Next Generation Sequencing Shared Resource

下一代测序共享资源

• 批准号: 10625767
• 负责人: David Moraga
• 金额: $ 7万
• 依托单位: UNIVERSITY OF FLORIDA
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-06-01 至 2027-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10625767
• 关键词: ATAC-seq; Abbreviations; Address; Adherence; Adopted; Advanced Malignant Neoplasm; Applications Grants; Automation; Bioinformatics; Biometry; Biotechnology; COVID-19 pandemic; Cancer Center; Cancer Center Support Grant; Cancer Control; Cell Survival; Cells; ChIP-seq; Chromatin Structure; Chromium; Clinical; Collaborations; Collection; Communities; Complex; Computer Analysis; Confocal Microscopy; Consultations; Cost Savings; Culicidae; DNA; DNA Library; DNA Methylation; DNA sequencing; Data; Data Analyses; Data Set; Educational workshop; Effectiveness; Ensure; Epigenetic Process; Equipment; Experimental Designs; Feedback; Florida; Flow Cytometry; Funding; Gene Expression Regulation; Genetic Research; Genomics; Health; High Performance Computing; Immune response; Immunobiology; Infrastructure; Institution; Investments; Laboratories; Last Name; Learning; Letters; Libraries; Liquid substance; Malignant Neoplasms; Messenger RNA; MicroRNAs; Miniaturization; Mission; Molecular Epidemiology; Multiomic Data; NCI Center for Cancer Research; Peer Review; Population Sciences; Preparation; Procedures; Proteins; Publications; Quality Control; RNA; RNA Splicing; Reaction; Recommendation; Reproducibility; Research; Research Project Grants; Research Support; Resource Sharing; Resources; Ribonucleases; Ribosomal RNA; Robot; Robotics; Running; Sampling; Schedule; Science; Services; Small RNA; Strategic Planning; Supervision; Surveys; System; Technology; Training; United States National Institutes of Health; Universities; Untranslated RNA; Variant; Vendor; Work; anticancer research; base; cancer cell; cluster computing; college; cost; cost effective; epigenomics; experience; genetic variant; genome sequencing; improved; instrument; instrumentation; meetings; member; metagenome; microbiome; nanolitre; nanopore; new technology; next generation sequencing; operation; programs; recruit; research study; response; sequencing platform; single-cell RNA sequencing; transcriptome sequencing; transcriptomics; treatment response; tumor; tumor microenvironment; tumorigenesis; whole genome

NEXT GENERATION SEQUENCING SHARED RESOURCE (NGS-SR): ABSTRACT The Next Generation Sequencing Shared Resource (NGS-SR) provides the University of Florida Health Cancer Center (UFHCC) members with access to centralized, state-of-the-art, cost-effective next generation sequencing services to advance cancer research. The NGS-SR is an institutionally-managed shared resource supported by UFHCC through a partnership with the UF Interdisciplinary Center for Biotechnology Research, a campus-wide shared biotechnology resource. Located within the Cancer & Genetics Research Complex providing convenient access for UFHCC members, NGS-SR includes 4 staff members under the supervision of Moraga, who has over 30 years of experience in DNA sequencing technologies. During the recent COVID-19 pandemic, the NGS-SR was identified as an essential campus resource and remained staffed and open to the UF research community. NGS-SR service requests and invoicing are managed via the CrossLab laboratory management system. Key sequencing technologies available include instruments from Illumina (NovaSeq6000, MiSeq), PacBio SEQUEL IIe, Oxford Nanopore PromethION, and the 10x Genomics Chromium single-cell RNA-Seq and VISIUM spatial transcriptomics platforms. Raw sequencing read data are directly transferred to the HiPerGator high- performance computing cluster for downstream bioinformatics analysis. UFHCC investments in instrumentation include the Illumina NovaSeq6000, PacBio SEQUEL IIe, mosquito® liquid handling robot, and 10x Genomics Chromium single cell platform. The NGS-SR works in collaboration with the UFHCC Biostatistics and Quantitative Sciences Shared Resource to provide no cost consultation in effective experimental design and best practices in computational analysis of large-scale multi-omic data sets. NGS-SR supports studies in DNA structural and gene variant analysis, microbiome and metagenome analysis, bulk and single cell ATAC-Seq and RNA-Seq, ChIP-Seq, and whole genome sequencing. Since 2016, 54 unique members have used NGS-SR, of which 45 have peer-reviewed funding. There has been an increase in the number of members using NGS-SR each year and an increase in sequencing runs, supporting 54 peer-reviewed publications, with 24% having IF >10. Mechanisms of Oncogenesis and the Cancer Therapeutics and Host Response members represent major users. The effectiveness of the NGS-SR in meeting member needs is assessed by annual surveys, feedback from the NGS-SR Scientific Advisory Group, and recommendations from the Shared Resources Oversight Committee. In response to user requests for lower costs, the acquisition of the NovaSeq6000 reduced sequencing costs by 50% and the use of robotics has reduced RNA-Seq library prep costs by 75%. In alignment with the UFHCC Strategic Plan, Momentum 2027, the demand for NGS-SR services is anticipated to grow with recruitments in molecular epidemiology, immunobiology, and RNA epigenetics. In response, NGS-SR will continue to lower costs through increased automation, expand services including spatial transcriptomics, and adopt new technologies to increase capabilities in cost effective single cell transcriptomics.

