoptic plate. The beads are then incubated with the genetic material of interest.