Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and ASIC1a-/- Hypothalamus Transcriptomes

Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare circadian gene expression in WT and ASIC1a-/- mice hypothalamusl transcriptome profiling at ZT1 and ZT13 Methods: hypothalamus mRNA profiles of 3-month-old wild-type (WT) and Acid-sensing ion channel 1a knockout (ASIC1a-/-) mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. Results: Using an optimized data analysis workflow, we mapped about 46 to 56 millions sequence reads per sample to the mouse genome and identified about 15,000 transcripts in the hypothalamus of WT and ASIC1a-/- mice. 3 genes expression changed at ZT1 and 13 genes expression changed at ZT13 Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that ASIC1a-/- mice only change 16 genes expression Hypothalamus mRNA profiles of 3-month old male wild type (WT) and ASIC1a-/- mice研究目的：下一代测序（Next-generation sequencing, NGS）已彻底革新了基于系统的细胞通路分析方法。本研究旨在对比授时因子时间ZT1与ZT13时刻，野生型（WT）与酸敏感离子通道1a敲除（ASIC1a-/-）小鼠下丘脑的节律基因表达转录组谱。 研究方法：采用Illumina GAIIx测序平台，对3月龄野生型（wild-type, WT）与酸敏感离子通道1a敲除（Acid-sensing ion channel 1a knockout, ASIC1a-/-）小鼠的下丘脑mRNA进行深度测序，设置3次生物学重复。 研究结果：通过优化的数据分析流程，我们将每个样本中4600万至5600万条序列读段比对至小鼠参考基因组，并在野生型与ASIC1a-/-小鼠的下丘脑中鉴定出约15000个转录本。在ZT1时刻，共有3个基因的表达发生改变；在ZT13时刻，则有13个基因的表达发生改变。 研究结论：本研究是首次通过RNA测序技术结合生物学重复开展的小鼠下丘脑转录组详细分析。本研究报道的优化数据分析流程，可为表达谱的比较研究提供分析框架。本研究结果显示，ASIC1a-/-小鼠仅存在16个基因的表达改变。 3月龄雄性野生型（WT）与ASIC1a-/-小鼠的下丘脑mRNA谱