array scanning protocol
Scanning and feature extraction was performed using GenePix scanner 4100A
nucleic acid hybridization to array protocol
300 ng of labeled cDNA was hybridized to an E. coli expression array (Agilent) according to Agilent standard protocols
nucleic acid labeling protocol
RNA samples were prepared for microarray analysis using the FairPlay III Labeling Kit (Agilent) according to the manufacturer’s instructions. Briefly, first strand cDNA was generated from 5 ?g of RNA by reverse transcription incorporating amino allyl dUTP. Cy5 or Cy3 monoreactive dyes (GE Healthcare) were coupled to the reactive amino allyl groups and the samples purified of unincorporated dye using Illustra™ Microspin G-50 Columns (GE Healthcare).
nucleic acid extraction protocol
Logarithmic-phase cultures were collected by centrifugation and adjusted to 3x108 CFU/ml in either LB, LB supplemented with 50 % normal human serum (NHS) or 50 % HIS. The samples were incubated at 37 ?C for 45 min after which RNA was extracted using TriZol (Invitrogen) according to the manufacturer's instructions. The RNA obtained was treated with DNase I (Ambion).
Experimental samples were exposed to 50% normal human serum for 45 min
Bacteria were routinely cultured at 37 °C in Lennox broth (LB)