COBRE: UID: DNA SEQUENCE ANALYSIS CORE FACILITY

COBRE：UID：DNA 序列分析核心设施

• 批准号: 8359573
• 负责人: LARRY J FORNEY
• 金额: $ 38.82万
• 依托单位: UNIVERSITY OF IDAHO
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-02-01 至 2012-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8359573
• 关键词: Base Sequence; Bioinformatics; Biological Sciences; Biomedical Research; Blood capillaries; Capillary Electrophoresis; Cells; Centers of Research Excellence; Communities; Computer software; Computers; Core Facility; Cytolysis; DNA; DNA Microarray Chip; DNA Resequencing; DNA Sequence; DNA Sequence Analysis; DNA analysis; Data Analyses; Equipment; Evolution; Fluorescence; Funding; Gene Expression; Genome; Grant; Heating; Idaho; Instruction; Internet; Laboratories; Length; Link; Linux; Location; Maintenance; Memory; Metagenomics; Microsatellite Repeats; Minor; Mutation Detection; National Center for Research Resources; Nucleic acid sequencing; Preparation; Principal Investigator; Process; RNA analysis; Reading; Reagent; Research; Research Infrastructure; Research Personnel; Research Project Grants; Resources; Robotics; Running; Sampling; Scanning; Series; Slide; Source; Speed; System; Titania; Titanium; United States National Institutes of Health; Universities; Vacuum; Vendor; arm; base; capillary; comparative genomics; computing resources; cost; foot; grasp; instrument; instrumentation; operation; tool

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The tools used for high throughput DNA sequencing, comparative genomics, SNP analysis, and the analysis of gene expression have become nearly indispensable in contemporary biomedical research. As a result of our current COBRE support we have been able to establish a high throughput multi-user DNA Sequence Analysis Core facility; the only one at the University of Idaho. This facility has greatly benefited both COBRE researchers and the larger biomedical research community at the University. In order for the University to remain competitive in biomedical research, and for COBRE funded researchers to achieve the aims of the proposed research projects, we must not only maintain the current capabilities of the core, but also add the capability to rapidly do whole genome re-sequencing and gene expression analysis. The existing DNA Sequence Analysis Core Facility provides researchers access to the instruments, equipment, and facilities needed for the analysis of nucleic acid sequences. The Core Facility occupies 850 sq. feet of newly renovated space in Life Sciences South. It is equipped with the major instrumentation and computational resources described below, as well as wet lab benches, biosafety cabinets, thermocyclers, centrifuges, microfuges, freezers, refrigerators, and other minor equipment needed for sample preparation. A portion of the laboratory is dedicated to data analysis and bioinformatics and has high-end workstations and printers that are linked via the internet to the software and hardware resources of the Bioinformatics Core Facility on campus. A technician oversees operation and maintenance of the instruments, and provides instruction, guidance, and trouble-shooting assistance to users of the facility. The major instrumentation now available in the Core Facility includes the following: Nimblegen Hybridization System. The Hybridization system is a four-bay system that can accommodate multiple array types to achieve consistent and reproducible microarray hybridization results GenePix 4000B Microarray Scanner. The GenePix Scanner is capable of scanning and quantifying DNA microarray slides from multiple different vendors including Nimblegen and Agilant microarrays Genome Sequencer FLX Titanium Series Instrument. The Genome Sequencer FLX Instrument, powered by GS FLX Titanium and Standard series reagents, features a groundbreaking combination of long reads, exceptional accuracy and high throughput. Applications include de novo sequencing, resequencing of whole genomes and target DNA regions, metagenomics and RNA analysis. + Applied Biosystems PRISM 3730 DNA Analyzer. The ABI 3730 is a 48 capillary system that can accommodate two array lengths, 50cm and 36cm for DNA fragment analysis applications such as microsatellites, AFLP, SNP analysis, mutation detection and traditional DNA sequencing + Applied Biosystems PRISM 3100 DNA Analyzer. The ABI 3100 is a fluorescence based DNA analysis system in which 16 electrophoresis capillaries are operated in parallel. The instrument is almost exclusively used for DNA fragment analysis. + Qiagen BioRobot 3000. The Qiagen BioRobot allows for high throughput sample processing using a 96-well microplate format. The customized workstation is equipped with a 4 microplate shaker system for efficient cell resuspension or lysis, two vacuum manifolds for simultaneous purification of 192 samples, a high-speed pipetting system with four dilutor units, one cooling and heating Peltier system for performing heat-dependent steps, and a T-grip robotic arm for moving items such as microplates between locations on the worktable. + Two Macintosh Power Mac G5 computers both of which have dual 2GHz processors with 512kb of cache per processor. For memory and storage each computer is equipped with 1GB of RAM, two 250GB hard drives and a Pioneer DVD-RW/CD-RW disc drive. This computer is connected to the high speed IBEST network with an internal gigabit Ethernet network card. + One Macintosh Mac Pro computer with two quad-Core Intel Xeon 2.8GHz processors with 12MB of cache per processor. For memory and storage it is equipped with 4GB of RAM, two 500GB hard drives and a Pioneer DVD-RW/DVR disc drive. This computer is connected to the high speed IBEST network with an internal gigabit Ethernet network card. + One Dell Computer with a Intel Pentium 4 CPU 1.6GHz processor with 256kb of cache For memory and storage it is equipped with 256MB of RAM, a 76GB hard drive and a CD-R/CD-RW disc drive. It is setup to run Ubuntu Linux and is also connected to the high speed IBEST network. + One Dell Computer with an Intel Pentium 4 3GHz processor. For memory and storage it is equipped with 1GB of RAM, a 300GB hard Drive and a DVD/CD-R disc drive. It is currently running Windows XP and is also connected to the high speed IBEST network. One Dell Computer with Dual Intel Xeon 2.26 Ghz Quad Core Processors. For memory and storage it is equiped with 24GB of RAM and 1TB Hard Drive and DVD/CD-R disc drive. It is currently running Ubuntu Linux 9.04 and is also connected to the high speed IBEST network.

