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"address2": "3720 15th Ave. NE, Foege Bldg. Rm. S310",
"address1": "Department of Genome Sciences and Medicine",
"state": "WA",
"institute_name": "University of Washington",
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"url": "http://projectreporter.nih.gov/project_info_details.cfm?aid=8330354",
"schema_version": "11",
"title": "DIGITAL DNASEI MAPPING AND FOOTPRINTING OF THE MOUSE GENOME",
"name": "RC2HG005654",
"description": "The goal of this project is to produce comprehensive, high-definition maps of mouse regulatory DNA marked by DNaseI hypersensitive sites to parallel the human catalogue currently under production by the ENCODE Project. Digital DNaseI technology enables efficient genome-wide mapping of accessible chromatin and DNaseI hypersensitive sites. The core regions of DNaseI hypersensitive sites are constitutively populated by regulatory factor binding sites, the nucleotide-resolution footprints of which may be systematically exposed on a genome-wide scale by ultra-deep sequencing. DNaseI hypersensitive sites exhibit marked cell-type variability; accordingly, production of a comprehensive catalog will require surveying a wide range of cell types. Cell types targeted under this proposal include murine analogues of the ENCODE Tier 1 and Tier 2 common reference cell lines; a broad spectrum of primary adult tissues; embryonic stem cells; and sentinel tissues amenable to sequential temporal profiling during development. The production of a parallel, high-quality, high-resolution compendium of mouse regulatory DNA will greatly enhance the value of the human ENCODE project and will provide a rich independent and unique resource for evolutionary, functional, and model organism genomics. PUBLIC HEALTH RELEVANCE: Relevance to Public Health Understanding the genetic basis of human disease requires detailed knowledge of the functional elements of the human genome which may be subject to polymorphism. The ENCODE Project seeks to identify all of the functional elements in the human genome, and present project seeks to greatly increase the value of the ENCODE data by providing a parallel catalogue of regulatory DNA in the mouse genome. This project is therefore expected to provide key insights into the importance of elements in the human genome, and to provide an unprecedented resource for rational functional modeling of human disease in the mouse.",
"start_date": "2009-09-29",
"end_date": "2013-01-31",
"pi": "/users/ec729133-c5f3-4c53-be5b-a5ea73a367dd/",
"rfa": "ENCODE2-Mouse",
"project": "ENCODE",
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"url": "http://projectreporter.nih.gov/project_info_details.cfm?aid=8402670",
"schema_version": "11",
"title": "A COMPREHENSIVE CATALOG OF DNASEI HYPERSENSITIVE SITES",
"name": "U54HG007010",
"description": "The overall aim of this proposal is to establish a comprehensive, high-quality, high-resolution catalogues of human and mouse DNasel hypersensitive sites (DHSs) spanning all major tissue lineages. Building on the prior success of the UW ENCODE center, we plan to localize DNasel hypersensitive sites, to define the locations of DNasel footprints therein, and to continue to provide relevant synergistic annotations including RNA-seq, histone modifications, and CTCF, as well as DNA methylation. The overriding focus of our production effort has been on data quality. Accordingly, samples will be rigorously screened in a pipeline fashion, with only a select set advancing to whole-genome data collection. To ensure the broadest possible coverage of both unique and non-unique genomic territories, we will employ a higher resolution, higher coverage sequencing strategy than the prior project period, significantly enhancing the information content of the data. This proposal integrates the UW-FHCRC Mouse ENCODE Center, which will be closely aligned with the human project to generate a comparative catalogue of regulatory DNA in carefully matched cells and tissues, providing an unparalleled resource. Since DNasel hypersensitive sites are generic markers of a broad spectrum of human cis-regulatory sequences, the utility of the catalogue will be greatly enhanced by the classification of DHSs into major functional categories including promoters, distal elements (enhancers, LCRs), and insulators. We plan to systematically connect distal DHSs with their cognate promoters and to perform in vivo validation of these connections using nuclease-mediated knockouts of distal DHSs in somatic cells.",
"start_date": "2012-09-21",
"end_date": "2014-07-31",
"pi": "/users/ec729133-c5f3-4c53-be5b-a5ea73a367dd/",
"rfa": "ENCODE3",
