Microarray analysis of RAW 264.7 cells treated with Kdo₂-Lipid A

Introduction

Experimental design

Microarray analysis was used to measure gene expression response in RAW264.7 cells over time. RAW 264.7 cells were harvested 0.5, 1.0, 1.5, 2.0, 4.0, 6.0, 8.0, 12.0, 18.0, and 24 hours after treatment with 100ng/ml Kdo₂-Lipid A. The experiment was performed three times, for three biological replicates. At each time point an Agilent array was hybridized, with Kdo₂-Lipid A on the green channel and the control on the red channel. One biological replicate was also run with Kdo₂-Lipid A on the red channel and the control on the green channel (i.e. dye-swapped). We evaluated the data and found no dye effects (data not shown). Cells were treated as described in LIPID MAPS Protocol PP0000001003: 10% Serum Kdo₂-Lipid A Treatment (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

Data Normalization

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