title: E. coli O157 Sakai oligonucleotide DNA microarray
status: Public on Aug 23 2007
contact.city: Kiyotake
contact.first: Yoshitoshi
contact.last: Ogura
contact.email: y-ogura@med.miyazaki-u.ac.jp
contact.state: Miyazaki
contact.address: Kihara 5200
contact.department: Frontier science reserch center
contact.country: Japan
contact.institute: University of Miyazaki
organism: Escherichia coli
manufacture_protocol: Oligonucleotide probes were prepared for all the protein-coding genes on the O157 Sakai genome (5,447 genes in total).  Principles for the probe design were 60-mer in length and two probes for each gene.  As for 542 repeated genes, we prepared a single probe for each repeated gene family.  Such probes totaled to 151 probes, each having two or more targets of more than 90% sequence identity on the O157 Sakai genome .  As for the singleton genes (4905 genes), we were able to design two different 60-mer probes for 4173 genes, but only one 60-mer probe for 725 genes and one 44 or 45-mer probes for 7 genes.  In total, 9,620 probes were synthesized (Sigma-Aldrich Japan, Tokyo, Japan), and each probe was spotted onto poly-L-Lysine coated glass slides (SD10011; Matsunami Glass Ind., Osaka, Japan) using SPBIO (Hitachi Software Engineering, Tokyo, Japan).