Data Core

数据核心

• 批准号: 10707551
• 负责人: Diana Tavares Ferreira
• 金额: $ 24.02万
• 依托单位: UNIVERSITY OF TEXAS DALLAS
• 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/10707551
• 关键词: ATAC-seq; Age; Algorithms; Archives; Bar Codes; Biological Assay; Cell Nucleus; Cells; Code; Collaborations; Communities; Computer software; DNA sequencing; Data; Data Analyses; Data Coordinating Center; Data Set; Data Storage and Retrieval; Databases; Decision Making; Detection; Encyclopedias; Ensure; Excision; Experimental Designs; Genes; Genetic Transcription; Genotype-Tissue Expression Project; Goals; Grant; Helping to End Addiction Long-term; Human; Informatics; Laboratories; Low Back Pain; Maps; Metadata; Mission; Molecular; Molecular Profiling; Neck Pain; Neurons; Neurosciences; Nociceptors; Organ Donor; Output; Pain; Pain Disorder; Pain management; Pathway interactions; Patients; Peripheral Nerves; Phenotype; Policies; Process; Protocols documentation; Quality Control; RNA; Records; Reproducibility; Research; Research Design; Research Personnel; Research Project Grants; Research Support; Resources; Ribosomes; Secure; Services; Site; Software Tools; Spinal Cord; Spinal Ganglia; Spine pain; Standardization; Synapses; System; Testing; Tissue Procurements; Tissue imaging; Tissues; United States National Institutes of Health; University of Texas M D Anderson Cancer Center; Vision; Work; analysis pipeline; bioinformatics tool; cell type; chronic painful condition; clinical phenotype; cohort; computational pipelines; data format; data infrastructure; data management; data sharing; data standards; database of Genotypes and Phenotypes; demographics; differential expression; high throughput screening; improved; insight; interoperability; nanopore; painful neuropathy; peripheral pain; phenotypic data; protocol development; reference genome; sex; tissue processing; tool; transcriptome; transcriptomics; usability; web site

This proposal aims to realize the vision of a “molecular encyclopedia” of pain-associated genes and cell types in the human dorsal root ganglia (hDRG), peripheral nerve, and spinal cord. The mission is to build data infrastructure and provide computational research support that will be needed for us to achieve our Center’s research goals and to effectively make our data accessible to all our cores, other PRECISE Centers and the broader community. This will facilitate discovery for diverse types of researchers. The first aim will be for the Core to provide standardized workflows for the creation and management of the raw data (including sequencing, tissue imaging, and functional datasets), along with associated metadata, and processed data. We will work closely with the Tissue Procurement and Processing Core to maintain records and de-identified metadata around the tissues collected and the data that will be generated. The second aim will be to create standardized workflows and pipelines to process bulk, single-cell/nucleus, and spatial RNA-seq (and associated ribosome footprinting and ATAC-seq) that will perform quality control (following ENCODE and GTEx standards), identify different cell types, their gene markers, and differentially expressed genes for clinical phenotype and demographics-based cohorts (from human DRGs, peripheral nerves, and spinal cords). Finally, the Core will develop algorithms (provided as software tools and scripts) to retrieve specific information and test specific hypotheses from different datasets in conjunction with each research project and to meet the scientific milestones of this grant. We will also develop tools to analyze data from multiple assays in our Research Projects, as well as from other PRECISE Centers in an integrative fashion. The work conducted in this Core will allow us to meet the proposed goals of this Center and fully characterize peripheral and spinal pain pathways across different tissues, chronic pain conditions, age, and sex. Our impact will also go beyond our Center as we plan to make our data and pipelines accessible to other researchers, facilitating collaborations, and integration of other datasets.

该建议旨在实现与疼痛相关基因和细胞类型的“分子百科全书”的愿景 人背根神经节（HDRG），周围神经和脊髓。任务是构建数据 基础架构并提供计算研究支持，我们将需要这项支持才能实现我们的中心 研究目标并有效地使我们的数据可访问我们所有的核心，其他精确的中心以及 更广泛的社区。这将促进潜水员类型的研究人员的发现。第一个目标是 核心提供标准化的工作流以创建和管理原始数据（包括排序， 组织成像和功能数据集）以及相关的元数据和处理的数据。我们将工作 与组织采购和加工核心紧密密切 收集的组织和将生成的数据。第二个目标是创建标准化的工作流程 和管道来处理散装，单细胞/核和空间RNA-seq（以及相关的核糖体足迹） 和将执行质量控制的ATAC-SEQ）（按照编码和GTEX标准），识别不同的单元格 类型，其基因标记物以及基于人口统计学的临床表型和人口统计学的不同表达基因 队列（来自人类DRG，外周神经和脊髓）。最后，核心将开发算法 （作为软件工具和脚本提供）检索特定信息并测试来自不同的假设 数据集与每个研究项目结合在一起，并满足这笔赠款的科学里程碑。我们将 还开发工具来分析我们的研究项目中多个评估的数据以及其他精确的工具 以整合的方式中心。在此核心中进行的工作将使我们能够实现 这个中心并完全表征了跨不同组织的外周和脊柱疼痛途径，慢性疼痛 条件，年龄和性别。当我们计划制作数据和管道时，我们的影响也将超越我们的中心 其他研究人员可以访问，支持其他数据集的协作和集成。