title: University of Minnesota - Streptomyces Microarray
status: Public on Jan 01 2014
contact.city: Powai, Mumbai
contact.first: Sarika
contact.last: Mehra
contact.state: MH
contact.address: IIT Bombay
contact.department: Chemical Engineering
contact.country: India
contact.institute: IIT Bombay
organism: Streptomyces coelicolor A3(2)
manufacture_protocol: A whole genome cDNA microarray was constructed for S. coelicolor. Gene-specific probes with an average length of 500 bp were designed based on the genomic sequence database at Sanger Center to represent the 7,825 genes. The primers to amplify these probes were designed to be 20 bp in length with a melting temperature around 62 deg C. An iterative primer/probe design process was adopted. The primers were first Blasted against the entire genome to check for the specificity to the corresponding genes. The probe sequences resulting from these primers were also blasted against the entire genome to check for possible cross-hybridization with sequences other than the corresponding gene. Any primer pair that may give rise to a potentially croshybridizing probe sequence was redesigned with alternate coordinates. This probe checking-redesign process minimized the possibility of cross-hybridization between a probe and other cDNA species. For some highly homologous genes, a unique probe was not attainable and a multigene probe was used. A multigene probe was designed in such cases. 7,581 genes were successfully amplified and spotted on the microarray. The microarray was fabricated on poly-L-lysine slides with duplicate spots for each probe.