Our RNA-seq study demonstrated that a known splice junction at exons 22-23 increased RPJM values in alcoholic brain. However, exons 14-16 and 5-6 did not show RPJM changes (Figure 7). Quantitative real-time PCR data also generated the same patterns as the RNA-seq splice junction study (Figure S4A in Supplement 1). RPGM changes at exons and introns were consistent with quantitative real-time PCR (Figure S4B in Supplement 1). Previous microarray studies using cDNA and oligonucleotide probes were also consistent with most of our RNA-seq data. The alcoholic and control groups used for the confirmation experiments are slightly different due to a limited sample number. Although the increase previously seen in one cDNA microarray probe signal at intron 4 was not confirmed in our RNA-seq data, four array probes targeting exon 23 and another probe for intron 5 showed no expression changes in agreement with our current RNA-seq data (5, 6, 17). Interestingly, an RNA-seq study of hippocampus found that GABAB1 transcripts decrease in human alcoholics and cocaine addicts as well as alcohol preferring rats that are genetically predisposed to excessive alcohol consumption (38). However, it is unknown which splice variants were detected and quantified in this study.
