Core B: Single cell and integrative genomics core

单细胞和综合基因组学核心将通过执行以下方式为个别项目提供支持 需要专业技术并提供独特的生物信息学方法的分析。更确切地说， 核心B将负责以下工作：(1)进行批量和单细胞RNA-Seq分析；(2) 运行批量和单细胞ATAC-Seq分析以评估染色质的可及性，以及(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 单个项目的能力。核心B由埃默里大学的史蒂文·博辛格博士和威尔博士共同领导 格林利夫在斯坦福大学担任关键的联合调查员。核心B将同时位于埃默里和斯坦福。 核心B的埃默里站点(博辛格)将进行批量和单细胞RNA-Seq文库的准备和 对每个项目中描述的实验进行排序。斯坦福大学核心B(格林利夫)的选址将是 负责批量和单细胞样品的ATAC-Seq文库的准备工作。这两个站点都将利用 支持单细胞RNA-Seq和sc-ATAC-Seq文库生成的新型液体处理平台工作流程 以高吞吐量、高成本效益的方式进行。因此，核心B将能够获得关于 个体免疫细胞在分辨率和规模上纵向接种后的表观遗传格局 这在以前是不可行的。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，这些分析方法允许预测表观遗传状态 转录状态需要准确识别。此外，核心B还制定了以下方法 构建淋巴细胞分化“轨迹”，对不同时期的表观遗传和转录变化进行排序 单细胞的发育阶段。这种分析方法将被应用于评估淋巴细胞 接种疫苗后和老化后的分化。总而言之，Core B提供的技术专长 将允许以高效和经济高效的方式生成高质量的单细胞基因组数据 举止。更重要的是，由Core B开发和提供的综合分析管道将是核心 达到每个项目的研究目标，特别是在构建高分辨率遗传状态模型方面 在获得记忆或衰老的过程中传递给淋巴细胞的分子，并识别 决定着这些长期的命运。

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.