title: NimbleGen Enterococcus faecalis OG1RF 12x135K version1
status: Public on Apr 15 2013
contact.city: Milwaukee
contact.first: Dusanka
contact.last: Vesic
contact.email: dvesic@mcw.edu
contact.state: Wisconsin
contact.address: 8701 Watertown Plank Road
contact.department: Microbiology and Molecular Genetics
contact.country: USA
contact.institute: Medical College of Wisconsin
organism: Enterococcus faecalis OG1RF
description: NimbleGen design  ID OID33524.  ORF-based expression design for 2,477 genes from Enterococcus faecalis OG1RF (derived from annotation via RAST - Aziz et. al. 2008. BMC 9:75 , as described by Frank et al (2012) Infect. Immun. 80:539) with eighteen 24-mer probe pairs (PM/MM) per gene.  Each probe is replicated 3 times.  The design includes random GC and other control probes.
  The ORF sequences used in design of this microarray were derived from a custom annotation of the E. faecalis OG1RF genome by RAST (Aziz et al 2008. BMC 9:75), as previously described by Frank et al (2012 Infect. Immun.  80:539), which was performed before the publicly available OG1RF annotation was completed. As a result of this RAST annotation, each ORF identified was assigned a unique RAST feature ID (see the OG1RF RAST output file provided). These ORFs were queried by BLAST against the E. faecalis V583 genome to identify the best hits (EFnnnn locus identifiers), which was the identifier that was subsequently used when assigning names to the array probes. If no clear hit was identified in the E. faecalis V583 genome by BLAST, the RAST-annotated ORFs were given arbitrary OG1RFnnnn identifiers, which were used when assigning names to the array probes.
manufacture_protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.