Hybridization and washing of microarray slides followed according to the manufacturer's protocols.
Examination of the slide followed.
Salmonella microarray slide preparation and general microarray analysis followed the procedures described by Porwollik et al. [63].
Following incubation, the microarray slide was washed for 5 minutes in aCGH/ChIP-on-chip Wash Buffer 1 (0.5X SSPE, 0.005% N-lauroylsarcosine; room temperature) and 5 minutes in a CGH/ChIP-on-chip Wash Buffer 2 (0.1X SSPE, 0.005% N-lauroylsarcosine; 31°C).
The investigated samples were all derived from the same PCR reactions and divided into two PrASE reactions followed by hybridization to one microarray slide.
This is determined by labelling genomic DNA from the test and reference sample with different fluorescent dyes followed by co-hybridisation to the microarray slide.
Data processing of the scanned microarray slide included signal intensity measurement with the ImaGene software program, followed by median pin-tip (c.q. sub array) normalization.
Following brief centrifugation, the samples were applied to the microarray slide, which was overlaid with a coverslip and incubated overnight at 42°C in a hybridisation chamber.
The dataset was first filtered to remove microarray slides with >50% missing values followed by a second filter to remove gene models containing >50% missing values, resulting in a final set of 602 arrays.
In parallel a control microarray slide probed with buffer and the mix of the detection antibodies was performed.
