{"lab": {"title": "Siyuan Wang, YALE", "uuid": "7f49b420-d2ae-4de4-820a-21403dc0749f", "display_title": "Siyuan Wang, YALE", "status": "current", "@type": ["Lab", "Item"], "correspondence": [{"contact_email": "c2l5dWFuLndhbmdAeWFsZS5lZHU=", "@id": "/users/774c29b8-db1e-48bc-9669-a3e380f435c2/", "display_title": "Siyuan Wang"}], "@id": "/labs/siyuan-wang-lab/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.7f49b420-d2ae-4de4-820a-21403dc0749f"]}}, "award": {"name": "1U01CA260701-01", "description": "OFHHD: During the humoral immune response, somatic hypermutation (SHM) introduces point mutations in rearranged immunoglobulin (Ig) genes of activated germinal center (GC) B cells. SHM is essential for the fine-tuning of antibody affinity, the generation of B cells expressing high-affinity antibody, and the efficacy of many vaccines. Mistargeted SHM activities can lead to mutations and chromosomal translocations that contribute to the development of B cell lymphoma. Recent studies suggest that the three-dimensional (3D) organization of the genome regulates SHM targeting and mistargeting. However, it is largely unknown how the genome is spatially organized across multiple length scales in GC B cell development and lymphoma, and how 3D genome architecture mechanistically affects the targeting and mistargeting of SHM. Conventional approaches cannot address these questions in the primary GC tissue environment due to technical limitations. Here, we propose to apply a new method recently developed by our team, termed Multiplexed Imaging of Nucleome Architectures (MINA), to primary human tonsil tissue samples and malignant GC-derived human B cell lymphomas. We will investigate and test the association between SHM susceptibility and a variety of 3D nucleome architectures, including topologically associating domain (TAD) architecture, phase separation, and nuclear positioning of genomic regions relative to nuclear lamina, nucleoli, and nuclear pores. Through targeted genomic perturbations in human B cell lymphomas, we will test specific hypotheses linking SHM targeting elements to elevated chromatin looping interactions, TAD phase separation, nuclear pore proximity, and mutation vulnerability. Our study will significantly advance our understanding of the role of 3D genome architecture and nuclear organization in GC B cells undergoing SHM in both the developmental and tumorigenesis contexts. We expect this study to establish a new research paradigm and transform 3D nucleome investigations in immunobiology.", "@id": "/awards/1U01CA260701-01/", "uuid": "f959fce7-bd94-4a8d-961d-8c72a4eaa1ad", "project": "4DN", "status": "current", "center_title": "OFHHD - Schatz", "display_title": "GENOME ARCHITECTURE IN HUMAN GERMINAL CENTER B CELL DEVELOPMENT, MALIGNANCY, AND SOMATIC HYPERMUTATION", "@type": ["Award", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["siyuan-wang-lab:exp_mouse_adenoma-LUAD_lung_B1_T1"], "protocol": {"status": "released", "uuid": "65b9317e-c172-4c47-a991-da8440965484", "display_title": "Experimental Protocol", "@type": ["Protocol", "Item"], "@id": "/protocols/65b9317e-c172-4c47-a991-da8440965484/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEX4F82R7B", "biosample": {"biosource_summary": "LUAD from mouse SA3440 and LUAD cells from mouse MM1433 and LUAD cells from mouse MM2030 and LUAD cells from mouse SA3501 and LUAD cells from mouse MM1690", "biosample_type": "primary cells", "display_title": "4DNBSGYLYO7P", "@id": "/biosamples/4DNBSGYLYO7P/", "uuid": "8256a662-4cf5-41ca-8028-d343a92c4f12", "modifications_summary": "Viral Transduction", "status": "released", "treatments_summary": "None", "accession": "4DNBSGYLYO7P", "@type": ["Biosample", "Item"], "biosource": [{"lab": {"@id": "/labs/siyuan-wang-lab/", "@type": ["Lab", "Item"], "status": "current", "display_title": "Siyuan Wang, YALE", "uuid": "7f49b420-d2ae-4de4-820a-21403dc0749f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.7f49b420-d2ae-4de4-820a-21403dc0749f"]}}, "award": {"@type": ["Award", "Item"], "status": "current", "uuid": "f959fce7-bd94-4a8d-961d-8c72a4eaa1ad", "display_title": "GENOME ARCHITECTURE IN HUMAN GERMINAL CENTER B CELL DEVELOPMENT, MALIGNANCY, AND