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).***

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 在本报告所述期间，核心B为第二次自愿委员会的四名调查员提供了实质性支助，并与另外三名调查员进行了协商。核心B服务包括一份出版物、三份准备中的手稿和一份提交的赠款申请。我们在上一份报告中讨论的VCII项目已经向前推进，新的项目已经开始，关于潜在项目的对话已经进行。 表一：核心B利用率。芯片是指核心B扫描的基因芯片数量。小时指的是生物信息学支持。 表示下面提供了更多详细信息。 马特拉伊特 从我们的最新进展报告： “Matrajt博士处理了九个阵列，他能够证明阵列为一系列拟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。" 该实验扩展到包括一个时间序列和六个额外的基因型（总共54个芯片）。 将分析扩展到包括来自同事提供的时间序列的5个芯片，并开发了混合模型（需要适应基因型与分化和未分化状态之间的样品中细胞分布之间的关联）。研究结果已在一次会议上提出，并构成了一个MS论文（帕梅拉莱斯科）的一章。 目前正在编写一份手稿，并正在进行后续实验。 德莱尼 完成了双向设计（基因型X处理，36个芯片）的初步分析。核心B与德莱尼博士和他的技术人员罗德里戈·奥拉特会面两次，讨论下一步行动。 Rincon 从我们之前的进度报告中：“为Rincon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Rincon博士或她的博士后研究员Dienz博士的三次会议。" 博士Dienz的手稿正在进行修改以重新提交。 在NIH拨款申请（现已提交）的初步结果的背景下，核心B咨询了公众可用（GEO）数据的使用，并分析了一位同事提供的数据（来自人类样本的激光捕获显微镜样本，66个芯片）。 Teuscher 从我们之前的进度报告中：“为Teuscher博士处理了38个阵列，正在准备手稿。 生物信息学支持（10.25小时）包括与Teuscher博士或他的博士后助理Changming Lu博士的五次会议。" 博士陆的手稿被接受出版。 核心B参与分析蛋白浓度数据（23种蛋白，42个样本，基因型X时间X治疗设计），将在4月期间提交供发表。核心B就组织来源X基因型X治疗设计的分析进行了三次会议;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个芯片比较接近分析阶段的结束，预计将被纳入手稿。 服务 核心B支持： - 基因表达谱分析 - 目标准备 - 真核和原核 - 单倍和双倍放大 - 基于Nugen的靶标制备用于低RNA靶标，即， LCM，细胞分选 - 杂交和扫描 -DNA Mapping靶标制备 - 外显子阵列靶标制备 -RNA完整性评估 - 核酸定量 -RNA提取协助和培训 - 为提供的所有服务制定SOP - 分析使用 线性建模 -GO注释 - 排列测试 科学或技术变化包括： - 购买AB 7500快速序列检测系统，允许快速循环实时PCR用于微阵列靶标验证，同时提高通量 - 优化方法并开发方案来量化荧光激活细胞分选中的低回收率RNA - 开发和优化用于下游分子分析的挑战性组织的均质化方法 * 有关图表，请参阅纸质副本（此处不复制）。