RNA-Seq of mouse liver female transcriptome: role of estrogens and hepatic ERa in the metabolic adaptation to dietary AA

The study was undertaken to evaluate the effects of dietary EAA (essential amino acids) on female liver metabolism and to elucidate to which extent the hepatic (Estrogen receptor alpha) ERa might account for the potential ability of female liver to modulate the metabolism in response to dietary EAA. To this aim, we adopted a specific diet formula, in which the enrichment in EAA did not affect the ratio among the macro-nutrients (carbohydrates/lipids/proteins). Overall design: at 2 months of age, mice were ovariectomized or sham operated. After 4 weeks, animals were assigned to a specific experimental group and fed with a control diet or a diet enriched in EAA for 12 weeks starting at 3 months of age. At the end of the experiment, mice were 6 months old. As the phase of the estrous cycle impacts on liver transcriptome, sham-operated female mice were collected when in the Estrus phase of the estrous cycle. Prior euthanasia, mice were fasted 6h to avoid diet-induced activation of the hepatic ERa. To verify the impact of hepatic ERa on liver transcriptome, RNA-seq analysis was also done on control (ERa floxed) or LERKO (liver ERa knockout) mice. Illumina TruSeq Stranded mRNA Library Prep was used for library construction and samples were sequenced on Illumina HiSeq platform, producing 2x150 bp paired end reads.