title: NRC-BRI_16S rRNA PsychroChip_528
status: Public on Aug 06 2009
contact.city: Montreal
contact.first: Etienne
contact.last: Yergeau
contact.email: Etienne.Yergeau@cnrc-nrc.gc.ca
contact.state: Qc
contact.address: 6100 Royalmount Ave
contact.department: Environmental Microbiology
contact.country: Canada
contact.institute: NRC-BRI
organism: Bacteria
  Archaea
manufacture_protocol: The 16S rRNA gene probe design for the microarray was as follows: 1) database searches in Greengenes (http://greengenes.lbl.gov) for 16S rRNA gene sequences with keywords "Arctic," "Antarctic," "Polar," "Cold," "Psychro" (2891 sequences retrieved, performed on April 15th, 2008); 2) clustering of the database sequences together with 16S rRNA gene sequences from strains isolated in our lab in previous studies of polar environments using Blastclust (NCBI, Bethesda, MD); 3) design of five 25-mer probes for each of the 99%-similarity clusters having 3 or more representatives using OligoPicker (32); 4) elimination of probes having a ΔG >-3 kJ; 5) BLAST comparison of the central 17 nucleotides of each probe against all the original sequences; 6) selection, for each cluster, of the probe that showed less significant hits to sequences outside the cluster and most significant hits within the cluster. Oligonucleotides (synthesized by IDT, Coralville) were printed in triplicate on amino-silane coated glass slides (Corning, Acton, MA) using a VersArray Chip Writer Pro printer (Bio-Rad, Hercules, CA). Including control spots, the microarray consisted of 528 spots. Each slide contained three identical sub-arrays.