Technology Core

技术核心

• 批准号: 10551464
• 负责人: Benjamin David Singer
• 金额: $ 51.16万
• 依托单位: NORTHWESTERN UNIVERSITY AT CHICAGO
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-01-17 至 2027-12-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10551464
• 关键词: 2019-nCoV; Alveolar; Alveolar Macrophages; Alveolus; Animal Model; B-Cell Antigen Receptor; Back; Bioinformatics; Biological; Biological Assay; Blood specimen; Bronchoalveolar Lavage; COVID-19 pneumonia; Cell Separation; Cells; Clinical; Clinical Trials; Complex; Cryopreservation; Curettage procedure; DNA Methylation; Data; Disease; Epithelial Cells; Epithelium; Epitopes; Expression Profiling; Flow Cytometry; Funding; Gene Expression; Gene Expression Profiling; Generations; Genomics; Goals; Hour; Immune; Immunophenotyping; Inflammatory; Interferon Type II; International; Knowledge; Laboratories; Lung; Mechanical ventilation; Modeling; Nature; Nose; Participant; Pathogenesis; Patients; Pneumonia; Population; Procedures; Process; Protocols documentation; Publishing; Research Personnel; Role; Running; Sampling; Signal Transduction; Structure; Systems Biology; T-Lymphocyte; T-Lymphocyte Subsets; Techniques; Technology; Work; biobank; cost; cytokine; genome-wide; immunopathology; indexing; information model; innovation; metagenomic sequencing; multiple omics; next generation sequencing; novel; novel therapeutics; pathogen; pneumonia treatment; process optimization; protein expression; response; sensor; severe COVID-19; single cell technology; single-cell RNA sequencing; success; transcriptome

PROJECT SUMMARY/ABSTRACT – Technology Core This innovative Systems Biology Center application seeks to model the complex host/pathogen interactions occurring in patients with severe pneumonia. The overall goals of the Technology Core (TechCore) are to provide sample processing, biobanking, and data generation support for all Projects and other Cores in the Super- Successful Clinical Response In Pneumonia Therapy (SCRIPT2) Systems Biology Center. Our Technology Core is uniquely poised to contribute to the success of the SCRIPT2 Study, as we possess expertise in flow cytometry, cell sorting, cryopreservation, and various next-generation sequencing (NGS) techniques, including bulk and single-cell technologies for gene expression (single-cell RNA-seq) and protein expression profiling (cellular indexing of transcriptomes and epitopes [CITE]-seq), T and B cell receptor (TCR and BCR) clonotyping, genome- wide DNA methylation analysis, metagenomics sequencing, and deep pathogen sequencing. The Technology Core will process clinical samples, cryopreserve them, and then cryorecover them for pre-designated NGS assays in close coordination with the Projects and other Cores. The data generated from the TechCore’s activities will feed back to the DMBI and Modeling Cores to support the aims of Projects 1 and 2 as well as iteratively inform sample selection to determine the most informative NGS assays to perform on a given sample. The Technology Core has conceptualized its activities into two Specific Aims: Aim 1. To immunophenotype and perform biobanking of BAL, nasal curettage, and blood samples obtained from patients with severe pneumonia for subsequent NGS analysis. In Aim 1.1, we will use multiparameter flow cytometry to immunophenotype subsets of epithelial and immune cells from samples obtained from patients with severe pneumonia. In Aim 1.2, we will perform cryopreservation of all samples using techniques that allow for downstream NGS assays on selected samples. Aim 2. To perform NGS assays, including single-cell RNA-seq, CITE-seq, single-cell TCR and BCR clonotyping, T cell subset DNA methylation analysis, metagenomics sequencing, and deep pathogen sequencing on selected cryopreserved samples. We will cryorecover samples selected by the Projects in conjunction with the DMBI and Modeling Cores to perform pre-designated NGS assays and subsequent bioinformatics processing. We will also perform other assays, such as cytokine profiling, as directed by the Projects.

项目概要/摘要-技术核心 这个创新的系统生物学中心应用程序旨在模拟复杂的宿主/病原体相互作用 发生在重症肺炎患者中。技术核心（TechCore）的总体目标是提供 样本处理、生物库和数据生成支持，适用于所有项目和超级 成功的临床反应在肺炎治疗（CITT 2）系统生物学中心。我们的技术核心 是独一无二的准备，有助于成功的CD 4 T2研究，因为我们拥有专业知识，在流式细胞术， 细胞分选、冷冻保存和各种下一代测序（NGS）技术，包括批量和 用于基因表达的单细胞技术（单细胞RNA-seq）和蛋白质表达谱分析（细胞 转录组和表位索引[CITE]-seq），T和B细胞受体（TCR和BCR）克隆分型，基因组- 广泛的DNA甲基化分析、宏基因组测序和深层病原体测序。技术 核心将处理临床样本，冷冻保存，然后冷冻复苏，用于预先指定的NGS 与项目和其他核心密切协调。从TechCore生成的数据 活动将反馈到DMBI和建模核心，以支持项目1和2的目标，以及 迭代地通知样品选择以确定对给定样品执行的信息量最大的NGS测定。 技术核心将其活动概念化为两个具体目标： 目标1.对BAL、鼻刮和血液样本进行免疫表型分析和生物库分析 用于随后的NGS分析。在目标1.1中，我们将使用 对来自样品的上皮细胞和免疫细胞的免疫表型亚群的多参数流式细胞术 从重症肺炎患者身上获得。在目标1.2中，我们将使用 这些技术允许对选定样品进行下游NGS测定。 目标二。进行NGS检测，包括单细胞RNA-seq、CITE-seq、单细胞TCR和BCR 克隆分型、T细胞亚群DNA甲基化分析、宏基因组测序和深层病原体 对选定的冷冻保存样品进行测序。我们会把由计划挑选的样本， 与DMBI和建模核心一起执行预先指定的NGS分析和随后的 生物信息学处理我们还将进行其他试验，如细胞因子谱分析，如指导下， 项目