GeneChip Arrays
The Affymetrix GeneChips are the high-density oligonucleotide arrays manufactured by a strictly controlled process combining photolitography and combinatorial chemistry, which resembles the production of microprocessor chips in the semi-conductor industry. Using these technologies it is possible to synthesize very precisely and reproducibly hundreds of thousands of oligonucleotide probes in high density manner. A typical chip contains several hundred of thousands probes, each probe of 5-11 microns in size. Each GeneChip is enclosed in a characteristic cartridge.
Several categories of chips are available depending on the type of analysis and probes present on the chip. The expression chips are the most commonly used chips for transcriptome analysis and contain 11-20 individual probe pairs for each examined transcript. The expression chips are available for variety of eukaryotic organisms including human, mouse, rat, chicken, Drosphila, C. elegans, yeast as well as for a large amount of bacterial organisms (as part of the NimbleExpress program).
The genotyping chips are used for the detection of SNPs (single nucleotide polymorphisms) in linkage and association studies. These chips are currently available only for human and allow collecting genotypes from as much as 10K, 100K or 500K SNPs.
Another type of chips are the resequencing chips, which contain probes designed according to the known genomic sequence of a particular organism. The purpose of these chips (currently available e.g. for human mitochondria) is to analyze polymorphism in genomic sequence in individuals.
The exon chips represent a new generation of chips for the transcriptome analysis. The probes on these chips are designed for individual exons of each transcripts, which allows to collect exon-level expression data and analysis of alternative splicing.
Using the tiling chips it is possible to perform the most comprehensive analysis of the whole genome combined with transcript mapping. The probes are designed (tiled) at an average resolution of 35-bp throughout the whole genome, thus enabling a more accurate view of the transcription and discovery of novel RNA transcripts.
Affymetrix is also able to produce the custom chips to study any genome (MyGeneChip Custom Array Services). The content of these chips is tailored according to the researchers requests.
For the whole catalogue of GeneChip arrays visit Affymetrix website.