Brain RNA-seq in the LXS RI strains: Saline and ethanol treatment

Purpose: To investigate the effect that acute ethanol tretament (5 g/kg) has on the brain transcriptome and relate that to ethanol-related behaviors. Methods: Male LXS recombinant inbred mice (40 strains; n=2 or 3 per strain) were treated with saline or ethanol (i.p.; 5 g/kg). Paired-end RNA-seq methods were employed to assess mRNA expression in whole brain 8 hours after the treatment. Results: The expression of thousands of transcripts was altered by the ethanol treatment. Thousands of expression QTLs (eQTLs) were mapped. A large percentage of the eQTLs were unique to the treatment. Poly-A RNA from whole brain (minus cerebellum, and olfactory bulbs) was profiled using Illumina HiSeq 2000 (2x100). Tissue was generated from 40 LXS recombinant inbred mouse strains; all mice were males. There were two treatment groups per strain: 1) saline (0.01 ml/g, ip) or 2) ethanol in saline (5 g/kg, ip; 20% v/v) with an an of 3 samples per strain/treatment condition (8 of the strain/treatment groups had an n of 2). Each sample consisted of pooled RNA from 3 individual mice. Mice were euthanized for tissue collection at 8 hours post treatment.