title: Candidatus Pelagibacter ubique OSU_SAR11_affychip
status: Public on Sep 01 2009
contact.city: Madison
contact.first: Michael
contact.middle: S
contact.last: Schwalbach
contact.state: WI
contact.address: 1550 Linden Dr
contact.department: Great Lakes Bioenergy Research Center
contact.country: USA
contact.institute: University of Wisconsin-Madison
organism: Candidatus Pelagibacter ubique HTCC1002
  Candidatus Pelagibacter ubique HTCC1062
  Candidatus Pelagibacter sp. HTCC7211
manufacture_protocol: Oligos designed using sequences from three SAR11 genomes (HTCC1062, 1002, 7211) as well as highly similar sequences from the first metagenomic GOS survey (Venter et al. 2004).  No mismatch probes are included on the chip.  All probes target biotin-labeled antisense-RNA.  Probes hard pruned against 16s and 23s rRNA genes.
  Affy description of production (from website):
  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.
  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.
  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.