title: Streptococcus gordonii Challis whole genome array SG-2
status: Public on Sep 01 2011
contact.city: Buffalo
contact.first: Anna
contact.last: Nikitkova
contact.email: an43@buffalo.edu
contact.state: NY
contact.address: 3435 Main St.
contact.country: USA
contact.institute: University at Buffalo
organism: Streptococcus gordonii str. Challis
manufacture_protocol: Unique 70-mer oligonucleotides were identified for each of the 2,186 open reading
  frames (ORFs) identified in the initial annotation of the Streptococcus gordonii CH1 Challis genome {Vickerman, 2007}. Oligonucleotides were resuspended at 25 uM final concentration in Nexterion Spot spotting solution (SCHOTT#1066029) and printed onto bar-coded Nexterion Epoxy coated slides (SCHOTT #1064016) using an QArray2 printer (Genetix USA Inc., Boston, MA) located in the genomics core at Roswell Park Cancer Institute (RPCI) in Buffalo. Print configuration is 48 blocks in a 4 X 12 arrangement. Spot diameters are approximately 90-100 microns. Control reporters included 10 Arabidopsis gene fragments. After printing, oligonucleotides were cross-linked to the slides by UV irradiation at 250 mJ/cm2 (Stratalinker UV Crosslinker, Stratagene) and subsequently stored at room temperature in a desiccated chamber until use. The oligonucleotides were spotted in four replicates each, which compensate for spot to spot variation within each slide and allows for greater overall precision of the data. Quality control consisted of self-self hybridizations and determination of total spot saturation using SYBR dyes (Molecular Probes, Eugene, OR) that intercalate between DNA strands and can be used to check spotting consistency. Quality control experiments were re-run on each new batch of printed microarray slides.