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
基本信息
- 批准号:7959814
- 负责人:
- 金额:$ 8.57万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 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:
- 关键词:Advisory CommitteesAntibody FormationApplications GrantsAwardBioconductorBioinformaticsBiological SciencesBiomedical ResearchBrainCD4 Positive T LymphocytesCell SeparationChargeClinicalCollaborationsCommunicable DiseasesComputer Retrieval of Information on Scientific Projects DatabaseComputer softwareConsultationsCore FacilityDNADNA Sequencing FacilityDNA mappingDatabasesDecontaminationDevelopmentDistrict of ColumbiaEducational workshopEmerging TechnologiesEndothelial CellsEvaluationEventExonsExperimental DesignsFacultyFundingGene Expression ProfilingGenesGeneticGenomicsGrantHourHousingHydrogen BondingImmunobiologyIndividualInformaticsInstitutionInterleukin-6InterviewLaboratoriesLeadershipLeftLettersMarketingMediatingMediationMemorial Sloan-Kettering Cancer CenterMessenger RNAMethodsMicroRNAsMicroarray AnalysisMolecular ProfilingNamesNational Center for Research ResourcesPaperPathway AnalysisPathway interactionsPertussis ToxinPlayPreparationPriceProceduresProcessProtocols documentationPubMedPublicationsRNAReagentRecommendationResearchResearch PersonnelResource SharingResourcesRibonucleasesRoentgen RaysRoleSamplingServicesSmall RNASorting - Cell MovementSourceStaff DevelopmentSystemTechniquesTechnologyTestingTextTimeTissuesUnited States National Institutes of HealthVermontVisitWorkangiogenesisbasecDNA Arraysdiscountflexibilityinstrumentationmeetingsnext generationpostersprogramspromoterresearch studyroutine practiceservice utilizationsuccess
项目摘要
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。
研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金,
因此可以出现在其他 CRISP 条目中 列出的机构是。
对于中心来说,它不一定是研究者的机构。
概述
***请注意,下面提到的表格和图表不会以这种格式复制,请参阅随纸质副本发送的附件。***
核心 B 通过向各个 VCII 实验室提供服务(参见利用和出版物)以及在引入对 VCII 研究人员重要的新兴技术(新兴技术)方面发挥核心作用来为 VCII 服务。还包括(一般背景信息)。
利用率
向各个 VCII 实验室提供的服务总计 65 个 Affymetrix GeneChips 和 25 小时的生物信息学服务(表 I,图 1)。
表 I 向各个实验室提供的服务“时间”是指生物信息学服务。
图 1 向 VCII 实验室提供的基因芯片(左)和 RNA 评估服务(右)占总服务的百分比。
微阵列设施的总利用率包括(另参见图 2)
- 与 18 位研究者进行实验设计咨询
-完成19个微阵列项目(277个基因芯片)
-进行了163个RNA评估:79个PicoChips、81个NanoChips、3个小RNA芯片(新服务,实施,2008年8月)
出版物
VCII 教师在核心 B 支持的 VCII 相关项目上发表的出版物:
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. 和 Rincon, M. (2009)“IL-6 诱导抗体产生是由 IL-21 间接介导的由 CD4 T 细胞产生”。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。百日咳毒素诱导脑微血管内皮细胞中的血管生成。
神经科学研究杂志,2008 年 9 月;86(12):2624-40。
PMID:18500752 [PubMed - 进行中]
新兴技术
新兴技术,特别是Affymetrix Exon和Gene阵列以及下一代测序对于VCII研究项目非常重要,例如,VCII外部咨询委员会(EAC)明确建议我们向VCII提供下一代测序技术。
下一代测序
Core B 积极参与将下一代测序引入 UVM(表 2),Budd 博士建议我们申请 NCRR 资助的佛蒙特州仪器奖,从而发起了这一过程。遗传学网络在这一过程中发挥了领导作用。
表 2. 与将下一代测序技术引入 UVM 相关的事件。
Affymetrix 外显子和基因阵列
