{"lab": {"correspondence": [{"contact_email": "am9iLmRla2tlckB1bWFzc21lZC5lZHU=", "@id": "/users/83b5073a-069b-4162-9b30-6f42d5551e34/", "display_title": "Job Dekker"}], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "title": "Job Dekker, UMMS", "display_title": "Job Dekker, UMMS", "@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "tags": ["4DN Joint Analysis 2018"], "award": {"center_title": "NOFIC - Dekker", "uuid": "ae6c618f-7a8c-441e-a886-e30bbbe591da", "description": "NOFIC: The spatial organization of the genome impinges on all genomic processes, including gene regulation, maintenance of genome stability and chromosome transmission to daughter cells. A detailed understanding of the spatial arrangement of the human genome, referred to as the 4D nucleome, and the biological and physical principles that drive chromosome folding requires combining approaches from the fields of molecular and cell biology, imaging, genetics and genomics with approaches from physics, computational biology, and computer simulation. We have assembled a highly interdisciplinary center with the goal of generating extensively validated maps of the 4D nucleome, its physical and dynamic properties and its role in regulating the activity of the genome. First, the center will further optimize and extensively validate a suite of genome-wide molecular methodologies, based on chromosome conformation capture (3C) that can probe the folding of chromosomes at the scale of single nucleosomes, chromatin fibers, chromosomes and the entire nucleus, across cell populations and in single cells. Given that chromosome and nuclear organization is tightly linked to biological state of the cell, the center will map the 4D nucleome for four key biological states representing different conformations during the cell cycle (interphase and mitosis), and during cell differentiation (pluripotent and differentiated states). We will obtain complementary data regarding the structure and dynamics of chromatin, at different length scales and in single cells using extensive high-throughput imaging, live cell imaging and super resolution microscopy. Data obtained with all approaches will be analyzed, integrated and modeled using a set of methods we will further develop to gain insights into the structure, physics and dynamics of chromosome folding over different length scales. Finally, a critical component of our proposal is the biological validation and further elaboration of the chromatin interaction maps that are generated from our conformational analyses. This validation will be achieved through site-specific editing of genomic sequence and epigenetic marks, the creation of new contact points within the genome, and the identification of factors (both protein and nucleic acid) that facilitat or restrict these interactions. 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If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) \nand the 4DN Data Portal paper \n([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).", "name": "item-page-headers.ExperimentSet.data-usage-guidelines", "award": {"@id": "/awards/1U01CA200059-01/", "status": "current", "@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Data Usage Guidelines", "status": "released", "aliases": [], "options": {"filetype": "md", "title_icon": "exclamation-circle", "collapsible": false, "default_open": true}, "date_created": "2018-08-06T03:09:55.543206+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-05-09T09:31:34.537494+00:00"}, "schema_version": "2", "@id": "/static-sections/621e8359-3885-40ce-965d-91894aa7b758/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "621e8359-3885-40ce-965d-91894aa7b758", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267228139"]}, "display_title": "Data Usage Guidelines", "external_references": [], "content": "\n**Data Use Guidelines:** This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) \nand the 4DN Data Portal paper \n([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p><strong>Data Use Guidelines:</strong> This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n(<a href=\"https://doi.org/10.1038/nature23884\" rel=\"noopener noreferrer\" target=\"_blank\">doi:10.1038/nature23884</a>) \nand the 4DN Data Portal paper \n(<a href=\"https://doi.org/10.1038/s41467-022-29697-4\" rel=\"noopener noreferrer\" target=\"_blank\">doi:10.1038/s41467-022-29697-4</a>), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the <a href=\"mailto:support@4dnucleome.org\">Data Coordination and Integration Center</a>.</p></div>"}, {"lab": {"@id": "/labs/4dn-dcic-lab/", "status": "current", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "This experiment set supercedes [4DNESGZ9A3FG](https://data.4dnucleome.org/experiment-set-replicates/79d1d2c6-a899-4383-a1fe-4a3c8a67ba97/) because a new biological replicate was added.", "name": " static-header.replacing_item_4DNESMBA9T3L", "award": {"@id": "/awards/2U01CA200059-06/", "status": "current", "@type": ["Award", "Item"], "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Note: This Experiment Set Supersedes 4DNESGZ9A3FG", "status": "released", "aliases": ["4dn-dcic-lab:dekker_lab_replacing_atac_seq"], "options": {"filetype": "md", "title_icon": "info", "collapsible": false, "default_open": true}, "date_created": "2018-09-12T17:21:50.609521+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-01-05T00:36:35.197881+00:00"}, "schema_version": "2", "@id": "/static-sections/83f79be6-eff5-4369-b36c-3cafeffdf6ae/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "83f79be6-eff5-4369-b36c-3cafeffdf6ae", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267111888"]}, "display_title": "Note: This Experiment Set Supersedes 4DNESGZ9A3FG", "external_references": [], "content": "This experiment set supercedes [4DNESGZ9A3FG](https://data.4dnucleome.org/experiment-set-replicates/79d1d2c6-a899-4383-a1fe-4a3c8a67ba97/) because a new biological replicate was added.", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p>This experiment set supercedes <a href=\"https://data.4dnucleome.org/experiment-set-replicates/79d1d2c6-a899-4383-a1fe-4a3c8a67ba97/\" rel=\"noopener noreferrer\" target=\"_blank\">4DNESGZ9A3FG</a> because a new biological replicate was added.</p></div>"}], "processed_files": [{"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/9c69ca32-a95c-441c-938d-bdaab6ddd3c8/4DNFI4R7BEGM.bb", "uuid": "9c69ca32-a95c-441c-938d-bdaab6ddd3c8", "status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI4R7BEGM.bb", "md5sum": "7cc806794937cfacb6a798a9dc7ea466", "file_type_detailed": "peaks (bigbed)", "file_size": 15708317, "file_format": {"@id": "/file-formats/bigbed/", "@type": ["FileFormat", "Item"], 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"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESMBA9T3L", "external_references": [], "pubs_using": [{"@type": ["Publication", "Item"], "status": "current", "@id": "/publications/dfc530f1-82c0-4ddc-8f95-6f40417f87a0/", "uuid": "dfc530f1-82c0-4ddc-8f95-6f40417f87a0", "display_title": "Akgol Oksuz B et al. 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We used this knowledge to develop a greatly improved Hi-C protocol (Hi-C 3.0) that can detect both loops and compartments relatively effectively. In addition to providing benchmarked protocols, this work produced ultra-deep chromatin interaction maps using Micro-C, conventional Hi-C and Hi-C 3.0 for key cell lines used by the 4D Nucleome project.", "journal": "Nature methods", "uuid": "dfc530f1-82c0-4ddc-8f95-6f40417f87a0", "authors": ["Akgol Oksuz B", "Yang L", "Abraham S", "Venev SV", "Krietenstein N", "Parsi KM", "Ozadam H", "Oomen ME", "Nand A", "Mao H", "Genga RMJ", "Maehr R", "Rando OJ", "Mirny LA", "Gibcus JH", "Dekker J"], "@id": "/publications/dfc530f1-82c0-4ddc-8f95-6f40417f87a0/", "display_title": "Akgol Oksuz B et al. 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