genomewide characterization of host-pathogen interactions by ...

infected; 2.5 h
infected; 6.5 h
mean intensity
mean intensity
infected; 6.5 h
medium control; 6.5 h
Maren Depke
Results
Host Cell Gene Expression Pattern in an in vitro Infection Model
medium control; 2.5 h
infected; 2.5 h
medium control; 6.5 h
medium control; 2.5 h
Fig. R.4.3: Scatter plots comparing mean signal intensities of treatment groups.
The signals of the four groups “medium control sample after 2.5 h”, “GFP-positive sorted infected sample after 2.5 h”, “medium
control sample after 6.5 h”, and “GFP-positive sorted infected sample after 2.5 h” were plotted after combining the four biological
replicates. Control sequences and sequences that were absent on all of the arrays used for each scatter plot are not shown. (Absence
of expression is defined via a p-value > 0.01 on intensity profile level in Rosetta Resolver).
When looking at examples of signal intensity data, gene expression pattern were recognized
that were characterized by similar expression in the three groups of infected GFP-positive sorted
cells after 2.5 h, medium control cells after 2.5 h, and infected GFP-positive sorted cells after
6.5 h. A divergent signal intensity, lower or higher than in the three other groups, was noticeable
for the last group of medium control cells after 6.5 h (Fig. R.4.4). However, the time-dependent
changes in the control samples’ gene expression were not in the focus of this study, but the
infection-dependent changes should be accessed. Therefore, a strategy was defined that allowed
to exclude genes which are mainly influenced by a differing value in the group of 6.5 h medium
control cells from the list of infection-dependent differential gene expression after 6.5 h of
infection.
A
Fkbp4 (EntrezGene ID 2288)
B
Cldn1 (EntrezGene ID 9076)
2500
3000
Fig. R.4.4:
Examples of mean signal
intensities characterized by a
higher (A) and lower value
(B) for the medium control
after 6.5 h compared to the
other three sample groups.
2000
1500
1000
500
0
pMEM control
tryps.
medium ActD/NaN3
control
2.5 h 6.5 h
2500
2000
1500
1000
500
2288 FKBP4
0
pMEM control
tryps.
ActD/NaN3 medium
control
RN1HG infected pMEM control RN1HG infected
RN1HG GFP wt GFP tryps. RN1HG GFP wt GFP
infected,
FACS sorted
GFP positive
GFPpositivpositive
medium ActD/NaN3
control
infected,
FACS sorted
GFP positive
GFP-
2.5 h 6.5 h
sorted
sorted
RN1HG infected pMEM control RN1HG infected
RN1HG GFP wt GFP tryps. RN1HG GFP wt GFP
FACS infected, sorted
GFP positive
GFPpositive
ActD/NaN3 medium
control
FACS infected, sorted
GFP positive
GFP-
6.5 h positive
2.5 h
sorted
sorted
2.5 h 6.5 h
9076 CLDN1
First, differential gene expression was determined with statistical testing for the comparison
of infected GFP-positive sorted cells vs. medium control, each after 6.5 h. Second, the differential
gene expression was calculated for the comparison of infected GFP-positive sorted cells after
6.5 h with medium control cells after 2.5 h. Third, only genes which featured differential gene
expression in both comparisons were included in the list of infection-dependent differential gene
expression 6.5 h after infection. For assessing the infection-dependent differential gene
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