VERMONT IMMUNOBIOL/INFECTIOUS DIS CTR: MICROARRAY & BIOINFORMATIC ANALYSIS CORE

佛蒙特州免疫生物学/传染性盘 CTR：微阵列

• 批准号: 7959814
• 负责人: JEFFREY P. BOND
• 金额: $ 8.57万
• 依托单位: UNIVERSITY OF VERMONT & ST AGRIC COLLEGE
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-07-01 至 2010-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7959814
• 关键词: Advisory Committees; Antibody Formation; Applications Grants; Award; Bioconductor; Bioinformatics; Biological Sciences; Biomedical Research; Brain; CD4 Positive T Lymphocytes; Cell Separation; Charge; Clinical; Collaborations; Communicable Diseases; Computer Retrieval of Information on Scientific Projects Database; Computer software; Consultations; Core Facility; DNA; DNA Sequencing Facility; DNA mapping; Databases; Decontamination; Development; District of Columbia; Educational workshop; Emerging Technologies; Endothelial Cells; Evaluation; Event; Exons; Experimental Designs; Faculty; Funding; Gene Expression Profiling; Genes; Genetic; Genomics; Grant; Hour; Housing; Hydrogen Bonding; Immunobiology; Individual; Informatics; Institution; Interleukin-6; Interview; Laboratories; Leadership; Left; Letters; Marketing; Mediating; Mediation; Memorial Sloan-Kettering Cancer Center; Messenger RNA; Methods; MicroRNAs; Microarray Analysis; Molecular Profiling; Names; National Center for Research Resources; Paper; Pathway Analysis; Pathway interactions; Pertussis Toxin; Play; Preparation; Price; Procedures; Process; Protocols documentation; PubMed; Publications; RNA; Reagent; Recommendation; Research; Research Personnel; Resource Sharing; Resources; Ribonucleases; Roentgen Rays; Role; Sampling; Services; Small RNA; Sorting - Cell Movement; Source; Staff Development; System; Techniques; Technology; Testing; Text; Time; Tissues; United States National Institutes of Health; Vermont; Visit; Work; angiogenesis; base; cDNA Arrays; discount; flexibility; instrumentation; meetings; next generation; posters; programs; promoter; research study; routine practice; service utilization; success

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. OVERVIEW ***Please note the Tables and Figures mentioned below would not reproduce in this format. Please see attachments sent with the paper copy.*** Core B served the VCII both by providing services to individual VCII laboratories (see Utilization and also Publications) as well as by playing a central role in bringing emerging technologies that are important for VCII investigators (Emerging Technologies). General background on the Microarray Facility is also included (General Background Information). UTILIZATION Services provided to individual VCII labs amounted to 65 Affymetrix GeneChips and 25 hours of bioinformatics service (Table I, Figure 1). Table I Services provided to individual laboratories. 