title: [Glyco_v4_Mm] Affymetrix Glyco v4 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: Mus musculus
description: The Glyco v4 array was designed in 2008 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 array also includes "GC bin" probes (100 for each bin) for use in background correction. These probes are used as an alternative to the PM/MM-based background correction methods. Mismatch probes are not used on this array.
  
  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: "GLYCOv4_Hs" and the mouse CDF file is named: "GLYCOv4_Mm".
  
  Probeset design: The v4 array uses 25 probes to target the first 600 bases from 3' end of each transcript. This region is called Probe Set Region 1 indicated by a psr1 in the probe set name. Up to 4 additional sets of  5 probes are used to target the transcript in 280 base increments upstream (towards the 5' end of the transcript) from the first 600 base region. These are indicated as psr2, psr3 and psr4 in the probeset name. If no psr appears in the probe set name, this indicates that probes are targeting Probe Set Region 1 and that no additional probe sets were designed upstream (towards the 5' end of the transcript) for this transcript accession. Generally only data from Probe Set Region 1 are shown. Data from psr2-4 is generally ignored. All probes are for antisense target and may include a suffix of "_s", "_x" consistent with Affymetrix probe design algorithms used for all commercial Affymetrix 3' arrays.
manufacture_protocol: see manufacturer's web site