{"lab": {"display_title": "Yijun Ruan, JAX", "@type": ["Lab", "Item"], "correspondence": [{"contact_email": "eWlqdW4ucnVhbkBqYXgub3Jn", "@id": "/users/d8ac229e-ec08-4411-be38-dc779520ea62/", "display_title": "Yijun Ruan"}], "title": "Yijun Ruan, JAX", "status": "current", "@id": "/labs/yijun-ruan-lab/", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "award": {"name": "1U54DK107967-01", "project": "4DN", "@type": ["Award", "Item"], "center_title": "NOFIC - Ruan", "@id": "/awards/1U54DK107967-01/", "uuid": "029a2578-43dc-4343-8f41-694518cce304", "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.", "status": "current", "display_title": "NUCLEOME POSITIONING SYSTEM FOR SPATIOTEMPORAL GENOME ORGANIZATION AND REGULATION", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["ruan-lab:biosample_WTC11-cl28-insituchiapet-ctcf_B2"], "accession": "4DNBSBVJQXH6", "biosource": [{"lab": {"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@id": "/labs/job-dekker-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "url": "https://www.allencell.org/cell-catalog.html", "award": {"@id": "/awards/1U54DK107980-01/", "status": "current", "uuid": "ae6c618f-7a8c-441e-a886-e30bbbe591da", "display_title": "CENTER FOR 3D STRUCTURE AND PHYSICS OF THE GENOME", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"@id": "/ontology-terms/CL:0000034/", "term_name": "stem cell", "preferred_name": "stem cell", "term_id": "CL:0000034", "term_url": "http://purl.obolibrary.org/obo/CL_0000034", "display_title": "stem cell", "status": "released", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "@type": ["OntologyTerm", "Item"], "synonyms": ["animal stem cell"], "slim_terms": [{"display_title": "cell", "term_url": "http://purl.obolibrary.org/obo/GO_0005623", "preferred_name": "cell", "term_name": "cell", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "status": "current", "term_id": "GO:0005623", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "term_url": "http://purl.obolibrary.org/obo/CL_0000000", "preferred_name": "cell", "term_name": "cell", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "status": "released", "term_id": "CL:0000000", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["dekker-lab:Biosource_wtc11_aavs1_gfp_c28"], "accession": "4DNSR8LE4JQF", "cell_line": {"status": "released", "term_name": "GM25256", "@id": "/ontology-terms/EFO:0009747/", "synonyms": ["WTC-11", "WTC11"], "term_url": "http://www.ebi.ac.uk/efo/EFO_0009747", "term_id": "EFO:0009747", "preferred_name": "WTC-11", "display_title": "WTC-11", "@type": ["OntologyTerm", "Item"], "uuid": "648cb723-fc6f-44b1-81a3-796c5d3e7868", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"sex": "male", "status": "released", "@id": "/individuals-human/4DNINKRIXJE2/", "uuid": "c5a25acb-fad0-4f15-a909-677b1eed995d", "display_title": "4DNINKRIXJE2", "@type": ["IndividualHuman", "Individual", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "Modified WTC-11 (GM25236) with GFP tagged AAVS1 locus - clone 28", "date_created": "2019-10-31T17:44:06.050287+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-06-16T15:19:27.844976+00:00"}, "modifications": [{"display_title": "Crispr insertion for AAVS1 gene with C-terminus mEGFP", "@id": "/modifications/25e102f7-e9a4-4be1-ae8b-1694b5a89041/", "@type": ["Modification", "Item"], "status": "released", "uuid": "25e102f7-e9a4-4be1-ae8b-1694b5a89041", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosource_type": "induced pluripotent stem cell", "cell_line_tier": "Unclassified", "public_release": "2019-11-22", "schema_version": "2", "project_release": "2019-11-22", "biosource_vendor": {"status": "released", "uuid": "f0e9a370-7451-40e3-9a35-c36d77ebdb4b", "name": "coriell-institute-for-medical-research", "display_title": "Coriell Institute for Medical Research", "@type": ["Vendor", "Item"], "@id": "/vendors/coriell-institute-for-medical-research/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "override_biosource_name": "WTC-11 