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
• 负责人: JEFFREY P. BOND
• 金额: $ 13.02万
• 依托单位: UNIVERSITY OF VERMONT & ST AGRIC COLLEGE
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-07-01 至 2009-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7720913
• 关键词: Applications Grants; Bioinformatics; Cell Separation; Cells; Computer Retrieval of Information on Scientific Projects Database; Consult; DNA mapping; Data; Data Analyses; Detection; Development; Exons; Fluorescence-Activated Cell Sorting; Funding; Gene Expression Profiling; Genotype; Grant; Hour; Human; Institution; Lasers; Linear Models; Manuscripts; Methods; Microscopy; Modeling; Molecular Analysis; Nucleic Acids; Numbers; Paper; Polymerase Chain Reaction; Postdoctoral Fellow; Preparation; Process; Progress Reports; Protein Analysis; Proteins; Protocols documentation; Publications; RNA; Recovery; Reporting; Research; Research Personnel; Resources; Sampling; Scanning; Series; Services; Source; Staging; Students; System; Techniques; Testing; Time; Tissues; Training; Undifferentiated; United States National Institutes of Health; Validation; Vermont; base; design; follow-up; research study; symposium; therapy design

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. Summary (Table I) During the reporting period Core B provided substantive support for four VCII investigators and consulted with three others. Core B service was associated a publication, three manuscripts in preparation, and a submitted grant application. VCII projects discussed during our previous report have moved forward, new projects have begun, and conversations about potential projects have taken place. Table I: Core B Utilization. Chips refers to the number of GeneChips scanned by Core B. Hours refers to bioinformatics support. indicates that additional detail is provided below. Matrajt From our last progress report: "Nine arrays were processed for Dr. Matrajt, who was able to demonstrate that arrays provide an appropriate technique for a series of proposed experiments. Bioinformatics support (16.5 hours) included six meetings with Dr. Matrajt or her student, Ms. Pamela Lescault." The experiment was expanded to include a time series and six additional genotypes (a total of 54 chips). The analysis was expanded to include 5 chips from a time series made available by a colleague and a mixture model was developed (required to accommodate an association between genotype and the distribution of cells in samples between differentiated and undifferentiated states). The results have been presented at a conference and constituted a chapter of an MS thesis (Pamela Lescault). A manuscript is in preparation and a follow-up experiment is in progress. Delaney Preliminary analysis of a two-way design (genotype X treatment, 36 chips) was completed. Core B met twice with Dr. Delaney and his technician, Rodrigo Olarte, to discuss next steps. Rincon From our previous progress report: "Six arrays were processed for Dr. Rincon, which resulted in a submitted manuscript. Bioinformatics support (17 hours) included three meetings with Dr. Rincon or Dr. Dienz, her postdoctoral fellow." Dr. Dienz' manuscript is undergoing revision for resubmission. In the context of preliminary results for of an NIH grant application (now submitted) Core B consulted