{"lab": {"uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "@id": "/labs/yijun-ruan-lab/", "title": "Yijun Ruan, JAX", "status": "current", "correspondence": [{"contact_email": "eWlqdW4ucnVhbkBqYXgub3Jn", "@id": "/users/d8ac229e-ec08-4411-be38-dc779520ea62/", "display_title": "Yijun Ruan"}], "display_title": "Yijun Ruan, JAX", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "award": {"@id": "/awards/1U54DK107967-01/", "display_title": "NUCLEOME POSITIONING SYSTEM FOR SPATIOTEMPORAL GENOME ORGANIZATION AND REGULATION", "status": "current", "center_title": "NOFIC - Ruan", "project": "4DN", "description": "NOFIC: This proposal seeks to fulfill a community need for a comprehensive, high-resolution genome-mapping platform that will enable investigation of the structural, functional and spatiotemporal organization of the human genome. Our ultimate goal is to deliver complex chromatin interaction network maps in the context of 3D genome structures from which the dynamics of individual genomic elements can be monitored and referenced. Here, we propose to develop a Nucleome Positioning System (NPS)-comprised of 1) a robust genome- wide mapping technology platform, 2) advanced computational modeling algorithms and 3) state-of-the-art nuclear imaging methods-that will allow users community-wide to uncover the regulatory functions of 3D genome organization in human cells. NPS will be based upon the established ChIA-PET method (1,2), enhanced by process optimizations-i.e., microfluidic-based miniaturization and Tn5-transposase-based library preparation-to facilitate the study of chromatin interactions mediated by protein factors across a broader range of human cell types (Aim 1, see also Mapping Technology Development Component). We will also optimize RICh-PET for the comprehensive mapping of chromatin interactions mediated by non-coding RNAs (Aim 1). The high-quality mapping data generated through these optimization efforts will be analyzed by a new computational platform (Three-Dimensional Nucleome Modeling Engine, or 3D-NOME) that makes use of hierarchical multi-scaling to model 3D genome structures (Aim 2, Data Analysis and Modeling component). We will also complement the 3D modeling with transcriptome, epigenome and SNP data associated with genetic diseases (GWAS) to provide functional annotation to structural units (Aim 2). We will continue by developing strategies to validate the nucleome geometry predicted by 3D-NOME both structurally, using new nuclear imaging technologies, and functionally, using cutting-edge genome- and epigenome-editing approaches, in both human cell lines and mouse models (Aim 3, Biological Validation Component). Finally, we will implement NPS to generate pilot 3D genome maps from a wide range of human cell lines and primary immune cells sorted from whole blood, to elucidate the spatiotemporal dynamics of human genome organization over major developmental and hematopoietic cell lineages, as well as among differentiating lymphocytes involved in the immune response (Aim 4, Data Generation Component). Together, these efforts will yield a powerful set of sophisticated, high-quality tools and mapping data for the larger research community, and will help establish the standards for future 3D/4D nucleome studies. They will also provide insights into the broad mechanisms that organize the structure and regulate the function of the human genome, as well as the specific mechanisms by which immune responses are regulated at the nuclear level.", "name": "1U54DK107967-01", "@type": ["Award", "Item"], "uuid": "029a2578-43dc-4343-8f41-694518cce304", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "pi": {"error": "no view permissions"}}, "status": "released", "aliases": ["ruan-lab:GM12878-insituchiapet-ctcf"], "accession": "4DNES7IB5LY9", "condition": "CTCF", "description": "Replicates of CTCF in situ ChIA-PET on  GM12878 cells.", "date_created": "2019-12-16T22:50:32.466311+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "in situ ChIA-PET on GM12878", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-10-11T15:12:00.903224+00:00"}, "public_release": "2020-02-06", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"uuid": "3ad4937a-4ac0-4d86-adbb-40dd8635b41e", "accession": "4DNEXKAMU4M6", "@id": "/experiments-chiapet/4DNEXKAMU4M6/", "display_title": "in situ ChIA-PET against CTCF protein on GM12878 - 4DNEXKAMU4M6", "@type": ["ExperimentChiapet", "Experiment", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"uuid": "8e926d29-e5ac-4237-8f3f-c0facbdcee85", "accession": "4DNEXFLO7R6M", "@id": "/experiments-chiapet/4DNEXFLO7R6M/", "display_title": "in