SOMATIC HYPERMUTATION", "@id": "/awards/1U01CA260701-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"term_id": "UBERON:0002048", "synonyms": ["pulmo"], "@id": "/ontology-terms/UBERON:0002048/", "uuid": "111186bc-8535-4448-903e-854af460a233", "slim_terms": [{"status": "released", "display_title": "respiratory system", "uuid": "111128bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0001004/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "lung", "uuid": "111186bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0002048/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "endoderm", "uuid": "111121bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000925/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "preferred_name": "lung", "status": "released", "display_title": "lung", "term_name": "lung", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["siyuan-wang-lab:biosource_K-MADM-Trp53_LUAD_mouse_SA3440"], "accession": "4DNSRD4JLYQD", "cell_line": {"synonyms": ["type II alveolar epithelial cell", "cuboidal type II cell", "AT2", "lung type 2 cell", "TII", "type 2 alveolar epithelial cell", "ATII", "granular pneumocyte", "type II alveolocyte", "type II alveolar cell", "type 2 alveolocyte", "great alveolar cell", "type 2 pneumocyte"], "@id": "/ontology-terms/CL:0002063/", "@type": ["OntologyTerm", "Item"], "status": "released", "term_name": "type II pneumocyte", "term_id": "CL:0002063", "display_title": "type II pneumocyte", "uuid": "784f2a76-e250-4981-9602-ef11411485bc", "preferred_name": "type II pneumocyte", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0000925/", "uuid": "111121bc-8535-4448-903e-854af460a233", "display_title": "endoderm", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "current", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0002048/", "uuid": "111186bc-8535-4448-903e-854af460a233", "display_title": "lung", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0001004/", "uuid": "111128bc-8535-4448-903e-854af460a233", "display_title": "respiratory system", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"uuid": "327742de-1601-4c71-ac0b-63e656236d93", "status": "released", "@type": ["IndividualMouse", "Individual", "Item"], "display_title": "4DNINXWW5J2D", "@id": "/individuals-mouse/4DNINXWW5J2D/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "Lung adenocarcinoma (LUAD) cells from mouse SA3440", "date_created": "2025-06-04T16:06:43.939791+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-06-12T16:09:08.119635+00:00"}, "biosource_type": "primary cell", "cell_line_tier": "Unclassified", "public_release": "2025-06-12", "schema_version": "2", "project_release": "2025-06-12", "override_biosource_name": "LUAD from mouse SA3440", "@id": "/biosources/4DNSRD4JLYQD/", "@type": ["Biosource", "Item"], "uuid": "f2be949f-f000-4a47-ba71-e6147fa47c39", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "LUAD from mouse SA3440 - 4DNSRD4JLYQD", "external_references": [], "biosource_name": "LUAD from mouse SA3440", "biosource_category": ["Primary Cells"], "organism": {"uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "display_title": "M. musculus", "name": "mouse", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"lab": {"@id": "/labs/siyuan-wang-lab/", "@type": ["Lab", "Item"], "status": "current", "display_title": "Siyuan Wang, YALE", "uuid": "7f49b420-d2ae-4de4-820a-21403dc0749f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.7f49b420-d2ae-4de4-820a-21403dc0749f"]}}, "award": {"@type": ["Award", "Item"], "status": "current", "uuid": "f959fce7-bd94-4a8d-961d-8c72a4eaa1ad", "display_title": "GENOME ARCHITECTURE IN HUMAN GERMINAL CENTER B CELL DEVELOPMENT, MALIGNANCY, AND SOMATIC HYPERMUTATION", "@id": "/awards/1U01CA260701-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"term_id": "UBERON:0002048", "synonyms": ["pulmo"], "@id": "/ontology-terms/UBERON:0002048/", "uuid": "111186bc-8535-4448-903e-854af460a233", "slim_terms": [{"status": "released", "display_title": "respiratory