AAVS1-GFP C28", "@id": "/biosources/4DNSR8LE4JQF/", "@type": ["Biosource", "Item"], "uuid": "d0f30ba8-3e43-4b72-b3cb-32b83c170785", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "WTC-11 AAVS1-GFP C28 - 4DNSR8LE4JQF", "external_references": [], "biosource_name": "WTC-11 AAVS1-GFP C28", "biosource_category": ["WTC-11", "Human stem cell"], "organism": {"@id": "/organisms/9606/", "display_title": "H. sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@type": ["Organism", "Item"], "status": "released", "name": "human", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "description": "WTC11 clone 28 cells prepared for in situ ChIA-PET bio replicate 2", "date_created": "2020-06-05T19:48:56.157365+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-10-26T18:20:11.634767+00:00"}, "public_release": "2020-06-16", "schema_version": "2", "project_release": "2020-06-16", "cell_culture_details": [{"lab": {"@id": "/labs/yijun-ruan-lab/", "status": "current", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "@type": ["Lab", "Item"], "display_title": "Yijun Ruan, JAX", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "award": {"@type": ["Award", "Item"], "display_title": "NUCLEOME POSITIONING SYSTEM FOR SPATIOTEMPORAL GENOME ORGANIZATION AND REGULATION", "status": "current", "uuid": "029a2578-43dc-4343-8f41-694518cce304", "@id": "/awards/1U54DK107967-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["ruan-lab:bcc_WTC11-cl28-insituchiapet-ctcf_B2"], "karyotype": "46,XY Normal Male Karyotype", "description": "Information on culturing WTC11 clone28 cells for CTCF in situ ChIA-PET bio replicate 2", "date_created": "2020-06-05T19:48:54.540803+00:00", "submitted_by": {"error": "no view permissions"}, "doubling_time": "~24h doubling time. Cells were moved to a larger flask once they reached 75% confluency", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-06-16T17:40:13.143521+00:00"}, "passage_number": 3, "public_release": "2020-06-16", "schema_version": "2", "doubling_number": "8", "project_release": "2020-06-16", "culture_duration": 10.0, "morphology_image": {"@id": "/images/0294cd3e-e3c6-4a8f-98ba-aca0027046ae/", "@type": ["Image", "Item"], "status": "released", "uuid": "0294cd3e-e3c6-4a8f-98ba-aca0027046ae", "caption": "Bright field image of WTC11 clone28 cell culture morphology", "display_title": "Replicate 2", "attachment": {"type": "image/png", "height": 641, "href": "@@download/attachment/WTC11-cl28biorep2.png", "md5sum": "65bed6e6b6964ae0e414b6ac3e281dba", "download": "WTC11-cl28biorep2.png", "width": 709}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "culture_start_date": "2020-01-03", "cell_line_lot_number": "AICS-0036-028\u00a0 LOT 0", "culture_harvest_date": "2020-01-13", "protocols_additional": [{"uuid": "1505a21e-b6b4-48f0-8321-6a223a8a5baf", "status": "archived", "display_title": "4DN_WTC-11_SOP_190124.pdf", "@type": ["Protocol", "Item"], "@id": "/protocols/1505a21e-b6b4-48f0-8321-6a223a8a5baf/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "in_vitro_differentiated": "No", "@id": "/biosample-cell-cultures/af8a5f62-4798-413c-ac3e-66ff744c77a6/", "@type": ["BiosampleCellCulture", "Item"], "uuid": "af8a5f62-4798-413c-ac3e-66ff744c77a6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "BiosampleCellCulture from 2020-06-05", "external_references": []}], "@id": "/biosamples/4DNBSBVJQXH6/", "@type": ["Biosample", "Item"], "uuid": "48ba6c89-2758-4748-bd8d-d2d2db9fe520", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNBSBVJQXH6", "external_references": [], "modifications_summary": "None", "modifications_summary_short": "None", "treatments_summary": "None", "tissue_organ_info": {"tissue_source": "stem cell"}, "biosource_summary": "WTC-11 AAVS1-GFP C28", "biosample_type": "induced pluripotent stem cells", "biosample_category": ["WTC-11", "Human stem cell"], "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}