Alcohol-induced temporal transcriptome remodeling in the prefrontal cortex in a mouse model of alcohol dependence

...............................................................................................................108 Introduction..........................................................................................................109 Materials and Methods.........................................................................................111 Animals and animal husbandry...................................................................111 Experimental design and tissue collection..................................................111 RNA isolation and quantification ...............................................................111 cDNA microarray fabrication and hybridization ........................................112 Normalization and storage of microarray data............................................113 Retrieval and standardization of microarray data .......................................113 Data analysis and statistical methods..........................................................114 Transcription Factor Binding Site (TFBS) overrepresentation analysis.....115 Functional overrepresentation analysis.......................................................116 Cellular classification of differentially expressed genes ............................117