Biotinylated cRNA was labeled with fluorescent dye at the Rockefeller University Gene Array Facility, hybridized onto a MouseRef-8 v2.0 Expression BeadChip expression array (Illumina, San Diego, CA) and scanned. Arrays were normalized by shift to 75th percentile and expression values below noise level were set to the minimum detection level. Expression data were then analyzed by Genespring software (Agilent Technologies, Santa Clara, CA). Quality

control was performed by analyzing gene expression correlation coefficients and samples Inhibitors,research,lifescience,medical with coefficients less than 0.95 were excluded. There were duplicate control samples, triplicate ethanol-treated samples, and duplicate heat-treated samples with correlation coefficients of >0.99 between biological replicates.

For the array analysis, biological Inhibitors,research,lifescience,medical replicate sample signals were averaged. The differences in gene expression were determined using analysis of variance (ANOVA) post hoc adjusted by Tukey test (P < 0.05), and multiple hypothesis testing adjustments were made using the Benjamini–Hochberg method at a false discovery rate (FDR) of less than 0.05. For gene array analysis, a hierarchical clustering algorithm was used to generate the dendrogram based on the squared Euclidian distance method with complete-linkage (Eisen et al. 1998). Genes differentially expressed following ethanol or heat treatments were subjected Inhibitors,research,lifescience,medical to Gene Ontology (GO) enrichment analysis using the hypergeometric method corrected by Benjamini–Yekuteili method at FDR ≤0.25. In order to identify genes regulated by both ethanol Inhibitors,research,lifescience,medical and heat shock in astrocytes, we analyzed the results of the microarray experiments looking for genes induced by both treatments. There was a substantial overlap between the transcriptional profiles of the two treatments, suggesting similar mechanisms of gene regulation (Fig. Inhibitors,research,lifescience,medical 1). Comparison of GO enrichment using differentially expressed genes after ethanol or heat treatment also showed striking similarities among upregulated categories (Fig. 2). Figure 1 Hierarchical

clustering by squared Euclidean distance algorithm on differentially expressed genes and Venn diagram of ethanol- and heat-induced genes in primary astrocyte culture. (A) The graph shows hierarchical clustering of the gene expression pattern … Figure 2 Heat-map of Gene Ontology categories enrichment analysis across the ethanol also (EtOH) and heat shock (HS) treatments. Only categories with an adjusted FDR-q-value of less than 0.25 in at least one condition are shown in the figure. Colors indicate downregulation … Real-time polymerase chain reaction analyses of mRNA levels Total RNA was isolated from cultured cells using TRIzol (Invitrogen, Grand Island, NY). cDNA was prepared from total RNA with the iScript cDNA AZD0530 ic50 synthesis kit (Bio-Rad, Hercules, CA).