system", "uuid": "111128bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0001004/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "lung", "uuid": "111186bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0002048/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "endoderm", "uuid": "111121bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000925/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "preferred_name": "lung", "status": "released", "display_title": "lung", "term_name": "lung", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["siyuan-wang-lab:biosource_K-MADM-Trp53_LUAD_mouse_MM1433"], "accession": "4DNSRBAWEU4R", "cell_line": {"synonyms": ["type II alveolar epithelial cell", "cuboidal type II cell", "AT2", "lung type 2 cell", "TII", "type 2 alveolar epithelial cell", "ATII", "granular pneumocyte", "type II alveolocyte", "type II alveolar cell", "type 2 alveolocyte", "great alveolar cell", "type 2 pneumocyte"], "@id": "/ontology-terms/CL:0002063/", "@type": ["OntologyTerm", "Item"], "status": "released", "term_name": "type II pneumocyte", "term_id": "CL:0002063", "display_title": "type II pneumocyte", "uuid": "784f2a76-e250-4981-9602-ef11411485bc", "preferred_name": "type II pneumocyte", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0000925/", "uuid": "111121bc-8535-4448-903e-854af460a233", "display_title": "endoderm", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "current", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0002048/", "uuid": "111186bc-8535-4448-903e-854af460a233", "display_title": "lung", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0001004/", "uuid": "111128bc-8535-4448-903e-854af460a233", "display_title": "respiratory system", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"uuid": "a2b3e2f9-e698-4530-bb91-00fd9031cf71", "status": "released", "@type": ["IndividualMouse", "Individual", "Item"], "display_title": "4DNINSCOGAYC", "@id": "/individuals-mouse/4DNINSCOGAYC/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "Lung adenocarcinoma (LUAD) cells from mouse MM1433", "date_created": "2025-05-27T17:40:20.658911+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-06-12T16:09:10.524272+00:00"}, "biosource_type": "primary cell", "cell_line_tier": "Unclassified", "public_release": "2025-06-12", "schema_version": "2", "project_release": "2025-06-12", "override_biosource_name": "LUAD cells from mouse MM1433", "@id": "/biosources/4DNSRBAWEU4R/", "@type": ["Biosource", "Item"], "uuid": "d05ee61a-020d-4ec8-9553-f0fbfb8e806d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "LUAD cells from mouse MM1433 - 4DNSRBAWEU4R", "external_references": [], "biosource_name": "LUAD cells from mouse MM1433", "biosource_category": ["Primary Cells"], "organism": {"uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "display_title": "M. musculus", "name": "mouse", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"lab": {"@id": "/labs/siyuan-wang-lab/", "@type": ["Lab", "Item"], "status": "current", "display_title": "Siyuan Wang, YALE", "uuid": "7f49b420-d2ae-4de4-820a-21403dc0749f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.7f49b420-d2ae-4de4-820a-21403dc0749f"]}}, "award": {"@type": ["Award", "Item"], "status": "current", "uuid": "f959fce7-bd94-4a8d-961d-8c72a4eaa1ad", "display_title": "GENOME ARCHITECTURE IN HUMAN GERMINAL CENTER B CELL DEVELOPMENT, MALIGNANCY, AND SOMATIC HYPERMUTATION", "@id": "/awards/1U01CA260701-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"term_id": "UBERON:0002048", "synonyms": ["pulmo"], "@id": "/ontology-terms/UBERON:0002048/", "uuid": "111186bc-8535-4448-903e-854af460a233", "slim_terms": [{"status": "released", "display_title": "respiratory system", "uuid": "111128bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0001004/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "lung", "uuid": "111186bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0002048/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "endoderm", "uuid": "111121bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000925/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "preferred_name": "lung", "status": "released", "display_title": "lung", "term_name": "lung", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["siyuan-wang-lab:biosource_K-MADM-Trp53_LUAD_mouse_MM2030"], "accession": "4DNSR7TX4JLS", "cell_line": {"synonyms": ["type II alveolar