Genomics, Biostatistics and Bioinformatics Core

基因组学、生物统计学和生物信息学核心

• 批准号: 10216632
• 负责人: Shannon K. McWeeney
• 金额: $ 21.09万
• 依托单位: OREGON HEALTH & SCIENCE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-15 至 2022-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10216632
• 关键词: Back; Bioinformatics; Biometry; CD34 gene; Candidate Disease Gene; Computer software; Cytomegalovirus; DNA Sequencing Facility; Data; Data Security; Data Set; Detection; Development; Dideoxy Chain Termination DNA Sequencing; Ensure; Evaluation; Experimental Designs; Generations; Genes; Genomics; Goals; Hematopoiesis; Hematopoietic stem cells; Human; Infection; Libraries; Life Cycle Stages; Maintenance; Maps; Massive Parallel Sequencing; Metadata; Methodology; Methods; Modeling; Molecular; Multiomic Data; Pathway interactions; Play; Poly A; Preparation; Process; Program Research Project Grants; Protocols documentation; RNA; Reproducibility; Research; Research Design; Research Personnel; Research Project Grants; Resource Sharing; Role; Running; Sampling; Signal Pathway; Signal Transduction; Standardization; Technology; Testing; Time; Transplantation; Validation; Viral; Virus; Virus Latency; Visualization; base; candidate validation; cell growth regulation; data integration; data integrity; data management; differential expression; experimental study; follow-up; genetic signature; mutant; novel; phosphoproteomics; transcriptome sequencing; transcriptomics; validation studies

CORE B PROJECT SUMMARY/ABSTRACT Consistent with the Overall aims of the PPG, the Genomics, Biostatistics and Bioinformatics core (Core B) will play a central role focused on robust identification and prioritization of candidate genes, pathways and gene signatures in order to elucidate how HCMV encoded genes regulate cellular signaling in HPCs to contribute to the establishment and maintenance of viral latency as well as hematopoiesis. Core B will support all five projects and will provide biostatistics and bioinformatics assistance, as well as critical expertise and standardization in sample and library preparation and initial confirmation to aid in prioritization of targets. Core B is responsible for the pre-processing, integration and modeling of the diverse readouts (e.g., transcriptomics, phosphoproteomics, secretomics etc.) generated by each project as well as across projects within the PPG. These data will be incorporated into probabilistic pathway models to provide a rigorous and reproducible framework for hypothesis testing. Follow-up validation and perturbation experiments will aid in the evaluation and refinement of the modeling in an iterative manner. To ensure the data from all PPG research projects will be generated in a standardized manner, the GBBC will play a critical role in facilitating PPG studies, managing and integrating the diverse experimental read-outs, assessing reproducibility and guiding identification of the most promising candidates for validation. The GBBC will regulate consistency and quality of the samples to be sequenced by performing both CD34+ HPC infection experiments with virus mutants generated by the different projects, and subsequent RNA isolations for RNA-seq to allow for cross-comparisons of datasets. This core will assist in prioritization of candidates for further perturbation and validation studies. Finally, the GBBC will provide bioinformatics and biostatistics support for PPG components throughout the “data life cycle” including assistance with experimental design, data pre-processing, QA/QC, analysis, modeling and visualization as well as data integration, storage, management, standards and dissemination for all data types utilized in the PPG.

核心B项目摘要/摘要 与PPG，基因组学，生物统计学和生物信息学核心（核心B）的总体目标一致 发挥着核心作用，专注于候选基因，途径和基因的强大识别和优先次序 为了阐明HCMV的编码基因如何调节HPC中的细胞信号传导以有助于 病毒潜伏期和造血的建立和维持。核心B将支持全部五个 项目并将提供生物统计学和生物信息学帮助，以及批判性专业知识和 样品和库准备和初步确认的标准化，以帮助目标优先级。核 B负责潜水员读数的预处理，集成和建模（例如，转录组学， 每个项目以及PPG中的跨项目产生的磷蛋白质组学，秘密组学等。 这些数据将纳入概率途径模型中，以提供严格且可重现的 假设检验的框架。后续验证和扰动实验将有助于评估 并以迭代方式对建模进行改进。为了确保所有PPG研究项目的数据将 GBBC以标准化的方式生成，将在促进PPG研究中发挥关键作用 并整合潜水员的实验读数，评估可重复性和指导识别 验证最有前途的候选人。 GBBC将调节样品的一致性和质量 通过用不同的病毒突变体进行CD34+ HPC感染实验测序 项目，以及随后的RNA-seq的RNA隔离，以允许数据集的跨综合子。这个核心将 协助优先考虑候选人进行进一步的扰动和验证研究。最后，GBBC将 在整个“数据生命周期”中为PPG组件提供生物信息学和生物统计学支持，包括 实验设计，数据预处理，QA/QC，分析，建模和可视化方面的帮助 作为PPG中所有数据类型的数据集成，存储，管理，标准和传播。