'Hours' refers to bioinformatics service. Figure 1 GeneChip (left) and RNA assessment services (right) provided to VCII laboratories as a percentage of total services. Total utilization of the Microarray Facility consisted of (see also Figure 2) -Experimental design consultations with 18 investigators -Completion of 19 microarray projects (277 GeneChips) -Performed 163 RNA assessments: 79 PicoChips, 81 NanoChips, 3 small RNA's chip (new service, implemented, August, 2008) PUBLICATIONS Publications by VCII Faculty on VCII-related projects that were supported by Core B: 1. Dienz, O., Eaton, S.M., Bond, J.P., Neveu, W., Moquin, D., Noubade, R., Briso, E.M. Charland, C., Leonard, W.J., Ciliberto, G., Teuscher, C., Haynes, L., and Rincon, M. (2009) " The induction of antibody production by IL-6 is indirectly mediated by IL-21 produced by CD4 T cells". J Exp Med. 2009 Jan 16;206(1):69-78. Epub 2009 Jan 12. 2: Lu C, Pelech S, Zhang H, Bond J, Spach K, Noubade R, Blankenhorn EP, Teuscher C. Pertussis toxin induces angiogenesis in brain microvascular endothelial cells. J Neurosci Res. 2008 Sep;86(12):2624-40. PMID: 18500752 [PubMed - in process] EMERGING TECHNOLOGIES Emerging technologies, particularly Affymetrix Exon and Gene arrays as well as next generation sequencing are important for VCII research programs, for example, the VCII external advisory committee (EAC) made a firm recommendation that we provide next generation sequencing technlogy to the VCII. Next generation sequencing Core B is heavily involved in efforts to bring next generation sequencing to UVM (Table 2). Tim Hunter of Core B initiated the process by inviting speakers to UVM. Dr. Budd suggested we apply for an NCRR instrumentation award. The INBRE-funded Vermont Genetics Network took on a leadership role in this process. Table 2. Events related to bringing next generation sequencing technology to UVM. Affymetrix exon and gene arrays Affymetrix exon and gene arrays are emerging as a replacement for Affymetrix 3' arrays. Tim Hunter and Scott Tighe brought these arrays to UVM. Scott Tighe identified a software platform (BioTique Systems XRAY) that supports this technology. The Vermont Genetics Network provided a part time bioinformatics analyst (Dr. Julie Dragon) who is in charge of the exon/gene array pipeline. Dr. Bond is developing an R/Bioconductor pipeline that will give our exon and gene array pipeline the flexibility that we provide for 3' arrays. Network Analysis Core B played a leadership role in bringing Ingenuity IPA to UVM. We evaluated products, coordinated the purchase, and offered special workshops for VCII laboratories. GENERAL BACKGROUND INFORMATION Staff Name Role VCII FTE Bond, Jeffrey Bioinformatics Facility Manager 0.1 Hunter, Timothy Microarray Facility Manager 0.1 Tighe, Scott Research Technician 0.25 Services Services Offered: -Integrated Approaches *Experimental design consultation Assistance in RNA and DNA Extractions *LCM, Flow sorted, difficult tissues -RNA Quality/Quantity assessment -Gene Expression Profiling -DNA Mapping (SNP, LOH, CNV) -Expression profiling using 3', Exon, and Gene Arrays -Hypothesis testing: gene or pathway-based -Support letters for grant applications; text for publication -Discounted pricing on many consumables and reagents through Core Facility negotiations Scientific or technical changes: -Implementation of NuGEN Ovation and Pico WT system for target prep. +Requires minimal RNA input +Useful for FACS sorted, Micro-dissected, and exon application input +Faster turn around time -Ability to assess integrity of small RNA's and miRNA's -Addition of Qubit Spectrofluorometer for accurate quantification -Implementation of Exon and Gene Arrays using NuGEN and AmpTec reagent -New software for Exon analysis: Biotique Systems XRAY -Scott Tighe established protocol for extracting intact RNA from flow sorted cells. Collaborative protocol from roundtable S.Tighe chaired at NERLSCD meeting 2006, Decontaminations procedures, RNase reduction steps, extraction techniques, and QA/QC of RNA Current developmental projects underway by the Microarray Facility: ¿Collaborative effort to develop stand alone software package for QA/QC of 3', Exon, and Gene arrays with Scott Tighe from UVM and John Burke at X-Ray Boutique ¿Comprehensive evaluation of current target preparations on market for working with slightly to severely degraded RNA for 3', gene, and exon arrays. ¿ Methods to re-synthesize sense RNA for microarray from cDNA constructed without a T7 promoter -Evaluation of Modified to Amp-Tec reagents -Evaluation of sRNA reagents from Epicenter -Evaluation of SenseAMP from Genisphere 4D Professional Development: Staff attended and participated at the following meetings: -Scott Tighe, Annual Affymetrix Users Meeting, Memphis, TN, Feb. 2009 -Tim Hunter and Scott Tighe: Advances in Microarray Technology, Visited Dr. Herbert Auer's lab, collaboration on DNA Mapping, Barcelona, ESP, May, 2008 -Tim Hunter and Scott Tighe: Association of Biomolecular Resource Facilities, Memphis, TN, 2009 Facility Promotion: -Hosted Open House, June 15, 2008. Over 100 attendees -Provided Workshop on sample requirements and handling for a successful array experiment, June 15, 2008 -Hosted Seminar: "The Challenges and Successes of Implementing Next Generation Sequencing in a Share Resource Facility" June, 2008, Agnes Viale, Director of Genomics Core Laboratory, Memorial Sloan Kettering Cancer Center -Hosted Technology Seminar: "Micro RNA profiling using miScript. Presented by Doug Last, Qiagen. March 14, 2008 -Hosted Technology Seminar, Selective mRNA Amplification using AmpTec Priming Strategies, Presented by Dr. Guido Krupp, August 23, 2008 Facility Presentations: Invited Speaker: -Tim Hunter, (2008) National IDeA States of Biomedical Research Excellence, co-moderator of Core Technology Breakout Session, Washington DC, August, 2008 -Tim Hunter, Northeast Regional Life Sciences Core Directors, "Leveraging Regional Resources", Burlington, VT, Oct., 2008 -Tim Hunter, NCRR Clinical and Translational Informatics Networking Meeting, "Vermont Genetics Network Searchable Core Database", Scottsdale, AZ, Feb., 2009 -Scott Tighe, (2009) Association of Biomolecular Resource Facilities, "Common Practices for Routine RNA Handling: A Three Part Story", Memphis, TN, Feb., 2009 Invited Interview: -Tim Hunter, (2008): "Real-Time PCR: Staying Power", Biotechniques Vol 44, No.2: pp179-183 (Feb 2008) Meeting presentations (Poster): -Scott Tighe and Tim Hunter, Northeast Regional Life Sciences Core Directors, Oct. 2008, Burlington, VT, Vermont Genetics Network Microarray Facility ***Please see attachment for tables and figures: would not reproduce here.***

