title: Escherichia coli O157:H7 virulence and regulatory array
status: Public on Jul 01 2006
contact.city: Lubbock
contact.first: Scot
contact.last: Dowd
contact.email: sdowd@pathogenresearch.org
contact.state: TX
contact.address: 4321 Marsha Sharp Fwy
contact.department: MBRI
contact.country: USA
contact.web_link: http://www.medicalbiofilm.org
contact.institute: MBRI
contact.phone: 806-789-6879
organism: Escherichia coli O157:H7 str. EDL933
description: epoxide coated
manufacture_protocol: Using the transcriptome of E. coli O157:H7 EDL933 an oligonucleotide microarray, made up of 43-45 mers, was designed.  Based upon available funding we were able to choose 610 genes originally, in the current submission 2 additional genes were added for a total of 612 genes [see Additional file 1] (including 10 negative control genes derived from pig EST sequences).  The genes on the O157 array were selected based upon their being associated with virulence or with regulation of virulence genes.  Specifications of oligos were based upon various design characteristics such as temperature of melting, 3’ location, specificity, lack of repeat nucleotides, etc. [32].  Oligos were synthesized and normalized in concentration by Integrated DNA Technologies Inc. (Coralville, IA).  Oligos were resuspended in Epoxide Slide Spotting Solution and printed onto Epoxide Coated Slides (Corning Inc., Corning, NY) using a GeneMachine’s Omnigrid Accent microarray printer (Genomic Solutions Ann Arbor, MI).  Each array consisted of duplicate elements for each gene and each slide contained a duplicate array with spot sizes of 170 µm, separated at a distance of 300 µm.
  
  The full array layout .gal file is available below as a supplementary file.