title: ORNL Clostridium thermocellum Oligoarray
status: Public on May 24 2011
contact.city: Oak Ridge
contact.first: Babu
contact.last: Raman
contact.email: raman.babu@gmail.com
contact.state: TN
contact.address: One Bethel Valley Road
contact.country: USA
contact.institute: Oak Ridge National Laboratory
organism: Acetivibrio thermocellus ATCC 27405
manufacture_protocol: DNA sequences for the 3163 C. thermocellum ATCC 27405 predicted protein-encoding genes were obtained from The Joint Genome Institute using sequence assembled in November 2003. Oligonucleotide probes that represented the whole genome of C. thermocellum were designed using the CommOligo software and were commercially synthesized without modification (MWG Biotech, High Point, NC) in 96-well plates. The concentration of the probes was adjusted to 100 pmol/JlL, transferred to 384-well printing plates in a final concentration of 50% dimethyl sulfoxide using a BioMek FX liquid handling robot (Beckman-Coulter, Fullerton, CA) and then spotted onto UltraGAPS glass slides (Corning Life Sciences, Corning, NY) using a BioRobotics Microgrid II microarrayer (Genomic Solutions, Ann Arbor, MI) in a dust-free clean room maintained at 21°C and 50% relative humidity. Spotted DNA was stabilized on slides by ultraviolet crosslinking using an Ultraviolet 1800 Stratalinker (Stratagene, La Jolla, CA) according to the slide manufacturer's instructions (Corning Life Sciences). Oligonucleotide probes originally designed based on the 2003 draft genome sequence were BLAST compared against the 2006 fully assembled genome to identify the corresponding open reading frames in the completed genome.