title: Clostridium beijerinckii NCIMB 8052 Spotted Oligonucleotide Array v1
status: Public on Jun 02 2009
contact.city: Urbana
contact.first: Zhen
contact.last: Shi
contact.email: zshi@illinois.edu
contact.state: IL
contact.address: 1206 West Gregory Drive
contact.department: Institute for Genomic Biology
contact.country: USA
contact.institute: University of Illinois
organism: Clostridium beijerinckii NCIMB 8052
description: The draft genome sequence assembly of Clostridium beijerinckii (whole genome shotgun [WGS] project accession AALO00000000) was used as a source of the genes used in this study. Note, this WGS project has been superceded by the complete genome in (non-WGS) GenBank record CP000721.
  The Platform data table reflects a condensed representation of the array's replicate features.  The full array layout representing all of the individual features is linked as a supplementary file at the foot of this record.
manufacture_protocol: An oligonucleotide of 70 bp was designed as a probe specific for each gene.  Each probe was made on the forward strand of the gene.  A probe was selected based on global optimization from all combinations of 70-mer within the target sequence by scoring simultaneously for a set of criteria including melting temperature, presence of hairpin/secondary structure, presence of low-complexity sequence and sequence specificity with respect to other genes.  Sequence specificity was examined by sequence alignment using BLAST to ensure that the selected probe is different from all other sequences in the set beyond a certain value.  All 70-mer probes have very similar melting temperature of ~65 oC.  The oligonucleotides were synthesized (Invitrogen) and printed as duplicates onto glass slides.  The slides were hybridized using probes generated by an aminoallyl-labeling and Cy dye-coupling procedure adapted from a TIGR protocol.  Hybridized slides were scanned on an Axon Microarray Scanner.  Features were extracted using GenePix Pro.