Total RNA was extracted using RNAeasy Miniprep Kit (Qiagen) . Double-stranded cDNA was synthesised using the double stranded cDNA synthesis kit (invitrogen)
Label
Cy3
Label protocol
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Hybridization protocol
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
Scan protocol
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Description
Multidrug resistant sequenced strain isolated from Massachusetts General (NC009648)
Data processing
After QC assessment to identify substandard arrays, raw data were subjected to quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.31 (Roche NimbleGen, Inc.). Probe level data were summarised to yield gene level data and differential expression analysis was carried out using Limma (Smyth Stat Appl Genet Mol Biol 3 article 3)
