Genomics-Bioinformatics Core

基因组学-生物信息学核心

• 批准号: 10385797
• 负责人: SUZANNE SANDMEYER
• 金额: $ 21.16万
• 依托单位: UNIVERSITY OF CALIFORNIA-IRVINE
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-04-01 至 2024-02-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10385797
• 关键词: ATAC-seq; Adult; Area; Automobile Driving; Back; Bioinformatics; Biology; Blood Vessels; Cell Communication; Cells; ChIP-seq; Chromatin; Collaborations; Communities; Complex; Computer software; Consultations; Custom; DNA; Data; Data Set; Dermal; Detection; Development; Disease; Educational workshop; Emerging Technologies; Epigenetic Process; Faculty; Fostering; Gene Expression; Gene Expression Profiling; Genomic approach; Genomics; Goals; Heterogeneity; High-Throughput Nucleotide Sequencing; Homeostasis; Human Resources; Image; In Situ; Individual; Informatics; Institutes; Laboratories; Machine Learning; Maps; Modeling; Molecular; Organ; Pathogenesis; Pigments; Process; Psoriasis; RNA; Research; Research Personnel; Resources; Scientist; Services; Skin; Skin Cancer; Skin Tissue; Speed; Statistical Data Interpretation; Systems Biology; Techniques; Technology; Testing; Time; Tissues; Training; Training Activity; Work; base; bioinformatics pipeline; bioinformatics tool; cell type; epigenome; epigenomics; experimental study; genomic data; imaging system; improved; innovation; insight; instrumentation; lectures; member; nano-string; next generation; novel; novel strategies; open source; programs; public database; ranpirnase; repaired; repository; single cell analysis; single cell technology; single-cell RNA sequencing; skin disorder; tool; transcriptome sequencing; transcriptomics; web based interface; web site; wound healing

PROJECT SUMMARY The ability to probe gene expression and chromatin landscape globally and at a single cell level has opened the door to seek unprecedented information and insight into the development, homeostasis, repair, and pathogenesis of skin as a complex organ. UC Irvine enjoys more than a critical mass of skin biologists with well- established research expertise and programs that aim at understanding the regulatory mechanisms underlying the biology of epidermal, dermal, pigment and vascular cells in skin, and how such mechanisms may go awry in diseases such as psoriasis and skin cancer. While these skin biologists all have access to general genomics techniques currently available on campus, there is an urgent need to adapt and develop unique and innovative techniques and services that are tailored to skin biology in order to speed up the process of scientific discoveries. The goal of the Genomics and Bioinformatics Core is to serve as a critical resource component of the Skin Center to place its member investigators at the cutting edge of new genomics and bioinformatics developments. The Core will leverage existing campus resources, such as technological instrumentation as well as genomics and bioinformatics expertise at both faculty and researcher levels, to develop new skin-specific services and provide technical and intellectual support to Center laboratories. The first specific aim of the Core is to provide state-of- the-art genomics technologies for gene expression and epigenome profiling (e.g., Illumina RNA-seq, NanoString nCounter, ATAC-seq, and ChIP-seq) along with dedicated staff time and associated statistical analyses (using both commercial and customized pipelines) to advance skin research. The second specific aim is to promote innovation in single cell analysis to foster understanding of cellular heterogeneities, differentiation hierarchies, and cell-cell interactions in skin, for example by testing and applying new instrumentation and technologies for single cell manipulation, developing new lineage-predicting bioinformatics tools for single cell data, as well as establishing and improving multiplexed in situ RNA detection to create spatial maps of gene expression and cell types or cellular states in the skin tissue. The third specific aim is to maintain a repository of all Center-generated skin sequencing data and create publically accessible databases, such as a new website containing single cell data with temporal and spatial information that is available to the skin research community at large. The last specific aim is to provide organized activities (e.g., seminars, workshops, mini-courses) as well as one-on-one consultation to train and educate Center skin biologists on basic genomics and bioinformatics. Collectively, these aims will make significant and long-lasting impact on skin research at UC Irvine to not only facilitate important scientific discoveries but also cultivate next-generation skin scientists with proficiency in genomics and bioinformatics.

项目概要 在全球和单细胞水平上探测基因表达和染色质景观的能力已经 打开了寻求前所未有的信息和洞察发展、稳态、修复和洞察的大门 皮肤作为一个复杂的器官的发病机制。加州大学欧文分校拥有超过临界数量的皮肤生物学家，他们具有良好的 建立旨在了解潜在监管机制的研究专业知识和计划 皮肤表皮、真皮、色素和血管细胞的生物学特性，以及这些机制如何出错 牛皮癣和皮肤癌等疾病。虽然这些皮肤生物学家都可以获得一般基因组学知识 校园中现有的技术，迫切需要适应和开发独特和创新的技术 针对皮肤生物学量身定制的技术和服务，以加快科学发现的进程。 基因组学和生物信息学核心的目标是作为皮肤中心的重要资源组成部分 使其成员研究人员处于新基因组学和生物信息学发展的前沿。这 核心将利用现有的校园资源，例如技术仪器以及基因组学和 教师和研究人员层面的生物信息学专业知识，开发新的皮肤特定服务并提供 为中心实验室提供技术和智力支持。核心的第一个具体目标是提供state-of- 用于基因表达和表观基因组分析的最先进的基因组学技术（例如 Illumina RNA-seq、NanoString nCounter、ATAC-seq 和 ChIP-seq）以及专门的工作人员时间和相关统计分析（使用 商业和定制管道）以推进皮肤研究。第二个具体目标是促进 单细胞分析创新，促进对细胞异质性、分化层次的理解， 以及皮肤中细胞与细胞的相互作用，例如通过测试和应用新的仪器和技术 单细胞操作，为单细胞数据开发新的谱系预测生物信息学工具，以及 建立和改进多重原位 RNA 检测，以创建基因表达和细胞的空间图 皮肤组织中的类型或细胞状态。第三个具体目标是维护所有中心生成的存储库 皮肤测序数据并创建可公开访问的数据库，例如包含单细胞的新网站 具有时间和空间信息的数据可供整个皮肤研究界使用。最后一个 具体目标是提供有组织的活动（例如研讨会、讲习班、迷你课程）以及一对一的活动 为中心皮肤生物学家提供基础基因组学和生物信息学方面的培训和教育咨询。总的来说，这些 目标将对加州大学欧文分校的皮肤研究产生重大和持久的影响，不仅促进重要的 科学发现，同时也培养精通基因组学和 生物信息学。