Multispecies NHP dGTEx Research Center

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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.