Sequencing Core

测序核心

基本信息

批准号：
10419452
负责人：
Gregory Seumois
金额：
$ 18.52万
依托单位：
LA JOLLA INSTITUTE FOR IMMUNOLOGY
依托单位国家：
美国
项目类别：
财政年份：
2015
资助国家：
美国
起止时间：
2015-06-15 至 2027-05-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10419452
关键词：
2019-nCoV ATAC-seq Antibodies Area Biological Assay Biology Blood COVID-19 vaccination Cell Count Cell Separation Cell Surface Proteins Cell physiology Cells Chromatin Collection DNA DNA Sequencing Facility Data Data Analyses Dengue Virus Disease Elements Enhancers Epigenetic Process Flow Cytometry Funding Future Gene Expression Profiling Genes Genome Genomics Guidelines Health Human Human Resources Immune Immunology Individual Infection Lead Length Libraries Methodology Methods Mission Molecular Profiling Mycobacterium tuberculosis Preparation Procedures Protocols documentation Publications RNA RNA analysis RNA library Reproducibility Research Personnel Resolution Role Sampling Services Site Small RNA Sorting - Cell Movement Stains Standardization T memory cell T-Cell Receptor T-Lymphocyte T-Lymphocyte Subsets T-cell receptor repertoire Technology Tissues Training Transposase Untranslated RNA Vaccination antibody detection data management design epigenomics genome-wide genomic platform high throughput analysis insight interest lung pathogen microgenomics next generation sequencing novel pathogen patient subsets peripheral blood programs promoter respiratory pathogen single cell sequencing single-cell RNA sequencing transcription factor transcription factor USF transcriptome transcriptome sequencing transcriptomics

项目摘要

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.

测序核心摘要 LJI的HIPC计划的任务是使用无假设的方法来定义综合分子在肺病原体的背景下，T细胞子集的轮廓。感兴趣的区域覆盖了极宽的范围 “ OMICS”分析包括：（i）全球基因表达（散装和单细胞RNA-Seq）的分析，（ii）分析 T细胞受体的高可变序列库库通过大量或单细胞TCR-Seq，（iii）分析的变化在T细胞存储器中，使用单细胞ATAC-SEQ，全局表观遗传学概况（全基因组增强子概况）感染和/或接种疫苗的患者的子集，SARS-COV-2，结核分枝杆菌（MTB）和其他肺病原体。所有这些“ OMICS”应用都依赖于标准化和验证的高通量下一代测序（NGS）方法 - 该核心提供的关键服务。测序核心将为该计划中涉及的所有三个项目提供所有NGS活动。这会由其人员的广泛基因组学专业知识和尖端的可用性做好准备技术和自动化平台，以生成高度可重现和健壮的测序数据样品数量。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，排序细胞，准备RNA/DNA，为高通量NGS准备库，并将结果数据传输到数据管理和分析核心进行后续分析。