Frozen strains were first grown on blood agar under aerobic conditions at 28°C 24 h. To prepare for DNA isolation the strains were grown in TSB-medium at 28°C 24 h.
Extracted molecule
genomic DNA
Extraction protocol
DNA was extracted as described by Pitcher et al. (1989). DNA quality was checked with Nanodrop device (Nanodrop Technologies, Wilmington, MA, USA)
Label
Cy5
Label protocol
DNA was labeled using the BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to the instructions of the manufacturer. Labeled DNA was purified with the DNA purification kit (QIAquick PCR Purification Kit, Qiagen, Hilden, Germany). The concentration of DNA and the incorporation of the dye were checked with Nanodrop device (Nanodrop Technologies, Wilmington, MA, USA)
Hybridization protocol
Agilent (Santa Clara, USA) 8x15K CGH protocol, 65°C for 18-20 h.
Scan protocol
GenePix 4200 AL (Axon Instruments) using pixel resolution of 5 µm, line average 2.
Description
253640110007_3_1.gpr
Data processing
Images were processed and checked manually using GenePix Pro 6.0/6.1 software. For data analysis R software LIMMA-package (Smyth et al 2005) was used. Background intensities were fixed using normexp-algorithm (threshold 50).
