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.

该副本是利用众多研究子项目之一 由NIH/NCRR资助的中心赠款提供的资源。子弹和 调查员（PI）可能已经从其他NIH来源获得了主要资金， 因此可以在其他清晰的条目中代表。列出的机构是 对于中心，这不一定是调查员的机构。 在当代生物医学研究中，用于高吞吐量DNA测序，比较基因组学，SNP分析和基因表达分析的工具几乎是必不可少的。由于我们目前的毛线支持，我们能够建立高吞吐量多用户DNA序列分析核心功能。爱达荷大学唯一的一家。这个设施极大地受益 大学的研究人员和大学的更大的生物医学研究界。为了使大学在生物医学研究中保持竞争力，并使毛cre资助的研究人员实现拟议的研究项目的目标，我们不仅必须保持核心当前的能力，而且还必须添加能够迅速完成整个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。核心设施占据了South Life Sciences的新装修空间的850平方英尺。它配备了下面描述的主要仪器和计算资源，以及湿实验室的长凳，生物安全柜，热循环器，离心机，微纤维，冰柜，冰箱和其他次要设备进行样品制备。实验室的一部分致力于数据分析和生物信息学，并具有高端工作站和打印机，这些工作站和打印机通过互联网链接到校园的生物信息学核心设施的软件和硬件资源。一名技术人员负责监督工具的操作和维护，并为设施的用户提供指导，指导和故障射击帮助。核心设施中现在可用的主要仪器包括以下内容： Nimblegen杂交系统。杂交系统是一个四湾系统，可以容纳多种阵列类型，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扫描仪能够扫描和量化来自多个不同供应商的DNA微阵列载玻片，包括Nimblegen和Agilant微阵列 基因组测序仪FLX钛系列仪器。由GS FLX钛和标准系列试剂提供动力的Genome Sequencer FLX仪器具有长读，出色精度和高吞吐量的突破性组合。应用包括从头测序，整个基因组和靶DNA区域的重新配置，宏基因组学和RNA分析。 +应用生物系统Prism 3730 DNA分析仪。 ABI 3730是一个48毛细管系统，可容纳两个阵列长度，50厘米和36厘米，用于DNA片段分析应用，例如微卫星，AFLP，SNP分析，突变检测和传统的DNA测序 +应用生物系统Prism 3100 DNA分析仪。 ABI 3100是一种基于荧光的DNA分析系统，其中16个电泳毛细血管并行操作。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吞吐量样品处理。定制的工作站配备了一个4微板振动板系统，可有效地重悬或裂解，两个真空歧管，用于同时净化192个样品，一个带有四个稀释器单元的高速移液器系统，一个冷却和暖气系统，用于执行热量的步骤，以及诸如t-Grip Robotic STEPS，以及一个T-Grip Robotic Marts，以及移动的物品， 在工作台上的位置之间。 +两台Macintosh Power Mac G5计算机都有每个处理器的双2GHz处理器，每个处理器的高速缓存。对于内存和存储，每台计算机配备了1GB RAM，两个250GB硬盘驱动器和一个先锋DVD-RW/CD-RW DISC驱动器。该计算机与内部千兆以太网网络卡连接到高速Ibest网络。 +一台MacIntosh Mac Pro计算机，带有两个四核Intel Xeon 2.8GHz处理器，每个处理器12MB的缓存。对于内存和存储，它配备了4GB RAM，两个500GB硬盘驱动器和一个先锋DVD-RW/DVR磁盘驱动器。该计算机与内部千兆以太网网络卡连接到高速Ibest网络。 +带有Intel Pentium 4 CPU 1.6GHz处理器的一台Dell计算机，带有256KB的存储器和存储，配备了256MB的RAM，76GB硬盘驱动器和CD-R/CD-RW DISC驱动器。它是运行Ubuntu Linux的设置，并且还连接到高速Ibest网络。 +带有Intel Pentium 4 3GHz处理器的一台戴尔计算机。对于内存和存储，它配备了1GB RAM，300GB硬盘驱动器和DVD/CD-R DISC驱动器。它当前正在运行Windows XP，并且还连接到高速Ibest网络。 一台带双Intel Xeon的Dell计算机2.26 GHz四核处理器。对于内存和存储，它配备了24GB的RAM和1TB硬盘驱动器以及DVD/CD-R DISC驱动器。它目前正在运行Ubuntu Linux 9.04，并且还连接到高速Ibest网络。