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研究所提供 中心（UFHCC）成员可获得集中、最先进、经济高效的下一代测序 促进癌症研究的服务。NGS-SR是一种由机构管理的共享资源， UFHCC通过与UF跨学科中心生物技术研究，一个校园范围内的合作伙伴关系 共享生物技术资源。位于癌症和遗传学研究中心内， 为方便UFHCC成员的访问，NGS-SR包括4名工作人员，由莫拉加监督，他有超过100名工作人员。 30年的DNA测序技术经验。在最近的COVID-19大流行期间，NGS-SR 被确定为一个必不可少的校园资源，并保持人员和开放的用友研究界。 NGS-SR服务请求和发票通过CrossLab实验室管理系统进行管理。关键 可用的测序技术包括来自Illumina（NovaSeq 6000，MiSeq）、PacBio SEQUEL IIe，Oxford Nanopore PromethION和10 x Genomics Chromium单细胞RNA-Seq和VISIUM空间 转录组学平台。原始测序读数数据直接传输至HiPerGator高- 用于下游生物信息学分析的高性能计算集群。UFHCC在仪器仪表方面的投资 包括Illumina NovaSeq 6000、PacBio SEQUEL IIe、mosquito®液体处理机器人和10 x Genomics Chromium单电池平台。NGS-SR与UFHCC生物统计学合作， 定量科学共享资源，提供有效的实验设计和免费咨询， 大规模多组学数据集计算分析的最佳做法。NGS-SR支持DNA研究 结构和基因变体分析、微生物组和宏基因组分析、本体和单细胞ATAC-Seq和 RNA-Seq、ChIP-Seq和全基因组测序。自2016年以来，已有54个独特成员使用了NGS-SR， 其中45个有同行评审的资金。使用NGS-SR的成员数量有所增加 每年都在增加，测序运行增加，支持54篇同行评审的出版物，其中24%具有IF >10.肿瘤发生机制和癌症治疗与宿主反应成员代表了主要的 用户.通过年度调查和反馈评估NGS-SR满足成员需求的有效性 NGS-SR科学咨询小组的建议，以及共享资源监督小组的建议 以马克思为了满足用户降低成本的要求， 测序成本降低了50%，机器人技术的使用使RNA-Seq文库制备成本降低了75%。对准 根据美国海军陆战队联合舰队的战略计划《2027年动力计划》，预计对NGS-SR服务的需求将随着 招募分子流行病学，免疫生物学和RNA表观遗传学。作为回应，NGS-SR将 通过提高自动化程度继续降低成本，扩大包括空间转录组学在内的服务， 采用新技术以提高成本效益高的单细胞转录组学的能力。