| VAMPIRE Analysis
| GOby Analysis
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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).
45,214 spots on the array
Data normalization was performed as described in J Mol Endocrinol Sasik et al. 33 (1): 1 (PDF)
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)