genomewide characterization of host-pathogen interactions by ...

More documents

Recommendations

Info

Maren Depke Results Host Cell Gene Expression Pattern in an in vitro Infection Model expression after 2.5 h, infected GFP-positive sorted cells after 2.5 h were statistically compared to their time matched medium control cells. Altogether, 86 genes were defined as differentially expressed in infection compared to control 2.5 h after infection. Of these genes, 40 possessed a minimal absolute fold change of 1.5, and 11 genes held a minimal absolute fold change of 2 (Table R.4.1 A). In comparison, for the 6.5 h time point differential expression in infection compared to control was made up of 2296 genes, of which 1196 passed an absolute fold change cutoff of 1.5 and still 495 passed a cutoff of 2 (Table R.4.1 B). Comparison of infection-dependent differentially expressed genes after 2.5 h and 6.5 h When comparing the infection-dependent changes in gene expression with a minimal absolute fold change of 1.5 after 2.5 h and after 6.5 h, an overlap of 26 genes was recorded. This corresponds to 65 % of the genes differentially expressed 2.5 h after infection (Fig. R.4.5 A). If genes that did not exhibit differential expression relative to the baseline of 2.5 h medium control had not been excluded from the list of infection-dependent regulated genes after 6.5 h, the overlap would have even increased by 6 genes to 80 %. A B 2.5 h repressed repressed 6.5 h 14 26 1170 induced 5 333 induced 9 2 837 genes differentially expressed in S9 cells between infection with RN1HG GFP and medium control 2.5 h after infection genes differentially expressed in S9 cells between infection with RN1HG GFP and medium control 6.5 h after infection 1 23 Fig. R.4.5: Comparison of infection-dependent regulated genes in S9 cells 2.5 h and 6.5 h after start of infection. After applying a minimal absolute fold change cutoff of 1.5, 40 genes were differentially expressed in infection compared to control 2.5 h after start of infection, while the number of differentially expressed genes 6.5 h after start of infection increased to 1196. The overlap between both lists contained 26 genes (A). This group of 26 genes in the overlap could be subdivided into 23 genes which were induced 2.5 h as well as 6.5 h after start of infection, 2 genes which were repressed in both time points and 1 genes which was induced 2.5 h after start of infection and repressed after 6.5 h. In general, a bigger fraction of differentially regulated genes was induced than repressed in each time point. This summed up to 33 or 860 induced genes 2.5 h or 6.5 h after start of infection, respectively. Repression occurred for 7 genes at the 2.5 h time point and 336 genes at the 6.5 h time point (B). In a finer resolution, also the direction of regulation was comparable between the two analyzed time points. Of the 26 genes, which were differentially expressed after 2.5 h as well as after 6.5 h, 23 were induced and 2 were repressed in both time points. Only for one gene induction was observed after 2.5 h while the expression was repressed after 6.5 h (Fig. R.4.5 B). Concluding from this high degree of conformance in the two time points, the RNA expression profiling 2.5 h after start of infection seemed to catch the very early beginning of the host cell’s reaction, which was very strongly aggravated during the following 4 hours until the measurement 6.5 h after start of infection. In each time point, induction of gene expression was more pronounced than repression. Induction summed up to 33 or 860 genes 2.5 h or 6.5 h after start of infection, respectively. Repression covered 7 genes at the 2.5 h time point and 336 genes at the 6.5 h time point (Fig. R.4.5 B). 114
Maren Depke Results Host Cell Gene Expression Pattern in an in vitro Infection Model A Genes displaying statistically different expression values in the corresponding comparisons. testing a significant with p*
