MRI: Acquisition of an Illumina/Solexa Genome Analyzer

犹他州大学获得了一笔赠款，用于获得下一代基因组分析机器，如Illumina/Solexa基因组分析仪。 这种设备使用新的方法，可以快速获得大量的DNA序列，成本大约是传统基因组中心的1%。 该设备将支持不同的用户群，并将为许多NSF支持的研究项目做出重大贡献。 此外，该设备还将用于本科教育。 该设备的主要研究者和主要用户将解决几个不同的基本研究问题：（1）自然变异和基因组进化-了解生物多样性需要了解个体或菌株之间的DNA序列差异以及这些序列差异如何影响表型。 使用这种新技术降低测序成本，以及获得DNA序列数据的速度，将允许几个PI和主要用户获得植物拟南芥，细菌内共生体，九棘鱼，赤狐和斑胸草雀的高质量基因组序列数据。 我们预计，基因组序列将使我们能够深入了解进化变化的模式，包括那些生物体对其环境的反应（例如，植物的干旱反应）。(2)遗传网络和基本分子机制-细胞和发育生物学的一个主要目标是了解特定基因如何在特定细胞类型中表达。 几个PI和主要用户正在关注RNA衰变的转录网络和机制，并将使用下一代测序仪来识别由于特定信号传导而产生的RNA以及积累的中间体。 有资金支持的仪器所可能采用的方法将允许在前所未有的详细程度上进行定性和定量分析。(3)微妙突变表型的行为遗传学和分子表征-一些遗传变异（突变）会导致非常微妙的表型，因此传统的方法，如遗传图谱，要么是困难的，要么是非常耗时的。 然而，这种突变对于理解行为的分子基础是非常有用的。 使用下一代测序仪，结合遗传学方法，将允许快速识别行为特征背后的DNA损伤（和基因）。 初步研究将使用线虫秀丽隐杆线虫进行。下一代序列分析仪将被放置在犹他州大学生物系的新基因组学设施中。 它将提供给大盆地地区（例如爱达荷州、怀俄明州、蒙大拿州、内华达州和新墨西哥州）的研究人员。 生物学系认为，对大型基因组学数据集的实际理解是基础本科教育的重要组成部分。 已经为三门本科课程制定了纳入这种新设备和分析所产生数据的具体计划。

A grant has been awarded to the University of Utah to obtain a next-generation genome analysis machine such as the Illumina/Solexa Genome Analyzer. This sort of equipment uses new methods that allow very large amounts of DNA sequence to be obtained rapidly, and at approximately 1% of the cost of traditional genome centers. The equipment will support a diverse base of users, and will contribute significantly to many NSF-supported research programs. In addition, the equipment will also be used for undergraduate education. The PIs and major users of this equipment will address several different basic research question: (1) Natural Variation and Genome Evolution- Making sense of biological diversity requires understanding the DNA sequence differences between individuals or strains and how these sequence differences influence phenotypes. The reduced cost of sequencing using this new technology, and the speed with which DNA sequence data can be obtained, will allow several PIs and major users to obtain high quality genomic sequence data for the plant Arabidopsis thaliana, bacterial endosymbionts, the ninespine stickleback, red fox, and zebra finch. We anticipate that the genome sequences will allow us to gain insights into modes of evolutionary change, including those that underlie response of organisms to their environments (e.g., drought response in plants). (2) Genetic Networks and Basic Molecular Mechanisms- A major goal of cellular and developmental biology is to understand how specific genes come to be expressed in specific cell types. Several PIs and major users are focusing on transcriptional networks and mechanisms of RNA decay, and will use the next-generation sequencer to identify the RNAs that are produced as a result of specific signaling, and the intermediates that accumulate. The approaches that are possible with the funded instrumentation will allow both qualitative and quantitative analyses at an unprecedented level of detail. (3) Behavioral Genetics and Molecular Characterization of Subtle Mutant Phenotypes- Some genetic variations (mutations) cause very subtle phenotypes, and so traditional approaches like genetic mapping are either difficult or extremely time-intensive. Nevertheless, such mutations are very informative for understanding the molecular basis of behaviors. Using the next-generation sequencer, in combination with genetic approaches, will allow rapid identification of the DNA lesions (and genes) underlying behavioral traits. Initial studies will be performed with the nematode Caenorhabditis elegans. The next-generation sequence analyzer will be placed into a new Genomics Facility in the Biology Department at the University of Utah. It will be made available to researchers in the Great Basin Region (e.g. Idaho, Wyoming, Montana, Nevada, and New Mexico). The Biology Department at the University of considers a hands-on understanding of large genomics datasets to be an essential component of a basic undergraduate education. Specific plans to incorporate this new equipment and analysis of the resulting data have already been developed for three undergraduate courses.