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.

单细胞和整合基因组学核心将通过执行以下操作为单个项目提供支持： 需要专门技术并提供独特的生物信息学方法的分析。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） 运行批量和单细胞ATAC-Seq测定以评估染色质可及性，和（iii）提供 计算专业知识和生物信息学，用于分析核心B生成的数据， 个别项目的能力。核心B由埃默里大学的史蒂文·博辛格博士领导， Greenleaf在斯坦福大学担任主要合作研究者。核心B将物理位于埃默里大学和斯坦福大学。 Core B（Bosinger）的Emory研究中心将进行批量和单细胞RNA-Seq文库制备， 为每个项目中描述的实验排序。核心B（Greenleaf）的斯坦福大学站点将 负责批量和单细胞样品的ATAC-Seq文库制备。两个网站都将利用 新的液体处理平台工作流程，使单细胞RNA-Seq和sc-ATAC-Seq文库产生， 以高通量、成本有效的方式进行。因此，核心B将能够获得以下信息 以一定的分辨率和规模纵向接种疫苗后单个免疫细胞的表观遗传景观 这在以前是不可行的。核心B还将提供分析sc-ATAC-Seq数据的独特专业知识 这将利用来自匹配样本的sc-RNA-Seq数据的可用性。通过整合 单细胞RNA-Seq和ATAC-Seq数据，这些分析方法允许预测 转录状态被准确地识别。此外，核心B还开发了方法， 构建淋巴细胞分化“轨迹”，以在不同时间点对表观遗传和转录变化进行排序， 单细胞的发育阶段。该分析方法将用于评估淋巴细胞 疫苗接种后和衰老过程中的分化。总之，核心B提供的技术专长 将允许高质量的单细胞基因组数据以高效和具有成本效益的方式生成， 方式更重要的是，核心B开发和提供的集成分析管道将成为核心 实现每个项目的研究目标，特别是建立高分辨率的遗传状态模型 在获得记忆或衰老过程中传递给淋巴细胞的信号， 决定了这些长期的命运。