Standard Illumina scanning protocol
The data were first raw-filtered in order to identify and remove probesets that were not detected and then normalised using robust spline normalization with FlexArray v1.6
ID_REF = VALUE = log2 robust spline normalized
Standard Illumina hybridization protocol
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
Mice were infected for 6h with 5 x 10^7 CFU of Streptococcus suis strain 89-1591 or mock-infected with bacterial growth medium (THB).
RNA was homogenized from RNAlater-stabilized spleen tissus, extracted and DNAse I treated using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Bacterial culture was prepared by transferring 10 μl of 1/1,000 dilutions of 8-h cultures into 30 ml of THB, which was incubated for 16 h at 37°C without agitation. Stationary-phase bacteria were washed twice in PBS (pH 7.3). The bacterial pellet was then resuspended and adjusted to a concentration of 5 × 10^8 c.f.u. ml-1.