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Bioinformatics and Computational Biology Core

生物信息学和计算生物学核心

基本信息

批准号：
10453789
负责人：
Wei Wang
金额：
$ 17.24万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN DIEGO
依托单位国家：
美国
项目类别：
财政年份：
2018
资助国家：
美国
起止时间：
2018-07-17 至 2024-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10453789
关键词：
ATAC-seq Acute Binding Sites Bioinformatics Biological Biology CD8-Positive T-Lymphocytes CD8B1 gene Cells Cellular biology ChIP-seq Chronic Collaborations Common Core Computational Biology Computer Analysis Computing Methodologies Data Data Analyses Data Set Databases Deposition Development Enhancers Ensure Epigenetic Process Experimental Designs Generations Genetic Genetic Transcription Glean Goals Growth Immune response Individual Laboratories Link Memory Methodology Methods Mission Molecular Mus Pathway Analysis Pathway interactions Process Quality Control Research Research Personnel Research Project Grants Sampling Supervision System T memory cell T-Lymphocyte T-Lymphocyte Subsets Techniques Tissues United States National Institutes of Health Virus Diseases Work acute infection base bioinformatics pipeline bioinformatics tool chronic infection computational platform computerized data processing data sharing data submission denoising epigenomics exhaustion experience experimental study histone modification innovation insight large datasets mouse development multidimensional data novel programs response single cell analysis single-cell RNA sequencing synergism transcription factor transcriptome sequencing transcriptomics web interface

项目摘要

SUMMARY-BIOINFORMATICS AND COMPUTATIONAL BIOLOGY CORE: The Bioinformatics and Computational Biology Core will support all three Projects and the Single-Cell Transcriptomics and Epigenetics Core (SCTE) in a range of activities related to data processing, storage, distribution and integrative analysis. A key role of the Core is to provide a centralized portal for integrative analysis of the different omics data (RNA-seq, ChIP-seq and ATAC-seq) to be generated by the Projects and SCTE Core. The goal is to illuminate the transcriptomic and epigenomic landscape of T cells in response to acute and chronic viral infection, and uncover the critical regulators that determine the state or fate of T cells. The Core will utilize advanced bioinformatics tools for the high-dimensional data matrices generated at different stages of the immune response and in distinct tissues by the Program Project and will apply innovative techniques to discover core regulators. The Core will assist the three Projects and SCTE Core for experimental design, and work closely with the other Investigators to analyze individual data sets and also the combined data set. In particular, the Core will establish a data deposit, tracking, storage and distribution system to allow data sharing and sample tracking among all the participating laboratories. The Core will also establish three bioinformatics pipelines to process RNA-seq, ChIP-seq and ATAC-seq data respectively, including sequencing read mapping, quality control and peak calling. Advanced analyses such as enhancer prediction, motif analysis and genetic network analysis will also be conducted to reveal the key regulators critical for defining particular T cell states.

摘要-生物信息学和计算生物学核心：生物信息学和计算生物学核心将支持所有三个项目和单细胞项目转录组学和表观遗传学核心 (SCTE) 从事与数据处理、存储、分布和综合分析。核心的一个关键作用是为集成提供一个集中的门户分析项目生成的不同组学数据（RNA-seq、ChIP-seq 和 ATAC-seq）和 SCTE 核心。目标是阐明 T 细胞的转录组和表观基因组景观对急性和慢性病毒感染的反应，并揭示决定状态或状态的关键调节因素 T细胞的命运。核心将利用先进的生物信息学工具来处理高维数据矩阵由该计划项目在免疫反应的不同阶段和不同组织中产生，将应用创新技术来发现核心监管机构。核心将协助这三个项目 SCTE Core 用于实验设计，并与其他研究人员密切合作来分析个人数据集以及组合数据集。特别是，核心将建立数据存放、跟踪、存储和分配系统，以允许所有参与实验室之间的数据共享和样本跟踪。该核心还将建立三个生物信息学管道来处理 RNA-seq、ChIP-seq 和 ATAC-seq 分别提供数据，包括测序读图谱、质量控制和峰调用。高级分析还将进行增强子预测、基序分析和遗传网络分析等以揭示对于定义特定 T 细胞状态至关重要的关键调节因子。