Sequencing Core

测序核心摘要 LJI重债穷国计划的使命是使用无假设的方法来定义全面的分子 在肺病原体的背景下的T细胞亚群的概况。感兴趣的领域涵盖了极其广泛的范围 “组学”分析包括：（i）分析整体基因表达（批量和单细胞RNA-seq），（ii）分析 （iii）通过批量或单细胞TCR-seq分析T细胞受体高可变序列库的变化， 在T细胞记忆中使用单细胞ATAC-seq的全局表观遗传学特征（全基因组增强子特征） 来自感染和/或接种SARS-CoV-2、结核分枝杆菌（Mtb）和 其他肺部病原体。所有这些“组学”应用都依赖于标准化和经过良好验证的高通量 下一代测序（NGS）方法-该核心提供的关键服务。 测序核心将支持该计划涉及的所有三个项目的所有NGS活动。这将 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， 技术和自动化平台，从大规模的 样本数量。实际上，测序核心将直接与所有三个项目接口，并提供一个 标准化和质量控制的管道，包括接收样品、分选细胞、制备RNA/DNA、 为高通量NGS准备库，并将结果数据传输到数据管理部门， 用于后续分析的分析核心。

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.