COBRE: UID: DNA SEQUENCE ANALYSIS CORE FACILITY

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 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经成为当代生物医学研究中几乎不可或缺的工具。由于我们目前对Cobre的支持，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；这是爱达荷州大学唯一的一个。这一设施极大地造福了Cobre研究人员和大学更大的生物医学研究社区。为了使该大学在生物医学研究方面保持竞争力，并使科布雷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目前的能力，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平方英尺。生命科学南区新装修的空间之脚。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、热循环器、离心机、微型熔断器、冰柜、冰箱和样品制备所需的其他次要设备。该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，这些工作站和打印机通过互联网连接到校园内生物信息学核心设施的软硬件资源。一名技术人员监督仪器的操作和维护，并为设施的用户提供指导、指导和故障排除帮助。核心基金目前提供的主要工具包括： 应用生物系统公司PRISM 3730 DNA分析仪。ABI 3730是一个48毛细管系统，可容纳50厘米和36厘米两个阵列长度，用于高通量DNA测序。 应用生物系统公司PRISM 3100 DNA分析仪。ABI 3100是一种基于荧光的DNA分析系统，其中16个毛细管平行运行。该仪器几乎完全用于DNA片段分析。 QIAGEN BioRobot 3000。Qiagen BioRobot使用96孔微孔板格式实现了高通量样品处理。定制的工作站配备了用于高效细胞再悬浮或裂解的4微板振荡器系统、用于同时提纯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、用于执行热依赖步骤的冷却和加热Peltier系统以及用于移动微板等物品的T-GRIP机械臂 在工作台上的各个位置之间。 两台Macintosh Power Mac G5电脑都有双2 GHz处理器，每个处理器有512KB的高速缓存。在内存和存储方面，每台计算机都配备了1 GB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。该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 2.8 GHz处理器，每个处理器具有12MB高速缓存。在内存和存储方面，它配备了4 GB的RAM，两个500 GB的硬盘驱动器和一个Pioneer DVD-RW/DVR光盘驱动器。该计算机通过内部千兆以太网卡连接到高速IBEST网络。 一台戴尔计算机，配备Intel Pentium 4 CPU 1.6 GHz处理器，256KB高速缓存用于内存和存储，配备256MB RAM、76 GB硬盘和CD-R/CD-RW光盘驱动器。它被设置为运行Ubuntu Linux，并且还连接到高速IBEST网络。 一台配备英特尔奔腾4 3 GHz处理器的戴尔计算机。在内存和存储方面，它配备了1 GB的RAM、300 GB的硬盘驱动器和DVD/CD-R光盘驱动器。它目前运行的是Windows XP，还连接到了高速的IBEST网络。

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: + Applied Biosystems PRISM 3730 DNA Analyzer. The ABI 3730 is a 48 capillary system that can accommodate two array lengths, 50cm and 36cm for high-throughput 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.