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 而子项目的主要调查员可能是由其他来源提供的， 包括其它NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， 而不是由NCRR赠款提供给子项目或子项目工作人员的直接资金。 用于高通量DNA测序、比较基因组学、SNP分析和基因表达分析的工具已成为当代生物医学研究中几乎不可或缺的工具。由于我们目前的COBRE支持，我们已经能够建立一个高通量的多用户DNA序列分析核心设施;唯一的一个在爱达荷州大学。这一举措使双方受益匪浅。 COBRE研究人员和大学更大的生物医学研究社区。为了使大学在生物医学研究方面保持竞争力，并使COBRE资助的研究人员实现拟议研究项目的目标，我们不仅必须保持现有的核心能力，而且还必须增加快速进行全基因组重新测序和基因表达分析的能力。 现有的DNA序列分析核心设施为研究人员提供了分析核酸序列所需的仪器、设备和设施。核心设施占地850平方米。新装修的空间在生命科学南部英尺。它配备了下文所述的主要仪器和计算资源，以及湿实验室工作台、生物安全柜、热循环仪、离心机、微量离心机、冷冻机、冰箱和样品制备所需的其他次要设备。实验室的一部分专门用于数据分析和生物信息学，并拥有高端工作站和打印机，通过互联网连接到校园生物信息学核心设施的软件和硬件资源。技术人员监督仪器的操作和维护，并为设施的用户提供说明、指导和故障排除帮助。核心设施现有的主要仪器包括： Nimblegen杂交系统。杂交系统是一个四机架系统，可容纳多种阵列类型，以获得一致和可重复的微阵列杂交结果 GenePix 4000 B微阵列扫描仪。GenePix扫描仪能够扫描和定量来自多个不同供应商的DNA微阵列载玻片，包括Nimblegen和Quantiant微阵列 基因组测序仪FLX钛系列仪器。基因组测序仪FLX仪器由GS FLX Titanium和Standard系列试剂提供支持，具有突破性的长读取、卓越的准确性和高通量组合。应用包括从头测序、全基因组和靶DNA区域的重测序、宏基因组学和RNA分析。 + Applied Biosystems PRISM 3730 DNA分析仪。ABI 3730是一个48毛细管系统，可容纳两种阵列长度，50 cm和36 cm，用于DNA片段分析应用，如微卫星、AFLP、SNP分析、突变检测和传统DNA测序 + Applied Biosystems PRISM 3100 DNA分析仪。ABI 3100是一种基于荧光的DNA分析系统，其中16个电泳毛细管并行操作。该仪器几乎完全用于DNA片段分析。 + 第3000章. Qiagen BioRobot允许使用96孔微孔板格式进行高通量样品处理。定制的工作站配备了一个4微孔板振荡器系统，用于有效的细胞重悬或裂解，两个真空歧管，用于同时纯化192个样品，一个高速移液系统，四个稀释器单元，一个冷却和加热Peltier系统，用于执行热依赖性步骤，以及一个T-grip机械臂，用于移动微孔板等物品 两个地点之间的联系 + 两台Macintosh Power Mac G5计算机，都有双2GHz处理器，每个处理器有512 kb的缓存。对于内存和存储，每台计算机都配备了1GB的RAM，两个250 GB的硬盘驱动器和一个Pioneer DVD-RW/CD-RW光盘驱动器。此计算机通过内部千兆以太网卡连接到高速IBEST网络。 + 一台Macintosh Mac Pro计算机，配备两个四核Intel Xeon 2.8GHz处理器，每个处理器12 MB缓存。对于内存和存储，它配备了4GB的RAM，两个500 GB的硬盘驱动器和先锋DVD-RW/DVR光盘驱动器。此计算机通过内部千兆以太网卡连接到高速IBEST网络。 + 一台戴尔电脑，配备英特尔奔腾4 CPU 1.6GHz处理器和256 kb高速缓存，内存和存储配备256 MB RAM、76 GB硬盘和CD-R/CD-RW光盘驱动器。它被设置为运行Ubuntu Linux，并连接到高速IBEST网络。 + 一台配备英特尔奔腾4 3GHz处理器的戴尔计算机。对于内存和存储，它配备了1GB的RAM，300 GB的硬盘和DVD/CD-R光盘驱动器。它目前运行Windows XP，并连接到高速IBEST网络。 一台配备双英特尔至强2.26 Ghz四核处理器的戴尔计算机。对于内存和存储，它配备了24 GB的RAM和1 TB的硬盘驱动器和DVD/CD-R光盘驱动器。它目前运行Ubuntu Linux 9.04，并连接到高速IBEST网络。