Multispecies NHP dGTEx Research Center

项目总结 这是一项建立非人灵长类发育基因-组织表达(NHP DGTEx)的建议 研究中心，由麻省理工学院俄勒冈州国家灵长类研究中心(ONPRC)的科学家开发， 布罗德学院和耶鲁大学。该中心将通过以下方式为NIH dGTEx计划提供重要资源 产生一种具有许多好处的两种非人类灵长类(NHP)资源，包括获得 产前发育阶段和发育表达程序进化分析的基础。 在这项提议中，我们选择从两个物种产生数据：恒河猴(猕猴)，一种古老的- Callithirix Jacchus(常见的绒猴)，一种新世界的猴子。我们将创造一种纸巾 这两个物种在6个发育阶段采集了30种不同组织类型的资源，总共 在这个过程中的198只动物。利用参考组织资源，我们将进行转录组测序 以及其他单细胞和大块组织的基因组分析。为了为rna-seq的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完整的转录测序，这将用于 给基因模型加注解。然后，我们将为每个物种生成30个组织的批量RNA测序，每个组织来自 12个个体，从6个时间点抽样。我们建议使用多组体SnRNA ATAC测序来生成 每个物种的第一代单细胞图谱，共涵盖20个组织，特别强调 大脑。这些RNA-seq资源将与ChIP-seq和Hi-seq的战略表观遗传学特征相辅相成。 C用于功能元素的注释。最后，将使用专门的技术从 最小的产前阶段。我们将调整布罗德研究所的GTEx RNA-SEQ分析管道，以适应 物种特有的信息和生物学，并使用产生的管道来分析散装的RNA-seq和 进行eQTL定位。我们建议为单细胞地图集开发一个公共、互动的平台， 支持探索性数据分析、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，识别进化受限的表达模式和功能元件，如 以及人类特有的特征，并调查这些特征与人类疾病的关系。我们会 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。促进关于资源可用性和实验的沟通 结果，中心将把NHP数据和组织库存数据库整合到dGTEx主要门户中，以 由远大研究所生成和维护。该项目的成功完成将创造一个独特的 资源包括一个涵盖早期产前到成年生活的全面的NHP生物谱系资料库，以及 相应的基因组数据库将被广泛获取，这将为 为未来的多项研究提供基础设施。

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.