Computational protocol: Metabolic and hepatic effects of liraglutide, obeticholic acid and elafibranor in diet-induced obese mouse models of biopsy-confirmed nonalcoholic steatohepatitis

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Protocol publication

[…] Hepatic transcriptome analysis was performed by RNA sequencing on RNA extracts from terminal liver samples (15 mg fresh tissue), as described in detail previously[]. The RNA quantity was measured using Qubit® (Thermo Scientific, Eugene, OR, United States). 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, United States) using Illumina TruSeq stranded mRNA Library kit for NeoPrep (Illumina, San Diego, CA, United States) and sequenced on the NextSeq 500 (Illumina, San Diego, CA, United States) with NSQ 500 hi-Output KT v2 (75 CYS, Illumina, San Diego, CA, United States). Reads were aligned to the GRCm38 v84 Ensembl Mus musculus genome using STAR v.2.5.2a with default parameters[]. Differential gene expression analysis was performed with DEseq2[]. Genes with a Benjamini and Hochberg adjusted P ≤ 0.05 (5% False Discovery Rate) were regarded as statistically significantly regulated. Enrichment analysis of KEGG pathways were performed using the clusterProfiler package for R[]. […]

Pipeline specifications

Software tools STAR, DESeq2, clusterProfiler
Databases KEGG
Applications Genome annotation, RNA-seq analysis
Organisms Mus musculus, Homo sapiens
Diseases Fatty Liver, Liver Diseases, Non-alcoholic Fatty Liver Disease
Chemicals Cholesterol, Fructose