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Background: The advancesin high-throughput technologies have allowed for the massive analysis of genomic data, providing benefits for the characterization of transcriptome architectures.Recent studies in rodent model of nonalcoholic fatty liver disease (NAFLD) employed RNA-Seq technique to explore the hepatic transcriptome in different pretreated conditions.The main goal of this study was to perform a large-scale gene expression profiling of liver in NAFLD rats intervened by supplementary fish oil rich in n-3 polyunsaturated fatty acids (DHA/EPA) by RNA-seq, to gain a deep insight into potential mechanisms of the effects of n-3 PUFA against NAFLD.