Next Generation Sequencing For Quantitative Analysis Of Hepatic Transcriptomes In Response To Txndc5

Purpose: The goal of this study was to determine the hepatic transcriptomic's difference in mice TXNDC5 KO Method: Hepatic mRNA profile of C57Bl/6J wild-type vs TXNDC5 KO mice fed over 4 weeks with a purified chow diet was analysed by Transcriptome sequencing using BGISEQ-500 platform. Sequence reads that passed quality filters were mapped onto reference genome, followed by novel gene prediction, SNP & INDEL calling and gene-splicing detection. Results: When using optimized Bioinformatics Workflow, mapping ratio for both tested groups was about 84,76%, 16,178 genes were identified in which 16,178 of them are known genes and 764 of them are novel genes. 5,419 novel transcipts were identified in which 4,115 of them are previously unknown splicing event for known genes, 764 of them are novel coding transcripts without any known features, and the remaining 540 are long noncoding RNA. Conclusions: This study represents the first analysis of hepatic transcriptome in respond to TXNDC5 absence. Result data confirm that RNA-Sequencing is a sensitive and accurate tool that provides a framework for comparative investigations of known and novel DEGs. 3 pools of hepatic wild-type RNA was compared versus 3 pools of hepatic TXNDC5 KO RNA. Mice sustrate was C67BL/6J, were feed during 4 weeks over a purified chow diet and sacrificed with a 16 hours fasting.### 研究目的 本研究旨在明确硫氧还蛋白结构域5（TXNDC5）敲除小鼠的肝脏转录组差异。 ### 实验方法 选取以纯化饲料喂养4周的C57Bl/6J野生型与TXNDC5敲除（KO）小鼠，采用BGISEQ-500平台开展转录组测序，分析其肝脏mRNA表达谱。对通过质量过滤的序列读数进行参考基因组比对，随后开展新基因预测、单核苷酸多态性（SNP）与插入缺失（INDEL）位点识别以及基因剪接事件检测。 ### 实验结果 采用优化后的生物信息学分析流程，两组受试样本的比对率均约为84.76%；共鉴定得到16178个基因，其中16178个为已知基因，764个为新基因。此外共鉴定得到5419个新转录本，其中4115个为已知基因的未知剪接事件，764个为无已知特征的新型编码转录本，剩余540个为长链非编码RNA（lncRNA）。 ### 研究结论 本研究首次针对TXNDC5缺失应答的肝脏转录组开展分析。研究结果证实，RNA测序（RNA-Sequencing）是一种灵敏且精准的技术工具，可为已知与新型差异表达基因（DEGs）的比较研究提供分析框架。本研究将3份肝脏野生型RNA混合样本与3份肝脏TXNDC5敲除RNA混合样本进行比对。实验所用小鼠品系为C67BL/6J，以纯化饲料喂养4周后，经16小时禁食并处死。