title: A genome proxy array for profiling marine micobial communities
status: Public on Oct 31 2007
contact.city: Tucson
contact.first: Virginia
contact.middle: Isabel
contact.last: Rich
contact.email: vrich@email.arizona.edu
contact.state: AZ
contact.address: 1041 E. Lowell St.
contact.country: USA
contact.institute: University of Arizona
organism: uncultured crenarchaeote 4B7
  Prochlorococcus marinus subsp. pastoris str. CCMP1986
  uncultured marine alpha proteobacterium
  uncultured marine gamma proteobacterium EBAC31A08
  uncultured marine group II euryarchaeote 37F11
  uncultured Pseudomonadota bacterium
  uncultured crenarchaeote 74A4
  uncultured marine bacterium 440
  uncultured marine bacterium 577
  uncultured marine bacterium 583
  uncultured gamma proteobacterium eBACHOT4E07
  uncultured marine bacterium EB0_41B09
  uncultured proteobacterium 60D04
  uncultured proteobacterium 65D09
  uncultured marine group II euryarchaeote EF100_57A08
  uncultured marine bacterium EB000_55B11
description: ***Design Overview***  The prototype microarray targeted thirteen BAC or fosmid genome fragments (20-160kb) from both bacteria and archaea (Table 1), recovered from a variety of marine habitats (Table 2), as well as the cyanobacterium Prochlorococcus MED4. These clones were originally sequenced because of the presence of taxonomic marker or specific functional genes. This array consisted of sets of 70-bp oligonucleotides targeting each genome or genome fragment (Fig. 1), dispersed along the target sequences with no more than one probe per gene, and excluding rRNA genes as targets. The probes were selected solely based on theoretical thermodynamic properties and GC content (~40%); that is, probe selection did not focus on specific genes or regions, but simply produced the “optimal” probes for each genome proxy based on the probes’ predicted hybridization properties. rRNA genes were excluded, because this probe design approach, which avoids sequence alignments and considerations of RNA secondary structure, would be unlikely to result in useful rRNA probes. Furthermore, rRNA probes of traditional design could not be included on the array because their appropriate hybridization conditions would be very different from those of this array’s probes.
manufacture_protocol: ***Microarray construction***  Oligonucleotides were synthesized (Illumina, San Diego, California), suspended in 3XSSC to a concentration of 40pmol/μl, and spotted on homemade poly-L-lysine-coated glass slides using a QArray 2 microarraying robot (Genetix, Hampshire, England). Six replicates of each probe were spotted.