Core 1: Genomics Core

核心 1：基因组学核心

• 批准号: 10153725
• 负责人: ADRIANA HEGUY
• 金额: $ 20.54万
• 依托单位: NEW YORK UNIVERSITY SCHOOL OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-06-12 至 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10153725
• 关键词: ATAC-seq; Architecture; Automation; Cancer Center Support Grant; Cells; ChIP-seq; Chemistry; Chromatin; Communities; DNA; Data; Data Storage and Retrieval; Deposition; Doctor of Philosophy; Equipment; Gene Expression; Generations; Genes; Genome; Genomics; Health; Hi-C; High Performance Computing; Human; Human Resources; International; Libraries; Liquid substance; Malignant Neoplasms; Methods; Molecular Conformation; Nucleic Acids; Pathology; Phenotype; Play; Preparation; Procedures; Process; Production; Protocols documentation; Publications; Quality Control; Resource Sharing; Resources; Robot; Role; Running; Sampling; Scientist; Standardization; Technical Expertise; Technology; Testing; Work; anticancer research; bisulfite; bisulfite sequencing; computing resources; cost effectiveness; data sharing; deep sequencing; distributed data; exome; exome sequencing; genome sequencing; genomic data; instrumentation; medical schools; mutational status; nanopore; professor; sequencing platform; single-cell RNA sequencing; transcriptome; transcriptome sequencing; tumor progression; whole genome

SUMMARY – GENOMICS CORE The Genomics Core will assist all three projects, through the standardization of protocols and sequencing platforms, thus resulting in shared expertise and economies of scale. This centralized resource will play a coordinating role for all aspects of genomic data production, including automated library preparation, sequencing, data storage and distribution. The Genomics Core will be led by Dr. Adriana Heguy, PhD, Professor of Pathology at the NYU School of Medicine and Director of the Genome Technology Center (GTC) at NYU Langone Health. She is an internationally known genomics scientist with >10 years running genomics facilities for cancer research. Her lab is a state-of-the-art fully equipped genomic facility staffed with expert personnel specializing in high volume Illumina deep sequencing and automated sample preparation for large numbers of samples and a variety of applications including RNA-Seq, ChIP-Seq, ATAC-Seq, bisulfite sequencing and chromatin conformation sequencing approaches. Dr. Heguy has worked extensively with Dr. Skok and Dr. Aifantis during the past 4 years, generating key data featured in numerous high impact publications. The specific aims of the Genomics Core are: 1) to standardize all sample preparation and sequencing, and facilitate data sharing and storage among P01 projects and cores through high performance computing (HPC) resources; 2) to provide chromatin profiling library preps (ChIP-Seq and ATAC-Seq) and sequencing; 3) to perform chromatin conformation library preps (HiC, 4-C, 5-C, Capture HiC) and sequencing; 4) to provide exome sequencing and transcriptome profiling (RNA-Seq, scRNA-Seq) and 5) to perform whole genome and reduced representation bisulfite library preps and sequencing. The Genomics Core will extend beyond the current capabilities of the existing GTC, which is a shared resource partly supported by an NCI Cancer Center Support Grant. The Skok and Aifantis labs will assist the Genomics Core with the standardization of chromatin conformation library prep protocols, and the Melnick lab and Aifantis lab will work closely with the Core to standardize genome bisulfite sequencing protocols as well. The Genomics Core will coordinate sample workflow with the Pathology Core led by Dr. Giorgio Inghirami, which will supply human cells and nucleic acids for the projects, and after sequencing, with the Computational Core, led by Dr. Aristotelis Tsirigos, with which the GTC is already seamlessly integrated. There will be two half FTEs dedicated to the generation of data for these three projects, and Dr. Heguy's effort at 10%.

摘要 – 基因组学核心 基因组学核心将通过协议和测序的标准化来协助所有三个项目 平台，从而实现共享专业知识和规模经济。这种集中的资源将发挥 协调基因组数据生产各个方面的作用，包括自动化文库制备， 排序、数据存储和分发。基因组学核心将由 Adriana Heguy 博士领导， 纽约大学医学院病理学教授兼基因组技术中心（GTC）主任 在纽约大学朗格健康中心。她是一位国际知名的基因组科学家，从事基因组学工作超过 10 年 癌症研究设施。她的实验室是一个设备齐全的最先进的基因组设施，配备了专家 专门从事大批量 Illumina 深度测序和自动化样品制备的人员 大量样品和各种应用，包括 RNA-Seq、ChIP-Seq、ATAC-Seq、亚硫酸氢盐 测序和染色质构象测序方法。 Heguy 博士与 Dr. Heguy 进行了广泛的合作。 Skok 和 Aifantis 博士在过去 4 年中生成了众多高影响力的关键数据 出版物。基因组学核心的具体目标是：1）标准化所有样品制备和 排序，并通过高性能促进 P01 项目和核心之间的数据共享和存储 计算（HPC）资源； 2) 提供染色质分析文库制备（ChIP-Seq 和 ATAC-Seq）以及 测序； 3) 进行染色质构象文库制备（HiC、4-C、5-C、Capture HiC）和测序； 4) 提供外显子组测序和转录组分析（RNA-Seq、scRNA-Seq），5) 执行整体分析 基因组和简化代表性亚硫酸氢盐文库制备和测序。基因组学核心将扩展 超出了现有 GTC 的当前功能，GTC 是由 NCI 部分支持的共享资源 癌症中心支持补助金。 Skok 和 Aifantis 实验室将协助基因组学核心 染色质构象文库制备方案的标准化，Melnick 实验室和 Aifantis 实验室将开展工作 与核心密切合作，以标准化基因组亚硫酸氢盐测序方案。基因组学核心将 与 Giorgio Inghirami 博士领导的病理学核心协调样本工作流程，该核心将提供人类 该项目的细胞和核酸，以及测序后，由由博士领导的计算核心。 Aristotelis Tsirigos，GTC 已与其无缝集成。将有两个半 FTE 专门 为这三个项目生成数据，Heguy 博士的工作量为 10%。