title: BC Cancer Agency_E.coli_H.influenzae_P.aeruginosa_HumanChr6_340K array v1
status: Public on Apr 05 2008
contact.city: Vancouver
contact.first: Rene
contact.middle: Louis
contact.last: Warren
contact.email: rwarren@bcgsc.ca
contact.state: British Columbia
contact.address: 570 West 7th avenue Suite 100
contact.department: Genome Sciences Centre
contact.country: Canada
contact.institute: BC Cancer Agency
organism: Pseudomonas aeruginosa
  Escherichia coli
  Haemophilus influenzae
  Homo sapiens
manufacture_protocol: Oligonucleotide array design
  An oligonucleotide microarray has been designed to simultaneously measure the RNA level from genes in three different bacterial species (H. influenzae, E. coli and P. aeruginosa) and probe the DNA from one human BACs.  DNA oligonucleotides of length 60 targeting most genes were selected with the help of various filters designed to maximize the sensitivity and specificity of each oligonucleotide and the resulting signal-to-noise ratio. The filters and associated computer codes were similar to the ones successfully used for arrays designed to study C. elegans (Maydan et al. 2007).  Briefly, oligonucleotides containing 20-mers appearing more than once in the genomes of interest or having an overall identity above 75% with non-target sequences were eliminated from the pool of potential probes. Oligonucleotides presenting a significant self-folding energy or homopolymer longer than 5 bases in length were also eliminated and only the oligonucleotides with GC content between 36% and 62% were kept for further consideration, which corresponds to a range of about 10 ºC in melting temperature Tm. In the case of the human BACs, the selection process also eliminated known DNA repeats. The oligonucleotides appearing in the final design were selected from the pool of potential probes obtained with the above-mentioned filters taking into consideration the 14-mer count, 15-mer count, GC content, overlap between neighboring probes, and the number of probes per gene. The k-mer count of an oligonucleotide is defined as the sum of the frequencies within the genomes of interest of all constituent k-mers within the oligonucleotide. NimbleGen Systems manufactured the microarrays with each selected 60-mer oligonucleotide synthesized at random positions.