Data Core

数据核心

• 批准号: 10707435
• 负责人: Xianjun Dong
• 金额: $ 28.03万
• 依托单位: BRIGHAM AND WOMEN'S HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-19 至 2027-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10707435
• 关键词: ATAC-seq; Bioinformatics; Biological; Biological Markers; Brain region; Cells; Chromatin; Clinical; Communities; DNA Sequencing Facility; Data; Data Analyses; Data Security; Data Set; Data Storage and Retrieval; Data Store; Databases; Diagnosis; Enhancers; Ensure; Epigenetic Process; Genotype; Guidelines; Helping to End Addiction Long-term; Human; Individual; Learning; Location; Metadata; Methods; Molecular; Multiomic Data; Nature; Neuroma; Pain; Pain Clinics; Pain management; Pathway interactions; Patients; Physiological; Physiology; Process; Quality Control; RNA; Reporting; Research Personnel; Research Project Grants; Research Support; Resources; SNP genotyping; Sampling; Secure; Services; Source Code; Statistical Data Interpretation; Technology; Tissues; Training; United States National Institutes of Health; analysis pipeline; analytical method; bioinformatics pipeline; cell type; clinical phenotype; cloud based; cost effective; data centers; data exchange; data harmonization; data infrastructure; data integration; data management; data portal; data sharing; data submission; demographics; differential expression; epigenomics; genetic element; genetic variant; multiple omics; pain score; power analysis; repository; single-cell RNA sequencing; tool; transcriptomics; transmission process; web based interface; web interface; web portal

PROJECT SUMMARY (Data Core) This U19 Center propose to use human TG/DRG tissue and painful neuromas to generate large-scale multi- omics datasets for the discovery and characterization of functional genetic elements, epigenetic signatures, and molecular/cellular pathways that underlie human pain transduction, transmission, and processing. As one of the key components of the Center, the Data Core aims to act as a data center by building data infrastructure, providing data management, coordination, analysis, and sharing to the investigators within the Center and other centers in the community. The projects will generate nearly 4,000 datasets of clinical (pain scores, demographics), single-cell RNA-seq, single-cell ATAC-seq, SNP genotyping, spatial transcriptomics from MERFISH, and physiology for over 1,700 samples from 150 donors. The Data Core will first harmonize the datasets and store in centralized MySQL database with accessible web interface for other cores in the Center. Standard bioinformatics pipelines will be developed to process the raw data in a systematic manner, including cell type annotation and spatial location in each brain region. The Data Core will also support the research Projects on their customized analysis, including power analysis, differential expression and chromatin accessibility across different cell types, brain regions, and diagnosis. It will also reveal the genetic variants that are associated with various molecular features via xQTL analysis. Last, all these computed blocks and tools will be integrated into a comprehensive, cloud-based, interactive web portal – Pain Data Portal, providing a generally useful resource for generating biological hypotheses, discovering effective diagnosis biomarkers, and developing new treatments for pain. The Data Core will also ensure a timely data transfer and expertise sharing with the other U19 and U24 centers in the community.

项目摘要(数据核心) 这个U19中心建议使用人的TG/DRG组织和疼痛神经瘤来产生大规模的多个 用于发现和表征功能性遗传元件、表观遗传特征和 分子/细胞通路是人类疼痛传导、传递和处理的基础。作为世界上 作为中心的关键组件，数据核心旨在通过构建数据基础设施来充当数据中心， 向中心内的调查人员和其他人员提供数据管理、协调、分析和共享 社区中的中心。这些项目将生成近4,000个临床数据集(疼痛评分， 人口学)、单细胞RNA-seq、单细胞atac-seq、SNP基因分型、来自 来自150个捐赠者的1700多个样本的生理学研究。 数据核心将首先协调数据集，并存储在具有可访问性的集中式MySQL数据库中 中心其他核心的Web界面。将开发标准生物信息学管道，以处理 系统的原始数据，包括细胞类型注释和每个脑区的空间位置。这个 数据核心还将支持研究项目的定制分析，包括电力分析， 不同细胞类型、不同脑区和不同诊断的差异表达和染色质可及性。会的 还通过xQTL分析揭示了与各种分子特征相关的遗传变异。最后，全部 这些计算块和工具将集成到一个全面的、基于云的交互式Web门户中- 疼痛数据门户，为生成生物假说、发现 有效的诊断生物标志物，以及开发新的疼痛治疗方法。数据核心还将确保及时 与社区中的其他U19和U24中心进行数据传输和专业知识共享。