Microarray analysis of RAW 264.7 cells treated with Kdo2-Lipid A (KLA) and compactin (full time course)

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Introduction

Experimental design

Compactin is a potent competitive inhibitor of hydroxymethylglutaryl coenzyme A reductase, the rate-limiting enzyme in cholesterol biosynthesis. Experiments were conducted with RAW264.7 cells fed 10% fetal calf serum, as per protocol PP0000002800 (pdf). Measurements were taken at 30m, 1h, 2h, 4h, 8h, 12h, and 24h for: (i) compactin, (ii) Kdo2-Lipid A, (iii) compactin + Kdo2-Lipid A. and (iv) control.

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)

References

  • Kdo2-Lipid A of Escherichia coli, a defined endotoxin that activates macrophages via TLR-4.

    Raetz C, Garrett T, Reynolds C, Shaw W, Moore J, Smith JD, Ribeiro A, Murphy R, Ulevitch R, Fearns C, Reichart D, Glass C, Benner C, Subramaniam S, Harkewicz R, Bowers-Gentry R, Buczynski M, Cooper J, Deems R and Dennis E.

    Journal of Lipid Research 47, 1097-1111 (2006)

    PMID:16479018 [doi:10.1194/jlr.M600027-JLR200]

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