title: SIU Streptococcus pyogenes 5K
status: Public on May 08 2009
contact.city: Carbondale
contact.first: KyuHong
contact.last: Cho
contact.email: cho@micro.siu.edu
contact.state: IL
contact.address: 1125 Lincoln Dr. Room 131
contact.department: Microbiology
contact.country: USA
contact.institute: Southern Illinois University Carbondale
organism: Streptococcus pyogenes
manufacture_protocol: An antisense oligonucleotide array based on the published
  genome of S. pyogenes SF370 (Ferretti et al., 2001) was
  made at the Microarray Core Facility in the Genome-
  Sequencing Center at Washington University (GSC, http://
  genome.wustl.edu/groups/microarray/main_page/). A single
  60–80 mer oligonucleotide was designed to hybridize to the
  putative transcripts from each annotated open reading frame
  using ‘TOP’ software that was created at the GSC. To reduce
  complexity, probes for rRNA, tRNA  genes were not included. The oligonucleotides
  were synthesized by Illumina and were deposited onto
  a MWG epoxy microarray slide by custom Linear Servo
  Arrayer so that each slide included triplicates spots for each
  probe. Quality of the array was validated by hybridization with
  a Cyanine 5-labelled random nonamer (Hybchecker, Sigma)
  to ensure that the frequency of missed spots were less than
  1.0% and by self-self hybridization using a single RNA sample
  to generate Cyanine 3- and Cyanine 5-labelled cDNAs, which were then co-hybridized on the slide. Slide
  batches were rejected if the average ratio of hybridization
  differed significantly from 1.0.