title: NimbleGen Moraxella catarrhalis BBH18 4x72K custom design GAF array (mapping)
status: Public on Jun 06 2013
contact.city: Nijmegen
contact.first: Hester
contact.last: Bootsma
contact.email: h.bootsma@cukz.umcn.nl
contact.address: Kapittelweg 29
contact.department: Pediatrics
contact.country: Netherlands
contact.institute: Radboud University Medical Centre
contact.phone: +31-243666332
organism: Moraxella catarrhalis BBH18
description: The custom-designed Nimblegen 4x72K GAF microarray design was based on the AluI-restriction fragments of the M. catarrhalis BBH18 genome (de Vries et al., 2010 J Bacteriol 192: 3574-3583).
  Nimblegen probes (50-72 nt) were designed on the 3’ and 5’ ends of all AluI fragments >70 nucleotides (nt) and in case of fragments >400 bp, spaced every ~ 200 bp on both strands. This allows mapping of the transposon insertion with a ~200 bp resolution. Of the 6,085 AluI fragments larger than 70 nt, probes could be designed for 6,003 fragments, resulting in a total of 20,078 experimental probes. In addition to three replicates of each experimental probe, the array contained 11,803 negative-control probes with a length distribution and G+C content similar to those of the experimental control probes.
  Moraxella catarrhalis GAF.ndf
  Moraxella catarrhalis GAF.pos
manufacture_protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.