A total of 25 putative genes were not represented on the array because no unique probe satisfying the selection criteria could be selected. Comparative genome hybridization (CGH) Chromosomal DNA (50 μg) was sheared in 1 ml shearing buffer (TE/10% PS-341 cell line glycerol), using Nebulizers (Invitrogen, Carlsbad, USA) under 1.7 bar air pressure for 3 minutes to yield fragments between 500 and 1500 bp. DNA was ethanol precipitated, taken up in water and 10 μg of DNA was column purified using Illustra Cyscribe GFX purification kit (GE Healthcare, Uppsala, Sweden) according to instructions
of the manufacturer. Differential DNA presence was determined by two-colour fluorescent hybridizations of the corresponding genomic DNAs on the 8 × 15 k S. suis oligo array. Genomic DNA of each strain was cohybridized once with the reference strain P1/7, that was always labeled with Cy3. The test strain was consequently labeled with Cy5. Labeling of DNA (2,5 μg) was done using the Bioprime Array CGH Genomic Labeling System (Invitrogen) with slight modifications as described by Molenaar et al., 2005 [29]. Labeling efficiency was measured using the Nanodrop (ThermoScientific, Wilmington, USA). Constant amounts of label (25 pmol each) were hybridized to the oligoarray in hybridization buffer of the In situ hybridization kit Plus (Agilent Technologies) following instructions of the manufacturer. During hybridization, slides
were incubated for 17 h at 65°C under rotation. Slides were washed for 10 min in 6 × SSC/0.05% Triton-X102 at room temperature, followed by 5 min in 0.1 × SSC/0.05% Triton-X102 at 4°C. Slides were dried using FG-4592 manufacturer Aldol condensation pressured air and scanned
in a GenePix 4200AL scanner (Molecular Devices, Sunnyvale, USA). Scans were analyzed using GenePix software (Molecular Devices). Local background values were subtracted from the intensity of each spot. Data were normalized using S-Lowess [30] at the webtool accessible from http://bioinformatics.biol.rug.nl/websoftware/s-lowess. Normalized data were selleckchem imported into Acuity software (Molecular Devices) for further analysis. Cut-off values for presence/absence of genes were empirically determined by comparing microarray results to classic hybridization results using about 100 radioactively labeled probes on spotted chromosomal DNA (data not shown). It was determined that a log ratio above -1.5 indicated the gene was present and very homologous to the gene in P1/7, whereas a log ratio above -4.5 indicated that the gene was present, but variation in nucleotide composition existed among isolates. A ratio between -1.5 and -3 indicated slight variation, whereas a ratio between -3 and -4.5 indicated large variation. A gene was designated “”absent”" from a genome when all probes for that gene had a normalized log ratio below -4.5. Dendrograms CGH data was clustered using Acuity software to determine similarity of isolates tested in the CGH.