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Microarray analysis of foam cells in wild-type and LDLR(-/-) mice

Introduction | VAMPIRE Analysis | GOby Analysis
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Experimental design

Foam cells were elicited and harvested from thioglycolate-stimulated wild-type (WT) mice maintained on normal and Western (High-fat, high cholesterol) diets, and from low-density lipoprotein receptor knockout (LDLR(-/-)) mice maintained on normal and Western diets according to protocols PP0000003000 and PP0000003100 (pdf).

Microarray analysis was used to measure gene expression response. An Agilent array was hybridized for each genotype, with normal diet represented on the green channel, and Western diet on the red channel. A second plate was also prepared for each genotype, with normal diet on the red channel, and Western diet on the green channel (i.e. dye-swapped). We evaluated the data and found no dye effects (data not shown).

Gene expression results are shown as ratios of measurements for high-cholesterol vs normal chow diets for knock-out and wild-type mice, respectively.

Array Design

45,214 spots on the array
41,034 data spots
38,838 unique probes (6428 probes have no gene id)
21,609 unique mouse genes

Each gene was represented by 1 - 9 probes
Each probe was spotted 1 or 10 times

Data Normalization

Data normalization was performed as described in J Mol Endocrinol Sasik et al. 33 (1): 1 (PDF)