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.

项目摘要 全球且在单个细胞水平上探测基因表达和染色质景观的能力具有 打开了大门，寻求空前的信息并了解开发，体内平衡，维修和 皮肤的发病机理作为复杂的器官。 UC Irvine不仅享受着批判性的皮肤生物学家 建立的研究专业知识和旨在了解监管机制的计划 皮肤表皮，皮肤，色素和血管细胞的生物学，以及这种机制如何出现在 牛皮癣和皮肤癌等疾病。尽管这些皮肤生物学家都可以使用一般基因组学 目前在校园可用的技术，迫切需要适应和发展独特而创新的技术 为了加快科学发现的过程，针对皮肤生物学量身定制的技术和服务。 基因组学和生物信息学核心的目标是作为皮肤中心的关键资源组成部分 将其成员研究人员处于新基因组学和生物信息学发展的最前沿。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 教师和研究人员级别的生物信息学专业知识，以开发新的皮肤服务并提供 中心实验室的技术和智力支持。核心的第一个具体目的是提供最新 用于基因表达和表观基因组分析的ART基因组学技术（例如Illumina RNA-Seq，纳米弦 ncounter，atac-seq和chip-seq）以及专门的员工时间和相关的统计分析（使用 商业和定制管道）以推进皮肤研究。第二个具体目的是促进 单细胞分析中的创新以促进对细胞异质性，分化层次结构的了解， 以及皮肤中的细胞细胞相互作用，例如通过测试和应用新的仪器和技术 单细胞操纵，开发新的谱系预测生物信息学工具，用于单细胞数据以及 建立和改进多路复用的原位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。第三个具体目的是维护所有中心生成的存储库 皮肤测序数据并创建公开访问的数据库，例如包含单个单元格的新网站 具有时间和空间信息的数据可供整个皮肤研究社区使用。最后 具体目的是提供有组织的活动（例如研讨会，讲习班，迷你场）以及一对一 咨询培训和教育中心皮肤生物学家就基本基因组学和生物信息学提供咨询。总的来说，这些 目的将对UC Irvine的皮肤研究产生重大和持久的影响，不仅有助于重要 科学发现，但还培养了熟练基因组学和的下一代皮肤科学家 生物信息学。