Data Core

数据核心

基本信息

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
项目类别：
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

项目摘要

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.

该提案旨在实现疼痛相关基因和细胞类型的“分子百科全书”的愿景人类背根神经节 (hDRG)、周围神经和脊髓的任务是构建数据。基础设施并提供我们实现中心所需的计算研究支持研究目标，并有效地使我们的数据可供我们的所有核心、其他 PRECISE 中心和这将促进不同类型的研究人员的发现。核心为原始数据的创建和管理提供标准化工作流程（包括测序、组织成像和功能数据集），以及相关的元数据和处理后的数据。与组织采购和处理核心密切合作，维护周围的记录和去识别化元数据收集的组织和将生成的数据的第二个目标是创建标准化的工作流程。和管道来处理批量、单细胞/细胞核和空间 RNA-seq（以及相关的核糖体足迹）和 ATAC-seq）将执行质量控制（遵循 ENCODE 和 GTEx 标准），识别不同的细胞类型、其基因标记以及基于临床表型和人口统计学的差异表达基因最后，核心将开发算法。（以软件工具和脚本形式提供）检索特定信息并测试来自不同领域的特定假设我们将与每个研究项目结合使用数据集，并实现这项资助的科学里程碑。还开发工具来分析来自我们研究项目以及其他 PRECISE 的多个测定的数据以综合方式开展的工作将使我们能够实现以下目标：该中心并全面描述不同组织的外周和脊髓疼痛通路、慢性疼痛当我们计划制作我们的数据和管道时，我们的影响也将超越我们的中心。其他研究人员可以访问，促进协作和其他数据集的集成。