15_mus musculus_c57bl_adult_male_Liver_Standard diet
The RNeasy Lipid Tissue Mini Kit (Qiagen) was used to extract total RNAs from the liver and WAT, while RNA from skeletal muscle was extracted using Trizol (Invitrogen). Seven animals were included in each experimental group. The RNAs were precipitated and their quality and quantity assessed using an Agilent Bioanalyzer 2100 and an RNA 6000 chip (Agilent Technologies). The cDNA libraries were then constructed using the TruSeq RNA Sample Prep Kit v2 (Illumina, Inc.) and their quality checked using an Agilent Bioanalyzer 2100 and a DNA 1000 chip (Agilent Technologies). The libraries were Paired End sequenced in a HiSeq 4000 system (Illumina, Inc.) at Macrogen Inc. We aimed for 45 Giga Bases outcome per sample. The quality of the resulting sequencing reads was assessed using FastQC. The GRCm39 fasta and gtf files of the reference mouse genome were downloaded from the Ensembl database and indexed using the bwtsw option of BWA. BWA, combined with xa2multi.pl and SAMtools, was also used for aligning the sequencing reads against the reference genome, and HTSeq was used for counting the number of reads aligned to each genomic locus. The alignments and counting were carried out in our local server following the protocols as described (Bakkali & Martin-Blazquez, 2018).