COBRE: UID: DNA SEQUENCE ANALYSIS CORE FACILITY

COBRE：UID：DNA 序列分析核心设施

• 批准号: 8167450
• 负责人: LARRY J FORNEY
• 金额: $ 17.14万
• 依托单位: UNIVERSITY OF IDAHO
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-02-01 至 2011-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8167450
• 关键词: Base Sequence; Bioinformatics; Biological Sciences; Biomedical Research; Blood capillaries; Capillary Electrophoresis; Cells; Centers of Research Excellence; Communities; Computer Retrieval of Information on Scientific Projects Database; Computer software; Computers; Core Facility; Cytolysis; DNA; DNA Microarray Chip; DNA Resequencing; DNA Sequence; DNA Sequence Analysis; DNA analysis; Data Analyses; Equipment; Fluorescence; Funding; Gene Expression; Genome; Grant; Heating; Idaho; Institution; Instruction; Internet; Laboratories; Length; Link; Linux; Location; Maintenance; Memory; Metagenomics; Microsatellite Repeats; Minor; Mutation Detection; Nucleic acid sequencing; Preparation; Process; RNA analysis; Reading; Reagent; Research; Research Personnel; Research Project Grants; Resources; Robotics; Running; Sampling; Scanning; Sequence Analysis; Series; Slide; Source; Speed; System; Titanium; United States National Institutes of Health; Universities; Vacuum; Vendor; arm; base; capillary; comparative genomics; computing resources; 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. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. 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.

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。子项目及 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以在其他 CRISP 条目中表示。列出的机构是 对于中心来说，它不一定是研究者的机构。 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。由于我们当前的 COBRE 支持，我们已经能够建立高通量多用户 DNA 序列分析核心设施；爱达荷大学唯一一所。这项设施使双方都受益匪浅 COBRE 研究人员和大学内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，我们不仅必须保持核心的现有能力，而且还必须增加快速进行全基因组重新研究的能力。 -测序和基因表达分析。 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 平方英尺，位于生命科学南区新装修的空间中。它配备了下述主要仪器和计算资源，以及湿式实验室工作台、生物安全柜、热循环仪、离心机、微量离心机、冰柜、冰箱和样品制备所需的其他小型设备。实验室的一部分致力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。技术人员负责监督仪器的操作和维护，并向设施用户提供说明、指导和故障排除帮助。核心设施中现有的主要仪器包括： Nimblegen 杂交系统。杂交系统是一个四槽系统，可容纳多种阵列类型，以实现一致且可重复的微阵列杂交结果 GenePix 4000B 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（包括 Nimblegen 和 Agilant 微阵列）的 DNA 微阵列载玻片 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 和标准系列试剂提供动力，具有长读数、卓越准确性和高通量的突破性组合。应用包括从头测序、全基因组和目标 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 厘米和 36 厘米），适用于 DNA 片段分析应用，例如微卫星、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 个电泳毛细管并行运行。该仪器几乎专门用于DNA片段分析。 + Qiagen BioRobot 3000。Qiagen BioRobot 允许使用 96 孔微孔板格式进行高通量样品处理。定制工作站配备用于高效细胞重悬或裂解的 4 微孔板摇床系统、用于同时纯化 192 个样品的两个真空歧管、带有四个稀释器单元的高速移液系统、用于执行热依赖的冷却和加热 Peltier 系统台阶和用于移动微孔板等物品的 T 形夹具机械臂 工作台上的位置之间。 + 两台 Macintosh Power Mac G5 计算机，均配备双 2GHz 处理器，每个处理器具有 512kb 缓存。对于内存和存储，每台计算机均配备 1GB RAM、两个 250GB 硬盘驱动器和一个 Pioneer DVD-RW/CD-RW 光盘驱动器。该计算机通过内部千兆位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，每个处理器具有 12MB 缓存。对于内存和存储，它配备了 4GB RAM、两个 500GB 硬盘驱动器和一个 Pioneer DVD-RW/DVR 光盘驱动器。该计算机通过内部千兆位以太网卡连接到高速 IBEST 网络。 + 一台配备 Intel Pentium 4 CPU 1.6GHz 处理器和 256kb 高速缓存的戴尔计算机 对于内存和存储，它配备了 256MB RAM、76GB 硬盘驱动器和 CD-R/CD-RW 光盘驱动器。它被设置为运行 Ubuntu Linux，并且还连接到高速 IBEST 网络。 + 一台配备 Intel Pentium 4 3GHz 处理器的戴尔计算机。对于内存和存储，它配备了 1GB RAM、300GB 硬盘和 DVD/CD-R 光盘驱动器。它当前运行的是 Windows XP，并且还连接到高速 IBEST 网络。 一台配备双 Intel Xeon 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 24GB RAM 和 1TB 硬盘以及 DVD/CD-R 光盘驱动器。它目前运行的是 Ubuntu Linux 9.04，并且还连接到高速 IBEST 网络。