Microarray analysis of bone marrow-derived macrophage cells treated with Kdo₂-Lipid A (KLA) and ATP

Introduction

Experimental design

Bone marrow-derived macrophages were obtained from tibias and femurs of mice as per protocol PP0000003500. Cell treatments consisted of a) Control (no treatment); b) Kdo₂-Lipid A (KLA) pretreatment only (4hr pretreamemt, no ATP); c) ATP only (with no Kdo₂-Lipid A pretreatment); d) Kdo₂-Lipid A pretreatment (4 hrs), followed by addition of ATP at t=0. Lipid/mRNA measurements were taken at t=0 (control only), 15m, 30m, 1h, 2h, 4h, 8h, and 20h (relative to ATP addition at t=0).

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