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Affymetrix |
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| The GeneChip technology platform consists of high-density microarrays and tools to help process and analyze those arrays, including standardized assays and reagents, instrumentation, and data management and analysis tools. |
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| GeneChip® Arrays |
| GeneChip microarrays consist of small DNA fragments (referred to here as probes), chemically synthesized at specific locations on a coated quartz surface. The precise location where each probe is synthesized is called a feature, and millions of features can be contained on one array. By extracting and labeling nucleic acids from experimental samples, and then hybridizing those prepared samples to the array, the amount of label can be monitored at each feature, enabling a wide range of applications on a whole-genome scale — including gene- and exon-level expression analysis, novel transcript discovery, genotyping, and resequencing. Microarray analysis can also be combined with chromatin immunoprecipitation to perform genome-wide identification of transcription factors and their respective binding sites.
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| Array Manufacturing |
| GeneChip microarrays are a classic Silicon Valley innovation, combining several disciplines to create a new technology and more useful research tool. The integration of semiconductor fabrication techniques, solid phase chemistry, combinatorial chemistry, molecular biology, and sophisticated robotics results in a unique photolithographic manufacturing process that produces GeneChip arrays with millions of probes on a small glass chip. |
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The photolithographic process begins by coating a 5″ x 5″ quartz wafer with a light-sensitive chemical compound that prevents coupling between the wafer and the first nucleotide of the DNA probe being created. Lithographic masks are used to either block or transmit light onto specific locations of the wafer surface. The surface is then flooded with a solution containing either adenine, thymine, cytosine, or guanine, and coupling occurs only in those regions on the glass that have been deprotected through illumination. |
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| The coupled nucleotide also bears a light-sensitive protecting group, so the cycle can be repeated. In this way, the microarray is built as the probes are synthesized through repeated cycles of deprotection and coupling. The process is repeated until the probes reach their full length, usually 25 nucleotides. Commercially available arrays are typically manufactured at a density of over 1.3 million unique features per array. Depending on the demands of the experiment and the number of probes required per array, each quartz wafer can be diced into tens or hundreds of individual arrays. |
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