Most of the studies to date in the field of ethanol transcriptomics have used cDNA or oligonucleotide arrays. Microarrays have incorporated an increasing number of probes over the years and the most advanced ones can now profile expression of more than 45,000 transcripts at a time. High-throughput sequencing of the whole transcriptome (dubbed RNA-seq or next-generation sequencing), however, is opening new avenues for the understanding of gene expression tuning by ethanol. First of all, RNA-seq quantifies expression levels more accurately and has a larger dynamic range than microarrays [88]. In addition, RNA-seq uncovers the existence of novel transcripts that are not referenced in databases and are therefore not interrogated by microarrays. For instance, in a recent study using RNA-seq to compare gene expression in the prefrontal cortex of alcoholics and matched controls, the number of reads that did not map to RefSeq sequences represented more than one third of mapped reads [89, and personal communication from R.D. Mayfield]. Moreover, RNA-seq reveals sequence variations (such as single nucleotide polymorphisms, SNPs) within the transcripts. In the future, it would be interesting to
