Core B: Single cell and integrative genomics core

核心 B：单细胞和整合基因组学核心

• 批准号: 9893785
• 负责人: Steven Edward Bosinger
• 金额: $ 31.65万
• 依托单位: EMORY UNIVERSITY
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/9893785
• 关键词: Acute; Address; Age; Aging; Antigens; Bioinformatics; Biological Assay; CD4 Positive T Lymphocytes; CD8-Positive T-Lymphocytes; Cells; Chromatin; Complement; Contracts; Custom; Data; Data Analytics; Development; Effector Cell; Epigenetic Process; Funding; Generations; Genetic Models; Genetic Transcription; Genomics; Goals; Growth; Immune; Immunophenotyping; Individual; Infection; Libraries; Liquid substance; Longevity; Lymphocyte; Memory; Methodology; Modeling; Molecular; Myelogenous; Phase; Population; Preparation; Research; Research Personnel; Resolution; Running; Sampling; Site; T-Lymphocyte; Technology; Universities; Vaccination; Vaccines; Work; acute infection; aged; antigen-specific T cells; cell age; cost effective; droplet sequencing; epigenetic profiling; epigenomics; experimental study; genomic data; innovation; memory acquisition; novel; response; senescence; single cell analysis; single-cell RNA sequencing; stemness; transcription factor; transcriptomics; vaccine-induced immunity

The Single Cell and Integrative Genomics Core will provide support for individual Projects by performing assays requiring specialized technology and offering unique bioinformatics methodology. More specifically, Core B will be responsible for the following work: (i) conducting bulk and single-cell RNA-Seq profiling; (ii) running bulk and single-cell ATAC-Seq assays to assess chromatin accessibility, and (iii) providing computational expertise and bioinformatics for the analysis of Core B generated data that is beyond the capabilities of individual Projects. Core B is led by Dr. Steven Bosinger at Emory University, with Dr. Will Greenleaf at Stanford as a key Co-Investigator. Core B will be physically located at both Emory and Stanford. The Emory site of Core B (Bosinger) will conduct bulk and single-cell RNA-Seq library preparation and sequencing for the experiments described in each project. The Stanford site of Core B (Greenleaf) will be responsible for ATAC-Seq library preparation on bulk and single-cell samples. Both sites will take advantage of novel liquid handling platform work-flows to enable single-cell RNA-Seq and sc-ATAC-Seq library generation to be performed in a high-throughput, cost-effective manner. Hence, Core B will be able to obtain information on the epigenetic landscape of individual immune cells longitudinally after vaccination at a resolution and scale that has previously not been feasible. Core B will also provide unique expertise in analyzing sc-ATAC-Seq data that will take advantage of the availability of the sc-RNA-Seq data from matching samples. By integrating single-cell RNA-Seq and ATAC-Seq data, these analytical approaches allow for epigenetic states that predict transcriptional states to be identified with accuracy. Additionally, Core B, has developed methodology to construct lymphocyte differentiation “trajectories” to order epigenetic and transcriptional changes at different stages of development in single cells. This analytical approach will be applied to assess lymphocyte differentiation following vaccination and in aging. In summary, the technological expertise offered by Core B will allow for high-quality single-cell genomic data to be generated in a highly efficient and cost-effective manner. More importantly, the integrated analytical pipelines developed and offered by Core B will be central to attaining the research aims of each Project, specifically in building high resolution models of genetic states that are imparted on lymphocytes during the acquisition of memory or senescence and identifying factors that dictate these long-term fates.

单细胞和综合基因组学核心将通过执行单个项目提供支持 需要专业技术并提供独特的生物信息学方法的测定方法。更具体地说， 核心B将负责以下工作：（i）进行批量和单细胞RNA-seq分析； （ii） 运行散装和单细胞ATAC-SEQ分析以评估染色质的可及性，并且（iii）提供 用于分析核心B生成的数据的计算专业知识和生物信息学超出 单个项目的功能。核心B由埃默里大学（Emory University）的史蒂文·博辛格（Steven Bosinger）博士领导，威尔博士 斯坦福大学的Greenleaf是关键的共同研究员。核心B将在埃默里（Emory）和斯坦福大学（Stanford）物理上。 Core B（Bosinger）的Emory站点将进行批量和单细胞RNA-seq库的准备和 每个项目中描述的实验的测序。核心B（Greenleaf）的Stanford遗址将是 负责在批量和单细胞样品上制备ATAC-SEQ库。两个站点都将利用 新颖的液体处理平台工作流程以使单细胞RNA-seq和SC-ATAC-Seq库生成 以高通量，具有成本效益的方式进行。因此，核心B将能够获取有关 疫苗接种后，单个免疫细胞的表观遗传景观以分辨率和尺度接种 以前这是不可行的。核心B还将在分析SC-ATAC-SEQ数据方面提供独特的专业知识 这将利用来自匹配样本的SC-RNA-seq数据的可用性。通过集成 单细胞RNA-SEQ和ATAC-SEQ数据，这些分析方法允许表观遗传状态预测 转录状态可以准确地识别。此外，Core B，还开发了方法论 构建淋巴细胞分化的“轨迹”，以在不同 单细胞的发育阶段。这种分析方法将用于评估淋巴细胞 疫苗和衰老后的分化。总而言之，核心B提供的技术专长 将允许高效且具有成本效益的高质量单细胞基因组数据 方式。更重要的是，核心B开发和提供的集成分析管道将是中心 为了达到每个项目的研究目标，特别是在建立遗传状态的高分辨率模型中 在获取记忆或感受期间，淋巴细胞赋予的这些因素以及识别因素 决定这些长期命运。