Sequencing Core

排序核心摘要 LJI的HIPC计划的任务是使用无假设的方法来定义全面的分子 T细胞亚群在肺部病原体中的分布。感兴趣的领域涉及非常广泛的领域 “组学”分析包括：(一)全球基因表达分析(散装和单细胞RNA序列)，(二)分析 批量或单细胞TCR-seq的T细胞受体高可变序列谱系，(Iii)变化分析 在T细胞存储器中使用单细胞ATAC-seq的全球表观遗传学简档(基因组范围的增强子简档) 来自感染和/或接种SARS-CoV-2、结核分枝杆菌(Mtb)的患者的亚群，以及 其他肺部病原体。所有这些“组学”应用程序都依赖于标准化且经过充分验证的高吞吐量 下一代测序(NGS)方法-该核心提供的关键服务。 测序核心将为该计划涉及的所有三个项目的所有NGS活动提供支持。这将是 通过其人员的广泛基因组学专业知识和尖端技术的可用性来促进 技术和自动化平台，从大量的数据中生成高度可重复性和健壮的测序数据 样本数。实际上，测序核心将直接与所有三个项目对接，并提供 标准化和质量控制的流水线，包括接收样品，分选细胞，制备RNA/DNA， 为高吞吐量NGS准备库，并将生成的数据传输到数据管理和 分析核心，用于后续分析。

Sequencing Core Summary The mission of the HIPC program at LJI is to use hypothesis-free approaches to define comprehensive molecular profiles of T cell subsets in the context of lung pathogens. The areas of interest cover an extremely wide spectrum of “omics” analysis including: (i) analysis of global gene expression (bulk and single-cell RNA-seq), (ii) analysis of T cell receptors high variable sequences repertoire by bulk or single-cell TCR-seq, (iii) analysis of changes in global epigenetics profiles (genome-wide enhancer profiles) using single-cell ATAC-seq, in T cell memory subsets from patients infected and/or vaccinated against, SARS-CoV-2, Mycobacterium tuberculosis (Mtb), and other lung pathogens. All these “omics” applications rely on standardized and well-validated high-throughput Next-Generation Sequencing (NGS) methods – a key service provided by this Core. The Sequencing Core will support all NGS activities for all the three projects involved in this program. This will be facilitated by the extensive genomics expertise of its personnel and the availability of cutting-edge technologies and automated platforms to generate highly reproducible and robust sequencing data from a large number of samples. Practically, the Sequencing Core will interface directly with all three Projects and provide a standardized and quality-controlled pipeline consisting of receiving samples, sorting cells, preparing RNA/DNA, preparing libraries for high-throughput NGS, and transferring the resulting data to the Data Management and Analysis Core for subsequent analysis.