Page 1 and 2:
G E N O M E W I D E C H A R A C T E
Page 3 and 4:
Maren Depke C O N T E N T S GENOMEW
Page 5 and 6:
Maren Depke Z U S A M M E N F A S S
Page 7 and 8:
Maren Depke Zusammenfassung der Dis
Page 9 and 10:
Maren Depke S U M M A R Y O F D I S
Page 11 and 12:
Maren Depke Summary of Dissertation
Page 13 and 14:
Maren Depke I N T R O D U C T I O N
Page 15 and 16:
Maren Depke Introduction Besides op
Page 17 and 18:
Maren Depke Introduction Extracellu
Page 19 and 20:
Maren Depke Introduction with heigh
Page 21 and 22:
Maren Depke Introduction 2005). SaP
Page 23 and 24:
Maren Depke Introduction contains a
Page 25 and 26:
Maren Depke Introduction via fibron
Page 27 and 28:
Maren Depke Introduction cathelicid
Page 29 and 30:
Maren Depke Introduction shock are
Page 31 and 32:
Maren Depke Introduction STUDIES OF
Page 33 and 34:
Maren Depke Introduction are effect
Page 35 and 36:
Maren Depke Introduction cell stimu
Page 37 and 38:
Maren Depke Introduction channel CF
Page 39 and 40:
Maren Depke M A T E R I A L A N D M
Page 41:
Maren Depke Material and Methods Li
Page 44 and 45:
Maren Depke Material and Methods Ki
Page 47 and 48:
Maren Depke Material and Methods GE
Page 49:
Maren Depke Material and Methods Ge
Page 52 and 53:
Maren Depke Material and Methods Ho
Page 54 and 55:
Maren Depke Material and Methods Ho
Page 56 and 57:
Maren Depke Material and Methods Pa
Page 58 and 59:
Page 60 and 61:
Page 63 and 64: corticosterone [pg/ml plasma] corti
Page 65 and 66: Maren Depke Results Liver Gene Expr
Page 67 and 68: lood glucose levels [nmol/l] resist
Page 69 and 70: LBP [ng/ml] CPR [ng/ml] Maren Depke
Page 71 and 72: Maren Depke Results Liver Gene Expr
Page 73 and 74: liver weight [g] Maren Depke Result
Page 75 and 76: infection rate cfu / 10 mg tissue c
Page 77 and 78: Maren Depke Results Kidney Gene Exp
Page 79 and 80: Table R.2.1: Genes displaying stati
Page 81 and 82: Maren Depke BR1 sign DsigB vs wt BR
Page 91 and 92: Maren Depke Results GENE EXPRESSION
Page 93 and 94: Maren Depke Results Gene Expression
Page 95 and 96: log2(ratio C57BL/6 / BALB/c) at IFN
Page 109: Maren Depke Results Gene Expression
Page 112 and 113: Maren Depke Results Host Cell Gene
Page 132 and 133: Maren Depke Results Pathogen Gene E
Page 138 and 139: S. aureus RN1HG sample conditions a
Page 148 and 149: mean normalized intensity mean norm
Page 158 and 159: mean normalized intensity Maren Dep
Page 164 and 165:
mean normalized intensity mean norm
Page 166 and 167:
mean normalized intensity mean norm
Page 168 and 169:
log 2 (ratio) log 2 (ratio) log 2 (
Page 171 and 172:
Maren Depke D I S C U S S I O N A N
Page 173 and 174:
Maren Depke Discussion and Conclusi
Page 175 and 176:
Page 177 and 178:
Page 179 and 180:
Page 181 and 182:
Page 183 and 184:
Page 185 and 186:
Page 187 and 188:
Page 189 and 190:
Page 191 and 192:
Page 193 and 194:
Page 195 and 196:
Page 197 and 198:
Page 199 and 200:
Page 201 and 202:
Page 203 and 204:
Page 205:
Page 208 and 209:
Maren Depke References Athanasopoul
Page 210 and 211:
Maren Depke References Byrne GI, Le
Page 212 and 213:
Maren Depke References Demling R. T
Page 214 and 215:
Maren Depke References Foss GS, Pry
Page 216 and 217:
Maren Depke References Hagopian K,
Page 218 and 219:
Maren Depke References Jin T, Bokar
Page 220 and 221:
Maren Depke References Kwan T, Liu
Page 222 and 223:
Maren Depke References Luster AD, U
Page 224 and 225:
Maren Depke References Namiki S, Na
Page 226 and 227:
Maren Depke References Puccetti P.
Page 228 and 229:
Maren Depke References Siewert E, B
Page 230 and 231:
Maren Depke References van den Akke
Page 232 and 233:
Maren Depke References Yang XL, Sch
Page 235:
Maren Depke A F F I D A V I T / E R
Page 238 and 239:
Maren Depke Acknowledgments Kidney
show all

genomewide characterization of host-pathogen interactions by ...

Create successful ePaper yourself

Delete template?

Save as template?