Affymetrix based applications:

Affymetrix technology includes a growing number of applications which exploit photolithographic/chemical coupled synthesis of oligonucleotides on silica wafer. Applications include:


 Affymetrix GeneChip® Arrays EXPRESSION

The use of Affymetrix GeneChip® expression arrays allows the simultaneous detection and quantitation of the expression levels of thousands of transcripts from a given sample. Expression arrays are available for many species, read the full list.

With the most recent human array, the HG-U133Plus 2.0 the expression level of over 47,000 human transcripts and variants, including 38,500 well-characterized human genes can be assessed in a single experiment.

With the recent Mouse Expression Set 430 2.0 (MOE430 2.0) 39,000 transcripts and variants corresponding to 34,000 mouse genes are represented on a single GeneChip.



 Affymetrix HuSNP Mapping Assay GENOTYPING

The GeneChip® Mapping 100K Set is the first in a family of products for whole-genome association studies. It is comprised of a set of two arrays that enable genotyping of greater than 100,000 SNPs with a single primer.

The GeneChip® Mapping Assay uses a simple approach for reducing complexity of the genome, allowing efficient genotyping with a microarray containing over 100,000 SNPs.

Total genomic DNA (250ng per array) is digested with a restriction enzyme (XbaI or HindIII) and ligated to adapters that recognize the cohesive four basepair (bp) overhangs. All fragments resulting from restriction enzyme digestion, regardless of size, are substrates for adapter ligation. A generic primer that recognizes the adapter sequence is used to amplify adapter ligated DNA fragments. PCR conditions have been optimized to preferentially amplify fragments in the 250 to 2000 bp size range. The amplified DNA is then fragmented, labeled, and hybridized to the specified GeneChip Mapping Array.