Functional Genomics and Bioinformatics Data management Core

功能基因组学和生物信息学数据管理核心

• 批准号: 10592221
• 负责人: Seyed Ali Mortazavi
• 金额: $ 228.3万
• 依托单位: UNIVERSITY OF CALIFORNIA-IRVINE
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-15 至 2027-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10592221
• 关键词: ATAC-seq; Affect; Alternative Splicing; Alzheimer' s disease model; Automobile Driving; Bioinformatics; Biological Assay; Brain; California; Cell Nucleus; Cells; Chromatin; Data; Deposition; Development; Disease; Disease Progression; Disease model; Female; Gene Expression; Gene Expression Profiling; Genes; Genetic; Global Change; Hippocampus (Brain); Human; Human Resources; Knowledge; Libraries; Maps; Measurement; Measures; Messenger RNA; MicroRNAs; Microglia; Modeling; Mus; Phenotype; Play; Preparation; Process; Production; Proteomics; Protocols documentation; RNA; Regulatory Element; Reproducibility; Resources; Robotics; Role; Running; Small Nuclear RNA; Source; Split-Pool Ligation Transcriptome sequencing; Synapses; Techniques; Technology; Time; Tissues; Translations; Universities; Untranslated RNA; Variant; Work; XCL1 gene; cell type; data management; design; differential expression; experimental study; functional genomics; genome wide association study; human data; interactive tool; interest; mRNA sequencing; male; metabolomics; microbiome; model development; mouse model; novel; predictive modeling; risk variant; sequencing platform; transcriptome sequencing; transcriptomics

FGBDMC ABSTRACT: The University of California, Irvine (UCI) MODEL-AD Functional Genomics and Bioinformatics Data Management Core (FGBDMC) will centralize all functional genomics as well as bioinformatics tasks to support the efforts of the UCI MODEL-AD Center. The core will characterize deeply UCI Late-Onset AD (LOAD) mouse models using bulk as well as single-cell techniques, and advise the UCI MODEL-AD Disease Model Development and Phenotyping Project (DMP) as to the best combination of variants and genetic backgrounds for subsequent models. Specifically, the FGBDMC will: 1) characterize novel mouse AD models using bulk RNA sequencing to identify model-specific changes in gene expression, 2) characterize selected mouse AD models using single-cell and single-nucleus RNA-seq and ATAC-seq to identify cell-type specific changes in gene expression and chromatin accessibility associated with AD GWAS risk-variant function, 3) analyze integratively all UCI MODEL-AD ‘omics data with AMP-AD and other publicly-available data in order to characterize the human AD relevance of the novel UCI mouse AD models as well as to predict the best variant combination to support DMP efforts, and 4) make UCI MODEL-AD results accessible on the Sage Bionetworks Synapse Portal.

FGBDMC摘要： 加州大学欧文分校（UCI）MODEL-AD功能基因组学和生物信息学数据 管理核心（FGBDMC）将集中所有功能基因组学以及生物信息学任务来支持 UCI模型广告中心的努力。核心将深入表征UCI晚发型AD（LOAD）小鼠 模型使用散装以及单细胞技术，并建议UCI模型AD疾病模型 开发和表型分析项目（ESTA）的最佳组合的变异和遗传背景 对于后续型号。具体而言，FGBDMC将：1）使用大量RNA表征新型小鼠AD模型 测序以鉴定基因表达中的模型特异性变化，2）表征选定的小鼠AD模型 使用单细胞和单核RNA-seq和ATAC-seq鉴定基因中的细胞类型特异性变化 与AD GWAS风险变异功能相关的表达和染色质可及性，3）综合分析 所有UCI MODEL-AD组学数据与AMP-AD和其他公开可用的数据，以表征 新的UCI小鼠AD模型的人AD相关性以及预测最佳变体组合， 支持可持续发展工作，以及4）在Sage Bionetworks Synapse门户网站上提供UCI MODEL-AD结果。