Core 1: Genomics Core

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 这是一个平台，从而产生共享的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的所有方面，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和基因组技术中心（GTC）主任 在纽约大学朗格尼健康中心她是国际知名的基因组学科学家，从事基因组学研究超过10年 癌症研究设施。她的实验室是最先进的设备齐全的基因组设施， 专业从事大批量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. Skok和Aifantis博士在过去的4年里，产生了许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， 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 3）进行染色质构象文库制备（HiC、4-C、5-C、捕获HiC）和测序; 4)提供外显子组测序和转录组分析（RNA-Seq，scRNA-Seq）和5）进行全基因组测序， 基因组和简化的亚硫酸氢盐文库制备和测序。基因组学核心将扩展 超出现有全球技术中心的现有能力，这是一种共享资源，部分由国家计算机基础设施提供支持 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 与由Giorgio Inghirami博士领导的病理学核心协调样本工作流程，该病理学核心将提供人类 细胞和核酸的项目，并在测序后，与计算核心，由博士领导。 Tsirigos，与GTC已经无缝集成。将有两名半全职员工专门负责 这三个项目的数据生成，和赫盖伊博士的努力在10%。

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%.