Microarray analysis of thioglycolate-elicited macrophage cells treated with Kdo₂-Lipid A (KLA) and compactin

Introduction

Experimental design

Peritoneal macrophages were obtained from thioglycolate-stimulated mice, as per protocols PP0000001401, PP0000001502 and PP0000001801 (pdf). Cells were treated with Kd0₂-Lipid A and/or compacin; measurements were taken at 30min, 1h, 2h, 4h, 8h, 12h, and 24h.

Data normalization

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

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