Affymetrix 外显子和基因阵列正在成为 Affymetrix 3' 阵列的替代品,Tim Hunter 和 Scott Tighe 将这些阵列引入 UVM,Scott Tighe 确定了支持该技术的软件平台 (BioTique Systems XRAY)。负责外显子/基因阵列管道的生物信息学分析师(Julie Dragon 博士)正在开发 R/Bioconductor 管道,该管道将提供我们的外显子和基因阵列管道我们为 3' 阵列提供的灵活性。
网络分析
Core B 在将 Ingenuity IPA 引入 UVM 方面发挥了领导作用。我们评估了产品,协调了采购,并为 VCII 实验室提供了特别研讨会。
一般背景信息
职员
名称 角色 VCII FTE
邦德,杰弗里生物信息学设施经理 0.1
Hunter, Timothy 微阵列设施经理 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
协助 RNA 和 DNA 提取
*LCM、流式分选、困难组织
-RNA质量/数量评估
-基因表达谱分析
-DNA 作图(SNP、LOH、CNV)
-使用 3'、外显子和基因阵列进行表达谱分析
-假设检验:基于基因或通路
-资助申请的支持信函文本;
-通过核心设施谈判,许多消耗品和试剂的折扣价格
科学或技术变化:
-实施 NuGEN Ovation 和 Pico WT 系统进行靶标准备。
+需要最少的RNA输入
+适用于 FACS 排序、显微解剖和外显子应用
输入
+更快的周转时间
-能够评估小RNA和miRNA的完整性
-添加 Qubit 荧光分光计以实现精确定量
-使用 NuGEN 和实施外显子和基因阵列
AmpTec 试剂
-用于外显子分析的新软件:Biotique Systems XRAY
-Scott Tighe 建立了从流式分选细胞中提取完整 RNA 的方案。
圆桌会议 S.Tighe 在 2006 年 NERLSCD 会议上主持的合作协议,
RNA 的净化程序、RNase 还原步骤、提取技术和 QA/QC
微阵列设施当前正在进行的开发项目:
¿与 UVM 的 Scott Tighe 和 X-Ray Boutique 的 John Burke 合作开发用于 3'、外显子和基因阵列 QA/QC 的独立软件包
¿对市场上当前用于处理 3'、基因和外显子阵列的轻度至严重降解 RNA 的目标制剂进行综合评估。
¿从无 T7 启动子构建的 cDNA 重新合成微阵列正义 RNA 的方法
-改良Amp-Tec试剂的评估
-Epicenter sRNA 试剂的评估
-Genisphere 4D 的 SenseAMP 评估
专业发展:
工作人员出席并参加了以下会议:
-Scott Tighe,年度 Affymetrix 用户会议,田纳西州孟菲斯,2009 年 2 月
-Tim Hunter 和 Scott Tighe:微阵列技术的进展,参观 Herbert Auer 博士的实验室,DNA 绘图合作,巴塞罗那,ESP,2008 年 5 月
-Tim Hunter 和 Scott Tighe:生物分子资源设施协会,田纳西州孟菲斯,2009 年
设施推广:
-2008 年 6 月 15 日举办开放日。超过 100 名与会者
- 举办了关于成功阵列实验的样品要求和处理的研讨会,2008 年 6 月 15 日
- 主持研讨会:“在共享资源设施中实施下一代测序的挑战和成功”,2008 年 6 月,Agnes Viale,纪念斯隆凯特琳癌症中心基因组学核心实验室主任
- 主办技术研讨会:“使用 miScript 进行 Micro RNA 分析。由 Qiagen 的 Doug Last 主持。2008 年 3 月 14 日
-主办的技术研讨会,使用 AmpTec 启动策略进行选择性 mRNA 扩增,由 Guido Krupp 博士主讲,2008 年 8 月 23 日
设施介绍:
特邀演讲嘉宾:
-Tim Hunter,(2008 年)国家 IDeA 生物医学研究卓越奖,核心技术突破会议联合主持人,华盛顿特区,2008 年 8 月
-Tim Hunter,东北地区生命科学核心总监,“利用地区资源”,佛蒙特州伯灵顿,2008 年 10 月
-Tim Hunter,NCRR 临床和转化信息学网络会议,“佛蒙特遗传学网络可搜索核心数据库”,亚利桑那州斯科茨代尔,2009 年 2 月
-Scott Tighe,(2009) 生物分子资源设施协会,“常规 RNA 处理的常见做法:三部分故事”,田纳西州孟菲斯,2009 年 2 月
采访邀请:
-Tim Hunter,(2008):“实时 PCR:保持力量”,《生物技术》第 44 卷,第 2 期:第 179-183 页(2008 年 2 月)
会议报告(海报):
-Scott Tighe 和 Tim Hunter,东北地区生命科学核心总监,2008 年 10 月,佛蒙特州伯灵顿,佛蒙特州遗传学网络微阵列设施
***请参阅附件中的表格和图形:此处不会复制。***
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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JEFFREY P. BOND其他文献
JEFFREY P. BOND的其他文献
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{{ truncateString('JEFFREY P. BOND', 18)}}的其他基金
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:
8360769 - 财政年份:2011
- 资助金额:
$ 8.57万 - 项目类别:
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:
8167728 - 财政年份:2010
- 资助金额:
$ 8.57万 - 项目类别:
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:
7720913 - 财政年份:2008
- 资助金额:
$ 8.57万 - 项目类别:
CORE--BIOINFORMATICS: BRIN: VERMONT BIOMED RES INFRASTRU
核心--生物信息学:BRIN:佛蒙特州生物医学研究基础设施
- 批准号:
7170629 - 财政年份:2005
- 资助金额:
$ 8.57万 - 项目类别:
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