epithelial cell", "cuboidal type II cell", "AT2", "lung type 2 cell", "TII", "type 2 alveolar epithelial cell", "ATII", "granular pneumocyte", "type II alveolocyte", "type II alveolar cell", "type 2 alveolocyte", "great alveolar cell", "type 2 pneumocyte"], "@id": "/ontology-terms/CL:0002063/", "@type": ["OntologyTerm", "Item"], "status": "released", "term_name": "type II pneumocyte", "term_id": "CL:0002063", "display_title": "type II pneumocyte", "uuid": "784f2a76-e250-4981-9602-ef11411485bc", "preferred_name": "type II pneumocyte", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0000925/", "uuid": "111121bc-8535-4448-903e-854af460a233", "display_title": "endoderm", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "current", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0002048/", "uuid": "111186bc-8535-4448-903e-854af460a233", "display_title": "lung", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0001004/", "uuid": "111128bc-8535-4448-903e-854af460a233", "display_title": "respiratory system", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"uuid": "90b02433-b377-4ac1-812c-6dceec39f560", "status": "released", "@type": ["IndividualMouse", "Individual", "Item"], "display_title": "4DNIN43SJ3QX", "@id": "/individuals-mouse/4DNIN43SJ3QX/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "Lung adenocarcinoma (LUAD) cells from mouse MM2030", "date_created": "2025-05-27T17:40:22.166468+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-06-12T16:09:09.316445+00:00"}, "biosource_type": "primary cell", "cell_line_tier": "Unclassified", "public_release": "2025-06-12", "schema_version": "2", "project_release": "2025-06-12", "override_biosource_name": "LUAD cells from mouse MM2030", "@id": "/biosources/4DNSR7TX4JLS/", "@type": ["Biosource", "Item"], "uuid": "6af0afcd-ec73-482e-b798-75914e03421b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "LUAD cells from mouse MM2030 - 4DNSR7TX4JLS", "external_references": [], "biosource_name": "LUAD cells from mouse MM2030", "biosource_category": ["Primary Cells"], "organism": {"uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "display_title": "M. musculus", "name": "mouse", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"lab": {"@id": "/labs/siyuan-wang-lab/", "@type": ["Lab", "Item"], "status": "current", "display_title": "Siyuan Wang, YALE", "uuid": "7f49b420-d2ae-4de4-820a-21403dc0749f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.7f49b420-d2ae-4de4-820a-21403dc0749f"]}}, "award": {"@type": ["Award", "Item"], "status": "current", "uuid": "f959fce7-bd94-4a8d-961d-8c72a4eaa1ad", "display_title": "GENOME ARCHITECTURE IN HUMAN GERMINAL CENTER B CELL DEVELOPMENT, MALIGNANCY, AND SOMATIC HYPERMUTATION", "@id": "/awards/1U01CA260701-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"term_id": "UBERON:0002048", "synonyms": ["pulmo"], "@id": "/ontology-terms/UBERON:0002048/", "uuid": "111186bc-8535-4448-903e-854af460a233", "slim_terms": [{"status": "released", "display_title": "respiratory system", "uuid": "111128bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0001004/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "lung", "uuid": "111186bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0002048/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "endoderm", "uuid": "111121bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000925/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "preferred_name": "lung", "status": "released", "display_title": "lung", "term_name": "lung", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["siyuan-wang-lab:biosource_K-MADM-Trp53_LUAD_mouse_SA3501"], "accession": "4DNSRQ63ELJQ", "cell_line": {"synonyms": ["type II alveolar epithelial cell", "cuboidal type II cell", "AT2", "lung type 2 cell", "TII", "type 2 alveolar epithelial cell", "ATII", "granular pneumocyte", "type II alveolocyte", "type II alveolar cell", "type 2 alveolocyte", "great alveolar cell", "type 2 pneumocyte"], "@id": "/ontology-terms/CL:0002063/", "@type": ["OntologyTerm", "Item"], "status": "released", "term_name": "type II pneumocyte", "term_id": "CL:0002063", "display_title": "type II pneumocyte", "uuid": "784f2a76-e250-4981-9602-ef11411485bc", "preferred_name": "type