Microbiomics and Functional Genomics Core

微生物组学和功能基因组学核心

• 批准号: 10395973
• 负责人: ROB KNIGHT
• 金额: $ 26.38万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-07-01 至 2024-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10395973
• 关键词: ATAC-seq; Base Pairing; Basic Science; Bioinformatics; Biological Assay; California; Cells; ChIP-seq; Complex; Computational Biology; Consult; Consultations; Data; Data Analyses; Data Set; Digestive System Disorders; Ensure; Environmental Risk Factor; Gene Expression; Genetic Polymorphism; Genomic medicine; Genomics; Glass; High-Throughput Nucleotide Sequencing; Human Resources; Inflammatory Bowel Diseases; Infrastructure; Institutes; International; Libraries; Liver; Location; Medicine; Metagenomics; Molecular Genetics; Pathogenesis; Preparation; Procedures; Process; Protocols documentation; Quality Control; Research; Research Design; Research Personnel; Resource Sharing; Resources; Ribosomal RNA; Sampling; Services; Shotgun Sequencing; Signal Pathway; Standardization; Statistical Data Interpretation; Susceptibility Gene; System; Techniques; Technology; Training; Translational Research; Universities; Validation; base; cost; cost effective; data visualization; design; exome sequencing; experience; functional genomics; genome sequencing; genomic data; global run on sequencing; innovation; member; miRNA expression profiling; microbial; microbial community; microbiome; microbiome research; next generation sequencing; non-alcoholic fatty liver disease; response; ribosome profiling; tool; transcriptome sequencing; transcriptomics; whole genome

Summary Complex interactions between numerous specialized host cells in gut, liver and other locations, polymorphisms of multiple susceptibility genes and their associated signaling pathways and functions, and a myriad of microbial and other environmental factors are emerging as central to the pathogenesis of many of the most important digestive diseases, as exemplified by inflammatory bowel disease (IBD) and non-alcoholic fatty liver disease (NAFLD). It is becomingly increasingly evident that more comprehensive views of the players and interactions are needed to unravel many of the most perplexing digestive diseases. Consequently, tools to characterize and define multiple host and microbial cells and their gene expression responses are increasingly important and essential for digestive diseases research. Most advanced among these tools are technologies based on high- throughput sequencing, as it is now routinely possible to obtain hundreds of millions of base pairs of sequence at modest costs. Next-generation sequencing technologies have revolutionized basic and translational research in medicine over the last several years, and are in increasing demand in digestive diseases research. Consequently, we have designed the Microbiomics and Functional Genomics Core to provide advanced microbiomics and genomics services to Center members, and offer consultation and training in genomics technologies to enhance the ability of members to implement these technologies in their research. Specifically, the Core will: 1) Conduct sequencing-based assays for microbiomics and functional genomics; 2) Perform bioinformatics analyses of sequencing-based assays; 3) Consult and advise in studies involving microbiomics and functional genomics; and 4) Provide validated experimental protocols and training. The Core leverages several established institutional shared resources, including the Center for Microbiome Innovation at the University of California, San Diego (UCSD), the Genomics Center of the Institute for Genomic Medicine at UCSD, and the UCSD Center for Computational Biology and Bioinformatics. This unique combination and integration of outstanding existing resources will ensure that Center members have access to cutting-edge technologies for studies involving microbiomics and functional genomics. The Core will be directed by internationally recognized experts in microbiomics (Dr. Rob Knight) and functional genomics (Dr. Christopher Glass), and other Core personnel are highly experienced in microbiome science, molecular genetics, bioinformatics and computational biology. The Core has established rigorous procedures for quality control and data validation. Together, this infrastructure and expertise will enable the Microbiomics and Functional Genomics Core to provide a range of high quality and cost-effective microbiomics and functional genomics services that greatly enhance the ability of Center members to advance digestive diseases research.

概括 肠道，肝脏和其他位置中众多专业宿主细胞之间的复杂相互作用，多态性 多敏感性基因及其相关的信号通路和功能，以及无数的微生物 其他环境因素也成为许多最重要的发病机理的核心 消化疾病，例如炎症性肠病（IBD）和非酒精性脂肪肝病的例证 （NAFLD）。越来越明显的是，对玩家和互动的观点越来越全面 需要揭开许多最困惑的消化疾病。因此，要表征和 定义多个宿主和微生物细胞，其基因表达反应越来越重要，并且 消化疾病研究至关重要。这些工具中最先进的是基于高的技术 吞吐量测序，因为现在通常可以获得数亿对序列的基本对 费用适中。下一代测序技术彻底改变了基础和转化研究 在过去几年中，医学领域正在增加消化疾病研究的需求。 因此，我们设计了微生物学和功能基因组学核心，以提供高级 微生物学和基因组学服务为中心成员，并提供基因组学咨询和培训 提高成员在研究中实施这些技术的能力的技术。具体来说， 核心将：1）对微生物学和功能基因组学进行基于测序的测定； 2）执行 基于测序测定的生物信息学分析； 3）咨询和建议涉及微生物学的研究 和功能基因组学； 4）提供经过验证的实验方案和培训。核心利用 一些已建立的机构共享资源，包括在 加州大学圣地亚哥分校（UCSD），UCSD基因组医学研究所的基因组学中心， 以及UCSD计算生物学和生物信息学中心。这种独特的组合和集成 出色的现有资源将确保中心成员能够获得尖端技术 涉及微生物学和功能基因组学的研究。核心将由国际认可的 微生物学专家（Rob Knight博士）和功能基因组学（Christopher Glass博士）和其他核心 人员在微生物组科学，分子遗传学，生物信息学和计算方面经验丰富 生物学。核心已经建立了严格的质量控制和数据验证程序。一起，这个 基础架构和专业知识将使微生物学和功能基因组学核心能够提供一系列 高质量和具有成本效益的微生物学和功能基因组学服务，可大大提高 中心成员推进消化系统疾病研究。