Liver Transcriptomic Profiling of Dietary Interventions

To reveal the liver transcriptomic profile of the four different diets, whole-genome gene expression was analyzed by microarray analysis. This analysis included seven mock-treated animals from each C, MF, and INT diet groups, and six animals from the CR diet group. One hundred nanograms of RNA was used for Whole Transcript cDNA synthesis (Affymetrix, Santa Clara, CA, USA). Hybridization, washing, and scanning of Affymetrix GeneChip Mouse Gene 1.1 ST arrays were carried out according to standard Affymetrix protocols. Arrays were normalized using the Robust Multiarray Average method [21 (link),22 (link)]. Probe sets were defined according to Dai et al. [23 (link)]. In this method probes are assigned to unique gene identifiers, in this case Entrez IDs. The probes on the Gene 1.1 ST arrays represent 21225 Entrez IDs. For the analysis, only genes having intensity value of >20 on at least five array were taken into account, which resulted in 14 758 genes. Array data have been submitted to the Gene Expression Omnibus, with accession number GSE61233. The hierarchical clustering plot depicting gene expression profile similarity was constructed by using Multiple Experiment Viewer [24 (link)] and the accompanying body weight heatmap was prepared in Excel.