下一代测序共享资源（NGS-SR）：摘要 下一代测序共享资源（NGS-SR）为佛罗里达大学健康癌症提供 中心（UFHCC）成员可以访问集中式，最先进的，具有成本效益的下一代测序 推进癌症研究的服务。 NGS-SR是由机构管理的共享资源，由 UFHCC通过与UF跨学科生物技术研究中心建立合作伙伴关系 共享生物技术资源。位于癌症和遗传学研究综合体中，可方便 NGS-SR访问UFHCC成员，在莫拉加（Moraga）的监督下包括4名工作人员 DNA测序技术的30年经验。在最近的Covid-19大流行期间，NGS-SR 被确定为必不可少的校园资源，并保持人员配备并向UF研究社区开放。 NGS-SR服务请求和发票通过CrossLab实验室管理系统管理。钥匙 可用的测序技术包括来自Illumina（Novaseq6000，Miseq）的仪器，PACBIO续集 IIE，牛津纳米波尔Promethion和10倍基因组学铬单细胞RNA-seq和visium空间 转录组学平台。原始测序读取数据直接传输到嘻哈高 - 性能计算集群用于下游生物信息学分析。 UFHCC仪器调查 包括Illumina Novaseq6000，Pacbio续集IIE，Mosquito®液体处理机器人和10倍基因组学 铬单细胞平台。 NGS-SR与UFHCC生物统计学合作和 定量科学共享资源，以在有效的实验设计和 大规模多态数据集的计算分析中的最佳实践。 NGS-SR支持DNA的研究 结构和基因变异分析，微生物组和元基因组分析，大量和单细胞ATAC-SEQ和 RNA-seq，chip-seq和整个基因组测序。自2016年以来，有54位独特的成员使用了NGS-SR 有45个经过同行评审的资金。使用NGS-SR的成员数量增加了 每年，测序运行的增加，支持54个同行评审的出版物，其中24％的IF > 10。肿瘤发生的机制和癌症治疗剂和宿主反应成员代表主要 用户。 NGS-SR在满足会员需求方面的有效性通过年度调查，反馈评估 来自NGS-SR科学咨询小组，以及共享资源监督的建议 委员会。为了响应用户要求降低成本的要求，降低了novaseq6000的收购 测序成本提高50％，使用机器人技术使RNA-Seq库准备成本降低了75％。在对齐中 随着UFHCC战略计划，动力2027，对NGS​​-SR服务的需求预计将随着 分子流行病学，免疫生物学和RNA表观遗传学的募集。作为回应，NGS-SR将 通过增加自动化，扩大包括空间转录组学的服务以及 采用新技术来提高成本有效的单细胞转录组学的能力。