{"lab": {"@type": ["Lab", "Item"], "@id": "/labs/bing-ren-lab/", "status": "current", "title": "Bing Ren, UCSD", "display_title": "Bing Ren, UCSD", "correspondence": [{"contact_email": "YmlyZW5AdWNzZC5lZHU=", "@id": "/users/e3159ffc-a5a9-43a1-8cfa-90b776c39788/", "display_title": "Bing Ren"}], "uuid": "795847de-20b6-4f8c-ba8d-185215469cbf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.795847de-20b6-4f8c-ba8d-185215469cbf"]}, "pi": {"error": "no view permissions"}}, "award": {"center_title": "NOFIC - Ren", "project": "4DN", "description": "NOFIC: The complete sequencing of the human genome has provided an unprecedented opportunity for the study of the structure and function of the human genome. While our genome has historically been viewed as a linear sequence of bases, it has progressively become clear that this is an inadequate way to represent our genetic information. Notably, research over the last 30 years has begun to shed light on the fact that the higher-order, 3-dimensional organization of our genome plays a critical role in the interpretation of the genetic information encoded in our genome. The structure of our genome in the nucleus has been clearly demonstrated to play influential roles in diverse nuclear processes including DNA replication and gene expression. Despite this, our understanding of the structure of our genome within the nucleus remains incomplete. The reasons for this include limitations in the resolution and throughput of existing tools in chromatin topology mapping, a scarcity of the analytical tools for studying genome structure datasets, and the difficulty to relate the nuclear structure to function. Due to recent advancements in molecular methods based on high-throughput DNA sequencing, single cell analytical approaches, and high-resolution microscopy, the time for breaking through these previous limitations has come. We will establish a highly collaborative, innovative team in order to develop the tools necessary to transform our understanding of chromatin architecture and function in mammalian cells. We will begin by developing datasets that establish gold standards for the study of nuclear structure and function using genetic, biochemical and imaging approaches. We will optimize current existing technologies for mapping genome wide chromatin interactions, while also developing novel, complementary approaches for studying chromatin structure. We will also develop innovative analytical methods to interpret the chromatin structural data, unraveling principles of structural- and temporal- chromatin organization. Our highly collaborative team will draw on the diverse experiences of its members to provide a synergistic environment to push the limits of our understanding of nuclear structure. 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Peaks of a specific cell type are represented using different track colors which can be visualized using HiGlass. Additionally, a zipped folder containing individual bed files specific for each cell type is also provided. The information on track colors and associated cell type can be accessed via a key file [**here**](https://data.4dnucleome.org/documents/42b3f69f-7bf7-458d-9c4b-2b0d53636c6c/)", "name": "supp_file_peaks", "award": {"status": "current", "@type": ["Award", "Item"], "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "@id": "/awards/2U01CA200059-06/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Aggregated non-redundant peaks", "status": "released", "aliases": ["4dn-dcic-lab:peak_bed_file"], "options": {"filetype": "md", "collapsible": false, "default_open": true, "convert_ext_links": true}, "date_created": "2024-08-06T16:58:13.323765+00:00", "section_type": "Page Section", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-09-23T17:00:51.044862+00:00"}, "schema_version": "2", "@id": "/static-sections/a7423de5-3a90-4969-9ede-ed9042c0cf3c/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "a7423de5-3a90-4969-9ede-ed9042c0cf3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.6f9809b1-b9b4-4f2f-8e6d-0762bce320ef"]}, "display_title": "Aggregated non-redundant peaks", "external_references": [], "content": "**NOTE** Non-redundant peaks aggregated from multiple donors in bed format is provided as a supplementary file. Peaks of a specific cell type are represented using different track colors which can be visualized using HiGlass. Additionally, a zipped folder containing individual bed files specific for each cell type is also provided. The information on track colors and associated cell type can be accessed via a key file [**here**](https://data.4dnucleome.org/documents/42b3f69f-7bf7-458d-9c4b-2b0d53636c6c/)", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p><strong>NOTE</strong> Non-redundant peaks aggregated from multiple donors in bed format is provided as a supplementary file. Peaks of a specific cell type are represented using different track colors which can be visualized using HiGlass. Additionally, a zipped folder containing individual bed files specific for each cell type is also provided. 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Transposable elements contribute to nearly 80%  of the human-specific candidate cis-regulatory elements in cortical cells.  Through machine learning, we develop sequence-based predictors of candidate  cis-regulatory elements in different species and demonstrate that the genomic  regulatory syntax is highly preserved from rodents to primates. Finally, we show  that epigenetic conservation combined with sequence similarity helps to uncover  functional cis-regulatory elements and enhances our ability to interpret genetic  variants contributing to neurological disease and traits.", "title": "Conserved and divergent gene regulatory programs of the mammalian neocortex.", "display_title": "Zemke NR et al. 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