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Transcriptomic profiling of non-alcoholic fatty liver induced by a high-fat and high-sucrose diet in the genetically diverse Collaborative Cross mice.

ABSTRACT: Transcriptomic profiling of non-alcoholic fatty liver induced by a high-fat and high-sucrose diet in the genetically diverse Collaborative Cross mice.

PROVIDER: PRJNA630290 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11687300.fastq.gz	Fastqsanger.gz
	SRR11687300_1.fastq.gz	Fastqsanger.gz
	SRR11687300_2.fastq.gz	Fastqsanger.gz
	SRR11687301.fastq.gz	Fastqsanger.gz
	SRR11687301_1.fastq.gz	Fastqsanger.gz

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Project description:Identification of molecular determinants of the inter-individual and sex variability in the development of nonalcoholic fatty liver disease (NAFLD) is of great importance. Next-generation sequencing (NGS) derived transcriptome profiling (RNA-seq) is a powerful technique to investigate gene transcripts and gene variants for the systems-based analysis of molecular and cellular pathways. The goal of this study was to determine transcriptomic profiles in the livers of male and female Collaborative Cross (CC) mice fed a high-fat and high-sucrose (HF/HS) diet or a control diet for 12 weeks and to identify inter-individual- and sex-specific gene expression differences during the development of NAFLD. Liver mRNA profiles of 10 CC mouse strains (CC003/Unc, CC011/Unc, CC013/GeniUnc, CC019/TauUnc, CC032/GeniUnc, CC040/TauUnc, CC041/TauUnc, CC042/GeniUnc, CC043/GeniUnc, and CC060/Unc) fed an HF/HS diet were generated by deep sequencing, in triplicate, using Illumina NextSeq 500 NGS system. The sequence reads that passed quality filters were analyzed at the transcript level using TopHat followed by Cufflinks. The total number of differentially expressed genes identified by RNA-seq varied between sexes and individual mouse strains and correlated with the severity of liver steatosis. Pathway analysis of differentially expressed genes showed dysregulation of genes involved in lipid metabolism, cell proliferation and death, inflammation, and fibrogenesis pathways in the livers of males and females CC mice. The RNA-seq data were validated and confirmed by qRT-PCR analysis of 27 selected genes associated with lipid metabolism and fibrogenesis using TaqMan assays. Our results show that RNA-seq based transcriptome analysis offers a comprehensive, quantitative, and qualitative evaluation of whole-genome expression that can be used for the identification of unique genes associated with the inter-individual and sex differences in susceptibility to NAFLD at the population level.

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Transcriptomic profiling of non-alcoholic fatty liver induced by a high-fat and high-sucrose diet in the genetically diverse Collaborative Cross mice.

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