RNAseq analysis was used to identify mRNAs regulated by exposure to alcohol. Of 17,327 genes in the rat reference genome, 15,062 mRNAs were identified having over 0.1 FPKM (Additional file 1: Table S6); of those, 312 were differentially expressed (DE) following ethanol treatment (“Alc-DEs”; Additional file 1: Table S1). The majority of Alc-DEs (230) were increased, while 82 were decreased by ethanol. Of those, 274 were changed by at least 20% and 19 changed by at least 50%. Gda (guanine deaminase) was the mRNA most decreased (to about 50% of control values), and Robo1 (roundabout guidance receptor 1) and Plxdc2 (plexin domain containing 2) were the most increased (to 170% of control values) by alcohol. Quantitative reverse-transcription PCR (qPCR) of the mRNAs showing the largest changes, as well as of several other mRNAs selected for having important functional consequences, validated RNAseq results (Fig. 2).
