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Chunk #20 — Materials and methods — Microarray analysis of stress and ethanol treatment groups

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A promoter polymorphism in the Per3 gene is associated with alcohol and stress response.
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Hippocampal gene expression was assayed using Illumina Sentrix Mouse-6 v1.1 arrays according to manufacturer's protocols (http://www.illumina.com/). Microarray runs for the five groups (RSE, RSS, NOE, NOS and NON) were carried out in a counterbalanced manner to avoid batch effects. Raw microarray data were normalized using the rank invariant method and background subtraction protocols provided by Illumina as part of the BeadStation software suite. We log-transformed the expression values and stabilized the variance of each array to a mean of 8 and a s.d. of 2 per array. A single unit on this scale (log2) corresponds to a twofold difference in expression.