situ ChIA-PET against CTCF protein on GM12878 - 4DNEXFLO7R6M", "@type": ["ExperimentChiapet", "Experiment", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_headers": [{"lab": {"display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "status": "current", "@id": "/labs/4dn-dcic-lab/", "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": "\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).", "name": "item-page-headers.ExperimentSet.data-usage-guidelines", "award": {"@type": ["Award", "Item"], "status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@id": "/awards/1U01CA200059-01/", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "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": {"display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "status": "current", "@id": "/labs/4dn-dcic-lab/", "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 ExperimentSet contains files that are also part of [4DNES9BAC4R2.](https://data.4dnucleome.org/experiment-set-replicates/4DNES9BAC4R2) <br>\nThe files 4DNFIA61WDTD and 4DNFIOZ6OJYL (of experiment [4DNEXKAMU4M6](https://data.4dnucleome.org/experiments-chiapet/4DNEXKAMU4M6/)) that were originally submitted as part of this dataset were added and analyzed as part of [4DNES9BAC4R2](https://data.4dnucleome.org/experiment-set-replicates/4DNES9BAC4R2) that contains  additional replicate experiments to enable a more in depth analysis.", "name": "static-header.some-relinked_item_4DNES7IB5LY9", "award": {"@type": ["Award", "Item"], "status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "@id": "/awards/2U01CA200059-06/", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Note: Experiment items linked to 2 experiment sets (4DNES7IB5LY9, 4DNES9BAC4R2)", "status": "released", "aliases": ["4dn-dcic-lab:static-header.some-relinked_item_4DNES7IB5LY9"], "options": {"filetype": "md", "collapsible": false, "default_open": true, "convert_ext_links": true}, "date_created": "2024-10-11T15:11:14.128546+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-10-15T20:46:37.365539+00:00"}, "schema_version": "2", "@id": "/static-sections/47bd2862-5776-46bd-85ea-ba8b008ec123/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "47bd2862-5776-46bd-85ea-ba8b008ec123", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.6f9809b1-b9b4-4f2f-8e6d-0762bce320ef"]}, "display_title": "Note: Experiment items linked to 2 experiment sets (4DNES7IB5LY9, 4DNES9BAC4R2)", "external_references": [], "content": "This ExperimentSet contains files that are also part of [4DNES9BAC4R2.](https://data.4dnucleome.org/experiment-set-replicates/4DNES9BAC4R2) <br>\nThe files 4DNFIA61WDTD and 4DNFIOZ6OJYL (of experiment [4DNEXKAMU4M6](https://data.4dnucleome.org/experiments-chiapet/4DNEXKAMU4M6/)) that were originally submitted as part of this dataset were added and analyzed as part of [4DNES9BAC4R2](https://data.4dnucleome.org/experiment-set-replicates/4DNES9BAC4R2) that contains  additional replicate experiments to enable a more in depth analysis.", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p>This ExperimentSet contains files that are also part of <a href=\"https://data.4dnucleome.org/experiment-set-replicates/4DNES9BAC4R2\" rel=\"noopener noreferrer\" target=\"_blank\">4DNES9BAC4R2.</a> <br/>\nThe files 4DNFIA61WDTD and 4DNFIOZ6OJYL (of experiment <a href=\"https://data.4dnucleome.org/experiments-chiapet/4DNEXKAMU4M6/\" rel=\"noopener noreferrer\" target=\"_blank\">4DNEXKAMU4M6</a>) that were originally submitted as part of this dataset were added and analyzed as part of <a href=\"https://data.4dnucleome.org/experiment-set-replicates/4DNES9BAC4R2\" rel=\"noopener noreferrer\" target=\"_blank\">4DNES9BAC4R2</a> that contains  additional replicate experiments to enable a more in depth analysis.</p></div>"}], "project_release": "2020-02-06", "experiments_in_set": [{"display_title": "in situ ChIA-PET against CTCF protein on GM12878 - 4DNEXKAMU4M6", "crosslinking_method": "1% Formaldehyde and 2mM EGS", "files": [{"@type": 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"/file-formats/fastq/", "file_format": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "in situ ChIA-PET", "experiment_bucket": "raw file", "assay_info": "CTCF protein", "dataset": "in situ ChIA-PET on GM12878", "condition": "CTCF", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "GM12878", "lab_name": "Yijun Ruan, JAX"}, "external_references": [], "principals_allowed": 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