Microarray Experiment

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Post mortem cattle biochips reveals the following. IL-8 & IFN ß up regulated in susceptible host (Boran) versus resistant strain (N'Dama) ß defensins upregulated ...
Microarray Experiment GENE LISTS Statistical Analysis Anova t-tests

RNA

aRNA Cluster analysis Labelled probe

QC Metrics

Hybridization Feature identity

Normalization

After

Before

= Chips #709 #221/ 213?

 dChip flagged !!  Poor Affy metrics

Day 0 +3

Day 17

Day 7 +9

Clear separation evident in terms of time However, not in terms of QTL

= Chips #754 #755

 dChip flagged !!  Poor Affy metrics

4 x Tir 2 d0 Outliers: # 1044_S_T2C_0_1 # 1045_S_T2C_0_2 # 1046_S_T2C_0_3 # 1048_S_T2A_0_1

Day 7, 9,17

Day 0 Day 0

Day 3 Day 9 &17 Day 3

Day 7

94

96 95

94

98 97

98 97

Strong amplification

weak amplification

ng/ul Affy_cRNA_BC_#6_9-1 Affy_cRNA_BC_#6_9-2 Affy_cRNA_BC_#6_10-1 Affy_cRNA_BC_#6_10-2 Affy_cRNA_BC_#6_11-1 Affy_cRNA_BC_#6_11-2 Affy_cRNA_BC_#6_1-1 Affy_cRNA_BC_#6_1-2 Affy_cRNA_BC_#6_2-1

96 95

38.93 17.22 33.54 19.54 36.97 18.18 80.88 32.51 177.92

260/280 260/230 2.03 1.24 2.04 0.8 2.13 1.25 2.02 0.88 2.05 1.19 1.99 0.92 2.05 0.43 1.93 0.51 2.1 1.85

Serial ID ng/ul 260/280 260/230 94 Affy_cRNA_BC_#8_rpt_9-1 711.85 2.07 2.05 Affy_cRNA_BC_#8_rpt_9-2 333.67 2.07 1.97 95 Affy_cRNA_BC_#8_rpt_10-1 585.54 2.03 2.19 Affy_cRNA_BC_#8_rpt_10-2 488.22 2.05 2.36 96 Affy_cRNA_BC_#8_rpt_11-1 808.04 2.08 2.33 Affy_cRNA_BC_#8_rpt_11-2 585.97 2.03 2.02 97 Affy_cRNA_BC_#8_rpt_15-1 808.29 2.1 1.59 Affy_cRNA_BC_#8_rpt_15-2 431.24 2.06 1.84 98 Affy_cRNA_BC_#8_rpt_16-1 675.39 2.11 1.95

Extra peak missing from repurified material: Trizol or 5S RNA ??

RNeasy

Extra peak missing from repurified material: Trizol or 5S RNA ??

Original amplified aRNA Culminating in outlying data

Repurified RNA

ND

BZ

Day 0 upto day 35

Spleen Liver Lymph node Statistical analysis of biochip data from Post mortem cattle biochips reveals the following IL-8 & IFN ß up regulated in susceptible host (Boran) versus resistant strain (N’Dama) ß defensins upregulated in N’Dama Significant expression differences manifested in spleen & lymph node but not liver Data concurs with knock out mice strains demonstrating inflammation differences to bacteria and in particular marked differences in Neutrophil recruitment

Hypothesis: Boran cattle up Regulate the Trif TLR4 pathway in the lymph node and Spleen, culminating in excessive inflammation and dys regulated neutrophil recruitment Excess neutrophil recruitment is known to Interfere with parasite clearance