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: 9753911
• 负责人: Shannon K. McWeeney
• 金额: $ 22.05万
• 依托单位: OREGON HEALTH & SCIENCE UNIVERSITY
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/9753911
• 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; Imagery; 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; 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