该副本是使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，这是调查员的机构。 概述 ***请注意，以下提到的表和数字不会以这种格式复制。请参阅带有纸质副本的附件。*** 核心B通过为个别VCII实验室（请参阅利用率和出版物）提供服务以及通过在带来对VCII研究人员（Emering Technologies）重要的新兴技术方面发挥核心作用来为VCII服务。还包括微阵列设施的一般背景（一般背景信息）。 利用率 提供给单个VCII实验室的服务，总计65个Affymetrix Genechips和25小时的生物信息学服务（表I，图1）。 表I提供给各个实验室的服务。 “小时”是指生物信息学服务。 图1向VCII实验室提供的genechip（左）和RNA评估服务（右）占总服务的百分比。 微阵列设施的全部利用包括（另见图2） - 与18个调查人员的实验设计咨询 - 19个微阵列项目（277个genechips）的结论 - 执行163个RNA评估：79个Picochips，81纳米芯片，3个小RNA芯片（新服务，实施，2008年8月） 出版物 VCII学院的出版物对VCII相关项目的出版物得到了核心B的支持： 1。Dienz，O.，Eaton，S.M.，Bond，J.P.，Neveu，W.，Moquin，D.，Noubade，R.由CD4 T细胞产生”。 J Exp Med。 2009年1月16日； 206（1）：69-78。 Epub 2009年1月12日。 2：Lu C，Pelech S，Zhang H，Bond J，Spach K，Noubade R，Blankenhorn EP，Teuscher C.百日咳毒素诱导脑微血管内皮细胞中的血管生成。 J Neurosci Res。 2008年9月； 86（12）：2624-40。 PMID：18500752 [PubMed-流程] 新兴技术 新兴技术，尤其是Affymetrix Exon和Gene阵列以及下一代测序对于VCII研究计划很重要，例如，VCII外部咨询委员会（EAC）提出了一个坚定的建议，即我们为VCII提供下一代测序技术。 下一代测序 Core B大量参与将下一代测序带入UVM的努力（表2）。 Core B的Tim Hunter通过邀请发言人向UVM发起了这一过程。 Budd博士建议我们申请NCRR仪器奖。 Inbre资助的佛蒙特州遗传学网络在此过程中扮演了领导角色。 表2。将下一代测序技术带到UVM有关的事件。 Affymetrix外显子和基因阵列 Affymetrix外显子和基因阵列正在替代Affymetrix 3'阵列。蒂姆·亨特（Tim Hunter）和斯科特·蒂格（Scott Tighe）将这些阵列带到了UVM。斯科特·蒂格（Scott Tighe）确定了支持该技术的软件平台（Biotique Systems XRAY）。佛蒙特州遗传学网络提供了负责外显子/基因阵列管道的兼职生物信息学分析师（Julie Dragon博士）。 Bond博士正在开发R/Bioconductor管道，该管道将使我们的外显子和基因阵列管道具有3'阵列提供的灵活性。 网络分析 核心B在将Ingenuity IPA带入UVM方面发挥了领导作用。我们评估了产品，协调购买，并为VCII实验室提供了特殊的研讨会。 一般背景信息 职员 姓名角色VCII FTE 邦德，杰弗里生物信息学设施经理0.1 蒂莫西微阵列设施经理亨特0.1 Tighe，Scott研究技术员0.25 服务 提供的服务： - 综合方法 *实验设计咨询 帮助RNA和DNA提取 *lcm，流量排序，困难的组织 - RNA质量/数量评估 - 基因表达分析 -DNA映射（SNP，LOH，CNV） - 使用3'，外显子和基因阵列进行表达分析 - 假设测试：基因或基于途径的测试 - 支持授予申请的信件；出版文字 - 通过核心设施谈判对许多消耗品和试剂进行定价 科学或技术变化： - 用于目标准备的Nugen Ovation和Pico WT系统的实施。 +需要最小的RNA输入 +对FACS分类，微观和外显子的应用有用 输入 +更快的时间 - 能够评估小RNA和miRNA的完整性 - 量子光谱荧光仪的调整以进行准确的定量 - 使用Nugen和基因阵列的实施 AMPTEC试剂 - 外显子分析的新软件：生物系统X射线 -Scott Tighe建立的方案，用于从流动的细胞中提取完整的RNA。 圆桌会议的协作协议S.Tighe主持了2006年的Nerlscd会议， RNA的demansations步骤，RNase还原步骤，提取技术和QA/QC 微阵列设施正在进行的当前发展项目： »与UVM的Scott Tighe和X射线精品店的Scott Tighe一起为3'，Exon和Gene Arrays的QA/QC开发独立的软件包的合作努力 »对当前市场目标制剂的全面评估，用于与3'，基因和外显子阵列的重量略微降解的RNA略有降低。 �在没有T7启动子的cDNA的微阵列中重新合成sense RNA的方法 - 对AMP-TEC试剂进行修饰的评估 - 从震中评估SRNA试剂 - 从GENISPHERE 4D评估Senseamp 专业发展： 工作人员参加并参加以下会议： -Scott Tighe，2009年2月，田纳西州孟菲斯的年度Affymetrix用户会议 -Tim Hunter和Scott Tighe：微阵列技术的进步，访问了Herbert Auer博士实验室，DNA映射合作，巴塞罗那，ESP，2008年5月， -Tim Hunter和Scott Tighe：田纳西州孟菲斯的生物分子资源设施协会，2009年 设施促销： - 开放日，2008年6月15日。超过100名与会者 - 2008年6月15日成功的阵列实验的样本要求和处理的讲习班 - 举办的研讨会：“在股票资源设施中实施下一代测序的挑战和成功”，2008年6月，基因组核心实验室主任Agnes Viale，纪念Sloan Sloan Kettering Cancer Center - 托管技术研讨会：“使用误文的微RNA分析。由Doug Last提出，Qiagen。2008年3月14日 - 培训技术研讨会，使用AMPTEC启动策略的选择性mRNA扩增，由Guido Krupp博士提出，2008年8月23日 设施演示： 邀请发言人： -Tim Hunter，（2008年）《国家思想卓越生物医学研究状态》，核心技术突破课程的联合调查员，华盛顿特区，2008年8月 -Tim Hunter，东北地区生命科学核心主管，“利用区域资源”，伯灵顿，弗吉尼亚州，2008年10月， -Tim Hunter，NCRR临床和翻译信息学网络会议，“佛蒙特州遗传网络可搜索的核心数据库”，亚利桑那州斯科茨代尔，2009年2月 -Scott Tighe，（2009年）生物分子资源设施协会，“常规RNA处理的常见实践：三部分故事”，田纳西州孟菲斯，2009年2月， 邀请采访： -Tim Hunter，（2008年）：“实时PCR：持久力”，《生物技术》第44卷，第2卷：PP179-183（2008年2月） 会议演讲（海报）： -Scott Tighe and Tim Hunter，东北地区生命科学核心主管，2008年10月，伯灵顿，弗吉尼亚州，佛蒙特州遗传学网络微阵列设施 ***请参阅表格和数字的附件：不会在这里复制。***