title: [GLYCOv3_Hs] Custom Affymetrix Glyco v3 GeneChip
status: Public on Oct 23 2010
contact.city: La Jolla
contact.first: Steven
contact.last: Head
contact.email: shead@scripps.edu
contact.state: CA
contact.address: 10550 N Torrey Pines Rd
contact.country: USA
contact.institute: The Scripps Research Institute
contact.phone: 858 784-2263
organism: Homo sapiens
description: The Glyco v3 array was designed in 2005 and consists of probesets targeting genes coding for glycosyl transferases, carbohydrate binding proteins, glycan degradation enzymes, nucleotide sugar transporters, mucins, adhesion molecules, chemokines, cytokines, growth factors and their receptors, interleukins and their receptors and proteoglycans. In addition, a set of "housekeeping" and control genes are included on the array. The array contains probe set for both mouse and human gene sequences and can be use to analyze RNA from both species.
  
  This custom chip is to tile pre-selected probes from the Affymetrix HGU133 set, the MOE430 sets, the v1 custom array, and the v2 custom array.  We kept the original 11 probepairs from these pre-selected probes, while adding 10 more newly designed probepairs for a total of 21 probepairs per probeset within the 3' terminal 600 bases of each targeted transcript. Standard Affy controls (houskeeping and normalization genes) remain at 11 probepairs per probe set.
  
  This array also includes 8505 "GC bin" probes for use in background correction. GC content ranges from 3/25 to 25/25. These probes can be used as an alternative to the PM/MM-based background correction methods.
  
  There are separate library files for human and mouse probesets. The human library file includes all probesets on the array except mouse probes and vis versa for the mouse library file.  The human CDF file is named: "GLYCOv3_Hs" and the mouse CDF file is named: "GLYCOv3_Mm".
manufacture_protocol: see manufacturer's web site