Immunomics Research Core

免疫组学和表观基因组学核心 项目摘要/摘要 免疫组学和表观基因组学核心(IEC)是整个计划的重要组成部分，该计划将 集中执行多项检测，以确定免疫反应的特征。这个 整体提案旨在了解甲氧西林耐药感染患者的表观遗传学变化 金黄色葡萄球菌或白色念珠菌与免疫功能塑造 抗生素-解决结果的持久性。IEC核心将提供熟练的技术和科学专业知识 通过进行以下测试，使私人投资机构能够实现他们的研究目标。我们将描述 从长途阅读患者标本中分离的MRSA和CAC的遗传学和表观遗传学。使用PacBio 我们将重建患者分离的金黄色葡萄球菌和念珠菌的基因组 样本，得出这些微生物的基因组和表观基因组，并将数据与患者结果相关联。我们会 从短阅读数据中分析转录本和表观基因组。这将包括整个基因组的生成 亚硫酸氢盐测序文库，以确定血液和血浆中的细胞类型及其丰度 DNA样本。染色质的可及性将使用ATC-seq进行分析。蛋白质-DNA相互作用也将是 使用切割和运行协议进行分析。最后，我们还将描述先天免疫反应和获得性免疫反应 CAC和MRSA患者样本以及PAMP刺激的巨噬细胞的表型和功能。《核心》 已验证标准化细胞培养、免疫表型鉴定面板、多重Luminex、超敏感SIMA 分析，以支持项目的研究。我们将负责执行这些分析，解释 数据和与生物信息和数据管理(BDM)核心合作来传输数据和 用于进一步分析的计算(CPM)核心。

IMMUNOMICS AND EPIGENOMICS CORE PROJECT SUMMARY/ABSTRACT The Immunomics and Epigenomics Core (IEC) is an essential component of the overall program that will centralize the execution of a number of assays that will enable the characterization of immune responses. The overall proposal aims to understand epigenetic changes in patients infected by methicillin-resistant Staphylococcus aureus (MRSA) or Candida albicans Candidemia (CAC) and the immunologic functions shaping antibiotic-persistent from resolving outcomes. The IEC Core will provide skilled technical and scientific expertise to enable the PIs to achieve their research goals by carrying out the following assays. We will characterize the genetics and epigenetics of MRSA and CAC isolated from patient samples from long reads. Using PacBio circular consensus sequences we will reconstruct the genomes of SA and Candida isolated derived from patient samples, derive genomes and epigenomes of these microbes and related the data to patient outcomes. We will profile transcriptomes and epigenomes from short read data. This will include the generation of whole genome bisulfite sequencing libraries in order to characterize the cell types and their abundance in blood and plasma DNA samples. Chromatin accessibility will be profiled using ATC-seq. Protein-DNA interaction will also be profiled using CUT&Run protocols. Finally, we will also characterize innate and adaptive immune responses in CAC and MRSA patient samples and the phenotype and function of PAMP-stimulated macrophages. The Core has validated standardized cell cultures, immunophenotyping panels, multiplex Luminex, ultrasensitive Simoa assay to support the research of the Projects. We will be responsible for performing these assays, interpreting the data and working with the Bioinformatic and Data Management (BDM) Core to transfer the data and the Computational (CPM) Core for further analysis.