"project": "ENCODE",
"viewing_group": "ENCODE3",
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"status": "current",
"url": "http://projectreporter.nih.gov/project_info_details.cfm?aid=7692977",
"schema_version": "11",
"title": "NORTHWEST REFERENCE EPIGENOME MAPPING CENTER",
"name": "U01ES017156",
"description": "The overall aim of this proposal is to establish an integrated Center for creating high-quality reference maps of key epigenotypes in pluripotent, differentiating, and primary differentiated human cells and tissues. The Northwest Reference Epigenome Mapping Center aggregates leading experts in human embryonic stem cell (hESC) biology, lineage-specific differentiation of hESCs, and well-established differentiating and differentiated adult primary tissue systems to establish a substantial capacity for the production of purified cells and tissues for large-scale epigenomic studies. The Center integrates this capacity with an existing high-throughput genomics and informatics infrastructure operating at scale, creating unique synergies that enable genome-scale epigenetic analyses of high-value human primary and progenitor cell types. The Center will perform high-resolution, whole-genome profiling of foundational epigenotypes in project cell types including high-resolution quantification of chromatin structural remodeling, and analysis of DNA methylation at both actively remodeled and silenced regulatory DNA templates. The Center will also profile both small RNA species and conventional gene expression from all study cell types. The Center's informatics and analytical arm will manage project data and its release into consortium and public repositories, and will perform integrative analyses to elucidate the connection between major epigenotypes and dynamic cellular programming of gene expression.",
"start_date": "2008-09-29",
"end_date": "2013-06-30",
"pi": "/users/ec729133-c5f3-4c53-be5b-a5ea73a367dd/",
"rfa": "Roadmap",
"project": "Roadmap",
"viewing_group": "REMC",
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"uuid": "1c247a26-b384-4cb1-be4f-bd48db6d7da0"
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{
"status": "current",
"url": "https://projectreporter.nih.gov/project_info_description.cfm?aid=9247732&icde=32922214&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC&pball=",
"schema_version": "11",
"title": "ENCODE MAPPING CENTER-A COMPREHENSIVE CATALOG OF DNASE I HYPERSENSITIVE SITES",
"name": "UM1HG009444",
"description": "The overall mission of this Mapping Center is to create and disseminate open access, comprehensive, high-quality, high-resolution reference maps of DNase I hypersensitive sites (DHSs) in the human and mouse genomes, at previously unattainable levels of cellular and anatomical definition. Regulatory DNA is actuated in an exceptionally state-specific manner;; accordingly, achieving a comprehensive map of DHSs necessitates the interrogation of an expansive and finely partitioned range of cell and tissue samples. Progressive technical improvements and recent innovations have resulted in dramatic (>100x) decreases in requisite input biological sample quantities coupled with equally dramatic (>100x) increases in assay throughput, and corresponding decreases in the incremental cost of generating reference-quality DHS maps. These advances have in turn opened the possibility of systematically addressing all well-defined physiologically and disease-relevant anatomic and cellular compartments. Four major Specific Aims are targeted: (1) To create open access, comprehensive high-quality, high- resolution reference maps of human DNase I hypersensitive sites; (2) To create and disseminate comprehensive high-quality, high-resolution reference maps of mouse DNase I hypersensitive sites; (3) To maintain and disseminate reference indices of DNase I hypersensitive sites and footprints in the human and mouse genomes; and (4) To enable large-scale intake of Consortium and Community samples for high-quality, high-throughput DHS mapping.",
"start_date": "2017-02-01",
"end_date": "2021-01-31",
"pi": "/users/ec729133-c5f3-4c53-be5b-a5ea73a367dd/",
"rfa": "ENCODE4",
"project": "ENCODE",
"viewing_group": "ENCODE4",
"component": "mapping",
"@id": "/awards/UM1HG009444/",
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"uuid": "b83ba6d4-9b8a-4e11-8818-fcb48e55c5e0"
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],
"title": "John Stamatoyannopoulos, UW",
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"city": "Seattle",
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"name": "john-stamatoyannopoulos",
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