on use of publicly available (GEO) data and analyzed data made available by a colleague (laser capture microscopy samples from human samples, 66 chips). Teuscher From our previous progress report: "Thirty-eight arrays were processed for Dr. Teuscher and a manuscript is in preparation. Bioinformatics support (10.25 hours) included five meetings with Dr. Teuscher or his postdoctoral associate, Dr. Changming Lu." Dr. Lu's manuscript was accepted for publication. Core B is involved in analysis of protein concentration data (23 proteins, 42 samples, genotype X time X treatment design) that will be submitted for publication during April. Core B met three times regarding analysis of a tissue source X genotype X treatment design; a follow-up 6 chip experiment was performed and being analyzed. A 10 chip comparison in expression among genotypes is nearing the end of the analysis stage and is expected to be included in a manuscript. Services Core B supports: -Gene Expression Profiling -target preparation -eukaryotic and prokaryotic -single and double amplification -Nugen based target preps for low RNA targets, i.e., LCM , cell sorting -Hybridization and scanning -DNA Mapping target preparation -Exon Array target preparation -RNA Integrity assessment -Nucleic Acid quantification -RNA extraction assistance and training -SOP's established for all services offered -Analysis using -linear modeling -GO annotation -Permutation tests Scientific or technical changes include: -Purchased AB 7500 Fast Sequence Detection System allowing fast cycling real-time PCR for microarray target validation while increasing throughput -Optimized methods and developed protocols to quantify low recovery RNA from fluorescence- activated cell sorting -Development and optimization of methods for homogenization of challenging tissues for downstream molecular analysis ***Please see paper copy for figures and tables (would not reproduce here).***

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。 摘要（表I）在报告期间核心B中为四名VCII调查人员提供了实质性的支持，并咨询了另外三个调查员。核心B服务是关联的出版物，准备了三个手稿以及提交的赠款申请。我们先前的报告中讨论的VCII项目已经发展，新项目已经开始，并且已经进行了有关潜在项目的对话。 表I：核心B利用率。芯片是指Core B扫描的Genechip的数量。小时是指生物信息学支持。 表示下面提供了其他细节。 Matrajt 从我们的上一个进度报告中： “为Matrajt博士处理了九个阵列，他能够证明阵列为一系列建议的实验提供了适当的技术。生物信息学支持（16.5小时）包括与Matrajt博士或她的学生Pamela Lescault女士的六次会议。” 该实验扩展到包括时间序列和六个其他基因型（总共54个芯片）。 将分析扩展到包括同事提供的时间序列的5个芯片，并开发了混合模型（为了适应基因型与分化和未分化状态之间样品中细胞分布之间的关联）。结果已在会议上提出，并构成了MS论文（Pamela Lescault）的一章。 手稿正在准备，并且正在进行后续实验。 德莱尼 双向设计（基因型X处理，36芯片）的初步分析已完成。 Core B与Delaney博士及其技术人员Rodrigo Olarte进行了两次会面，讨论了下一步。 林肯 从我们先前的进度报告中：“林肯博士处理了六个阵列，这导致了一份提交的手稿。生物信息学支持（17小时）包括与林肯博士或她的博士后研究员迪恩斯博士的三次会议。” Dienz博士的手稿正在修订重新提交。 在使用公共可用数据（GEO）数据的NIH赠款应用程序（现已提交的）核心B的初步结果中，同事提供的数据（Laser捕获了人类样本中的显微镜样本，66个芯片）。 Teuscher 从我们先前的进度报告中：“为Teuscher博士处理了38个阵列，并正在准备手稿。生物信息学支持（10.25小时）包括与Teuscher博士或他的博士后合伙人Changming Lu博士的五次会议。” Lu博士的手稿被接受出版。 Core B参与了蛋白质浓度数据的分析（23种蛋白质，42个样品，基因型X Time X治疗设计），该数据将在4月份提交出版。 Core B在分析组织源X基因型X治疗设计方面需要3次；进行了后续6芯片实验并进行了分析。 基因型之间表达的10芯片比较接近分析阶段的结束，预计将包括在手稿中。 服务 核心B支持： - 基因表达分析 - 目标准备 - 核核和原核生物 - 单个和双重扩增 - 基于NUGEN的低RNA靶标的靶标，即 LCM，细胞分类 - 杂交和扫描 -DNA映射目标准备 -EXON阵列目标准备 - RNA完整性评估 - 核酸定量 - RNA提取协助和培训 - 为提供的所有服务建立 - 使用 - 线性建模 - 注释 - 末期测试 科学或技术变化包括： - 购买的AB 7500快速序列检测系统允许快速循环实时PCR进行微阵列目标验证，同时增加吞吐量 - 优化方法和开发的方案，以量化荧光激活的细胞分选的低回收RNA - 开发和优化具有挑战组织均质的方法用于下游分子分析 ***请参阅纸质副本以获取图形和表格（在这里不会复制）。***