Liver Transcriptome Analysis by RNA-seq

Liver transcriptome analysis was performed by RNA sequencing on RNA extracts from terminal liver samples (15 mg fresh tissue), as described in detail elsewhere^{34 (link)}. The RNA quantity was measured using Qubit® (Thermo Scientific, Eugene, OR). The RNA quality was determined using a bioanalyzer with RNA 6000 Nano kit (Agilent, Waldbronn, Germany). RNA sequence libraries were prepared with NeoPrep (Illumina, San Diego, CA) using Illumina TruSeq stranded mRNA Library kit for NeoPrep (Illumina, San Diego, CA) and sequenced on the NextSeq. 500 (Illumina, San Diego, CA) with NSQ 500 hi-Output KT v2 (75 CYS, Illumina, San Diego, CA). Reads were aligned to the GRCm38 v84 Ensembl Mus musculus genome using STAR v.2.5.2a with default parameters^{36 (link)}. Differential gene expression analysis was performed with DEseq2^{37 (link)}. Genes with a Benjamini and Hochberg adjusted P ≤ 0.05 (5% False Discovery Rate, FDR) were regarded as statistically significantly regulated.