genomewide characterization of host-pathogen interactions by ...

exponential growth phase
2.5 h internalized
2.5 h anaerobic incubation
2.5 h serum/CO 2 control
1 h non-adherent
6.5 h internalized
6.5 h serum/CO 2 control
Maren Depke
Results
Pathogen Gene Expression Profiling
The comparisons were visualized using scatter plots (Fig. R.5.9). Comparable to the clustering
results, a high concordance between expression values of 1 h serum/CO 2 controls and
exponential phase samples, which represent the inoculation condition (Fig. R.5.9, panel ), and
even more striking between 1 h serum/CO 2 controls and non-adherent staphylococcal samples
after 1 h (Fig. R.5.9, panel ) was observed. Strong effects of treatment in comparison to 1 h
serum/CO 2 controls emerged in 2.5 h internalized (Fig. R.5.9, panel ), 6.5 h internalized
(Fig. R.5.9, panel ), 2.5 h serum/CO 2 controls (Fig. R.5.9, panel ), 6.5 h serum/CO 2 controls
(Fig. R.5.9, panel ), and in 2.5 h anaerobically incubated samples (Fig. R.5.9, panel ). Most
variation was detectable in the comparison of 1 h and 6.5 h serum/CO 2 controls (Fig. R.5.9,
panel ), but this can be due to the lower number of only two replicates for the 6.5 h serum/CO 2
control, which led to a lesser compensation for variation in the mean value than in the mean of
three replicates in the other sample condition/time point groups.
1 h serum/CO 2 control
1 h serum/CO 2 control
1 h serum/CO 2 control
1 h serum/CO 2 control
1 h serum/CO 2 control
1 h serum/CO 2 control
1 h serum/CO 2 control
Fig. R.5.9: Scatter plots comparing mean signal intensities
of treatment groups.
The signals of the eight groups of “1 h serum/CO 2
controls”, “exponential growth phase”, “1 h nonadherent
staphylococci”, “2.5 h internalization”, “6.5 h
internalization”, “2.5 h serum/CO 2 controls”, “6.5 h
serum/CO 2 controls”, and “2.5 h anaerobic incubation”
were plotted after combining the three biological
replicates. In case of “6.5 h serum/CO 2 controls” only two
biological replicates were available. All sequences
available on the array are shown. Numbers in the first
column refer to the comparison scheme in Fig. R.5.8.
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