Next Generation Sequencing For Quantitative Analysis Of Hepatic Transcriptomes In Response To Squalene in Swine model

Purpose: The goal of this study was to determine squalene effect on hepatic transcriptome by comparing high-throughput data for tested group vs. control group in male Large White x Landrace Large swine animals Method: Study the Hepatic mRNA profile of swine animals in response to a steatotic diet supplied with 0.5% squalene over a month by Transcriptome sequencing using DNBseq platform. Sequence reads that passed quality filters were mapped onto reference genome, followed by SNP & INDEL variants calling and Gene expression detection. Results: Squalene intake did not significantly influence single nucleotide polymorphisms. When alternative splicing events were tested, squalene administration had significant influence on splicing events including alternative 5' splicing, alternative 3' splicing , retained intron, skipped exons and mutually exclusive exons. Splicing patterns led to variety of differentially splicing genes and a variety of different isoforms from one gene. Differentially expressed genes were 18,659 in the squalene group and 18,602 in control group. Overall design: Comparative gene expression profiling analysis of RNA-seq data for Pig consuming a steatotic diet and their counterparts consuming the same diet enriched in 0.5% squalene研究目的：本研究旨在通过比较雄性大白×长白杂交猪受试组与对照组的高通量测序数据，解析角鲨烯对肝脏转录组的影响。 研究方法：采用DNBseq测序平台开展转录组测序，分析受试猪在饲喂添加0.5%角鲨烯的致脂肪变性日粮1个月后的肝脏mRNA表达谱。将通过质量过滤的测序读数比对至参考基因组，随后进行单核苷酸多态性（Single Nucleotide Polymorphism, SNP）与插入缺失变异（Insertion-Deletion, INDEL）的变异检出，以及基因表达量检测。 研究结果：角鲨烯摄入对单核苷酸多态性无显著影响。在检测可变剪接事件时发现，角鲨烯给药对多种剪接事件具有显著影响，包括可变5'剪接、可变3'剪接、内含子保留、外显子跳跃及互斥外显子。不同的剪接模式可产生多种差异剪接基因，以及单个基因编码的多种不同转录本异构体。角鲨烯组与对照组的差异表达基因数量分别为18659个与18602个。 整体实验设计：本研究针对饲喂致脂肪变性日粮的猪与饲喂添加0.5%角鲨烯的同型致脂肪变性日粮的对照猪的RNA-seq数据，开展对比基因表达谱分析。