Multispecies NHP dGTEx Research Center

多物种 NHP dGTEx 研究中心

• 批准号: 10460849
• 负责人: KRISTIN ARDLIE
• 金额: $ 321.64万
• 依托单位: OREGON HEALTH & SCIENCE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-08-15 至 2027-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10460849
• 关键词: Address; Adult; Animals; Atlases; Biological Specimen Banks; Biology; Brain; Breeding; Callithrix; Callithrix jacchus jacchus; Cebidae; Cells; Cercopithecidae; ChIP-seq; Communication; Communities; Comparative Study; Complement; Data; Data Analyses; Databases; Defect; Development; Developmental Process; Disease; Dissection; Elements; Equipment and supply inventories; Fetus; Gene Expression Profile; Generations; Genes; Genetic; Genomics; Genotype; Genotype-Tissue Expression Project; Hi-C; Human; Human Development; Individual; Infrastructure; Institutes; Laboratories; Life; Macaca; Macaca mulatta; Modeling; Molecular; Oregon; Pan troglodytes; Papio; Partner in relationship; Pathology; Pattern; Positioning Attribute; Pregnancy; Primates; Process; Protocols documentation; RNA analysis; Research; Research Personnel; Resources; Rhesus; Sampling; Scientist; Small Nuclear RNA; Standardization; Techniques; Testing; Time; Tissue Sample; Tissues; Transcript; United States National Institutes of Health; Universities; XCL1 gene; analysis pipeline; animal colony; base; comparative genomics; data integration; epigenetic profiling; human disease; improved; insight; nonhuman primate; postnatal; prenatal; programs; research study; single cell analysis; tissue resource; transcriptome sequencing; transcriptomics

PROJECT SUMMARY This is a proposal to establish a Nonhuman Primate Developmental Genotype-Tissue Expression (NHP dGTEx) Research Center, developed by scientists at the Oregon National Primate Research Center (ONPRC), MIT, the Broad Institute, and Yale University. This Center will provide a vital resource to the NIH dGTEx program by generating a two-species nonhuman primate (NHP) resource with numerous benefits, including access to prenatal developmental stages and a basis for evolutionary analysis of developmental expression programs. For this proposal we have elected to generate data from two species: Macaca mulata (rhesus macaque), an old- world monkey, and Callithirix jacchus (common marmoset), a new-world monkey. We will create a tissue resource of 30 different tissues types sampled across 6 developmental stages in both species, profiling a total of 198 animals in the process. Using the reference tissue resource, we will perform transcriptome sequencing and other genomic analysis of single-cell and bulk tissues. To form a robust basis for analysis of RNA-seq, we begin by generating full-transcript sequencing from a panel of tissues of each species, which will be used for annotating gene models. For each species we will then generate bulk RNA-sequencing of 30 tissues each from 12 individuals, sampled from 6 timepoints. We propose to use multiome snRNA+ATAC sequencing to generate a first generation single-cell atlas for each species, covering 20 total tissues, with a special emphasis on the brain. These RNA-seq resources will be complemented with strategic epigenetic profiling by CHIP-seq and Hi- C for annotation of functional elements. Finally, specialized techniques will be used to generate data from the smallest prenatal stages. We will adapt the Broad Institute’s GTEx RNA-seq analysis pipeline to accommodate species-specific information and biology, and use the resulting pipelines to analyze the bulk RNA-seq and perform eQTL mapping. We propose to develop a public, interactive platform for the single-cell atlases that enables exploratory data analysis, hypothesis testing, and comparison across species. We will use our expertise in comparative genomics to identify evolutionarily constrained expression patterns and functional elements, as well as human-specific features, and investigate the relationship of these features to human disease. We will create a searchable inventory of all NHP tissues sampled in the project, and standardize NHP data types to match the human dGTEx specifications. To facilitate communicationabout resource availabilityand experimental results, the Center will integrate the NHP data and tissue inventory database into the primary dGTEx portal to be generated and maintained by the Broad Institute. The successful completionof the project will create a unique resource comprising a comprehensive NHP biospecimen repository spanning early prenatal to adult life, and a corresponding genomic database to be made widely accessible which will provide the groundwork and infrastructure for multiple future research studies.

项目概要 这是建立非人类灵长类动物发育基因型组织表达 (NHP dGTEx) 的提案 研究中心，由俄勒冈国家灵长类研究中心 (ONPRC)、麻省理工学院、 布罗德研究所和耶鲁大学。该中心将为 NIH dGTEx 计划提供重要资源 产生两种非人类灵长类动物 (NHP) 资源，具有诸多好处，包括获得 产前发育阶段和发育表达程序进化分析的基础。 对于本提案，我们选择生成两个物种的数据：恒河猴（Macaca mulata），一种古老的猕猴。 世界猴和Callithirix jacchus（普通狨猴），一种新世界猴。我们将制作一张纸巾 对两个物种的 6 个发育阶段采样的 30 种不同组织类型的资源，分析了总共 198 只动物在此过程中。使用参考组织资源，我们将进行转录组测序 以及单细胞和大块组织的其他基因组分析。为了为 RNA-seq 分析奠定坚实的基础，我们 首先从每个物种的一组组织中生成全转录本测序，这将用于 注释基因模型。对于每个物种，我们将对每个物种的 30 个组织进行批量 RNA 测序。 12 个人，从 6 个时间点采样。我们建议使用多组snRNA+ATAC测序来生成 每个物种的第一代单细胞图谱，涵盖 20 个总组织，特别强调 脑。这些 RNA-seq 资源将得到 CHIP-seq 和 Hi-seq 的战略表观遗传分析的补充。 C 用于功能元素的注释。最后，将使用专门的技术来生成数据 最小的产前阶段。我们将调整 Broad Institute 的 GTEx RNA-seq 分析流程以适应 物种特异性信息和生物学，并使用由此产生的管道来分析批量 RNA-seq 和 执行 eQTL 映射。我们建议为单细胞图谱开发一个公共的交互式平台 实现探索性数据分析、假设检验和跨物种比较。我们将利用我们的专业知识 在比较基因组学中识别进化限制的表达模式和功能元件，如 以及人类特有的特征，并研究这些特征与人类疾病的关系。我们将 创建项目中采样的所有 NHP 组织的可搜索清单，并将 NHP 数据类型标准化为 符合人类 dGTEx 规范。促进有关资源可用性和实验的沟通 根据结果​​，中心将把 NHP 数据和组织库存数据库整合到主要 dGTEx 门户中，以 由布罗德研究所生成和维护。该项目的成功完成将打造独一无二的 资源包括涵盖早期产前到成年的综合 NHP 生物样本存储库，以及 相应的基因组数据库将被广泛访问，这将提供基础和 多项未来研究的基础设施。