II pneumocyte", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0000925/", "uuid": "111121bc-8535-4448-903e-854af460a233", "display_title": "endoderm", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "current", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0002048/", "uuid": "111186bc-8535-4448-903e-854af460a233", "display_title": "lung", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0001004/", "uuid": "111128bc-8535-4448-903e-854af460a233", "display_title": "respiratory system", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"uuid": "862cbfd0-9b85-4957-b26e-70adae76552c", "status": "released", "@type": ["IndividualMouse", "Individual", "Item"], "display_title": "4DNINAPJRK7Q", "@id": "/individuals-mouse/4DNINAPJRK7Q/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "Lung adenocarcinoma (LUAD) cells from mouse SA3501", "date_created": "2025-05-27T17:40:23.679539+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-06-12T16:09:10.678447+00:00"}, "biosource_type": "primary cell", "cell_line_tier": "Unclassified", "public_release": "2025-06-12", "schema_version": "2", "project_release": "2025-06-12", "override_biosource_name": "LUAD cells from mouse SA3501", "@id": "/biosources/4DNSRQ63ELJQ/", "@type": ["Biosource", "Item"], "uuid": "9b68b829-cb33-4524-aa34-be4902c304d7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "LUAD cells from mouse SA3501 - 4DNSRQ63ELJQ", "external_references": [], "biosource_name": "LUAD cells from mouse SA3501", "biosource_category": ["Primary Cells"], "organism": {"uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "display_title": "M. musculus", "name": "mouse", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"lab": {"@id": "/labs/siyuan-wang-lab/", "@type": ["Lab", "Item"], "status": "current", "display_title": "Siyuan Wang, YALE", "uuid": "7f49b420-d2ae-4de4-820a-21403dc0749f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.7f49b420-d2ae-4de4-820a-21403dc0749f"]}}, "award": {"@type": ["Award", "Item"], "status": "current", "uuid": "f959fce7-bd94-4a8d-961d-8c72a4eaa1ad", "display_title": "GENOME ARCHITECTURE IN HUMAN GERMINAL CENTER B CELL DEVELOPMENT, MALIGNANCY, AND SOMATIC HYPERMUTATION", "@id": "/awards/1U01CA260701-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"term_id": "UBERON:0002048", "synonyms": ["pulmo"], "@id": "/ontology-terms/UBERON:0002048/", "uuid": "111186bc-8535-4448-903e-854af460a233", "slim_terms": [{"status": "released", "display_title": "respiratory system", "uuid": "111128bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0001004/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "lung", "uuid": "111186bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0002048/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "endoderm", "uuid": "111121bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000925/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "preferred_name": "lung", "status": "released", "display_title": "lung", "term_name": "lung", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["siyuan-wang-lab:biosource_K-MADM-Trp53_LUAD_mouse_MM1690"], "accession": "4DNSRV8GSS44", "cell_line": {"synonyms": ["type II alveolar epithelial cell", "cuboidal type II cell", "AT2", "lung type 2 cell", "TII", "type 2 alveolar epithelial cell", "ATII", "granular pneumocyte", "type II alveolocyte", "type II alveolar cell", "type 2 alveolocyte", "great alveolar cell", "type 2 pneumocyte"], "@id": "/ontology-terms/CL:0002063/", "@type": ["OntologyTerm", "Item"], "status": "released", "term_name": "type II pneumocyte", "term_id": "CL:0002063", "display_title": "type II pneumocyte", "uuid": "784f2a76-e250-4981-9602-ef11411485bc", "preferred_name": "type II pneumocyte", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0000925/", "uuid": "111121bc-8535-4448-903e-854af460a233", "display_title": "endoderm", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "current", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0002048/", "uuid": "111186bc-8535-4448-903e-854af460a233", "display_title": "lung", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0001004/", "uuid": "111128bc-8535-4448-903e-854af460a233", "display_title": "respiratory system", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"uuid": "54af05fa-9805-466c-a4d9-e2b7445009ca", "status": "released", "@type": ["IndividualMouse", "Individual", "Item"], "display_title": "4DNINQ139XGR", "@id": "/individuals-mouse/4DNINQ139XGR/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "Lung adenocarcinoma (LUAD) cells from mouse MM1690", "date_created": "2025-05-27T17:40:25.183600+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-06-12T16:09:11.104899+00:00"}, "biosource_type": "primary cell", "cell_line_tier": "Unclassified", "public_release": "2025-06-12", "schema_version": "2", "project_release": "2025-06-12", "override_biosource_name": "LUAD cells from mouse MM1690", "@id": "/biosources/4DNSRV8GSS44/", "@type": ["Biosource", "Item"], "uuid": "53e190e0-ba2d-45c0-8d9e-801ffa8fdc4f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "LUAD cells from mouse MM1690 - 4DNSRV8GSS44", "external_references": [], "biosource_name": "LUAD cells from mouse MM1690", "biosource_category": ["Primary Cells"], "organism": {"uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "display_title": "M. musculus", "name": "mouse", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "modifications": [{"status": "released", "@id": "/modifications/4b7121f3-2ddd-49bb-95ba-48e618a3917c/", "uuid": "4b7121f3-2ddd-49bb-95ba-48e618a3917c", "display_title": "Viral Transduction", "@type": ["Modification", "Item"], "modification_type": "Viral Transduction", "description": "MADM system (allowing unambiguous coupling of genotype to fluorescence labeling) in KRAS G12D/WT homozygous mutant (Trp53 -/-) cells expressing GFP+ green-fluorescent protein", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "Multiplexed FISH in GFP+ expressing (green) homozygous mutant (Trp53 -/-)  LUAD cells from K-MADM-Trp53 mouse, Biological Relicate 1, Technical Replicate 1", "sop_mapping": {"has_sop": "No"}, "date_created": "2025-05-27T17:41:46.619324+00:00", "submitted_by": {"error": "no view permissions"}, "imaging_paths": [{"path": {"@type": ["ImagingPath", "Item"], "imaging_rounds": "0", "labeled_probe": "Fiducial beads", "display_title": "Yellow-green fiducial beads for drift correction", "@id": "/imaging-paths/9cfbe934-5945-4a55-b1d0-47605053f0dc/", "override_display_title": "Yellow-green fiducial beads for drift correction", "uuid": "9cfbe934-5945-4a55-b1d0-47605053f0dc", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch00"}, {"path": {"@type": ["ImagingPath", "Item"], "imaging_rounds": "0", "labeled_probe": "DAPI", "display_title": "Chromosomes targeted by DAPI", "@id": "/imaging-paths/6270823b-4cf5-41df-94e5-7b10395961a2/", "override_display_title": "Chromosomes targeted by DAPI", "uuid": "6270823b-4cf5-41df-94e5-7b10395961a2", "status": "released", "target": [{"display_title": "Chromosomes", "status": "released", "@type": ["BioFeature", "Item"], "organism_name": "unspecified", "uuid": "655728f9-d4ab-4dd2-971c-1627ab2c8d33", "@id": "/bio-features/655728f9-d4ab-4dd2-971c-1627ab2c8d33/", "cellular_structure": "Chromosomes", "feature_type": {"uuid": "e47e2bea-bc1e-4989-881c-521fc0b33529", "display_title": "cellular_component", "preferred_name": "cellular_component", "@id": "/ontology-terms/GO:0005575/", "term_name": "cellular_component", "@type": ["OntologyTerm", "Item"], "status": "released", "term_id": "GO:0005575", "term_url": "http://purl.obolibrary.org/obo/GO_0005575", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch01"}, {"path": {"@type": ["ImagingPath", "Item"], "imaging_rounds": "1-50", "display_title": "~60kb feature-containing or central region of each of 473 TADs spanning from Chr1 to Ch19 targeted by Alexa 647-labelled imaging oligos", "@id": "/imaging-paths/bd423df1-91c3-4b25-8cd2-9bf4e061cdb8/", "override_display_title": "~60kb feature-containing or central region of each of 473 TADs spanning from Chr1 to Ch19 targeted by Alexa 647-labelled imaging oligos", "uuid": "bd423df1-91c3-4b25-8cd2-9bf4e061cdb8", "status": "released", "target": [{"display_title": "Total 473 TADs spanning between Chr1-Chr19 (mouse)", "status": "released", "@type": ["BioFeature", "Item"], "organism_name": "mouse", "uuid": "dc6a4e96-eb3d-4225-8d3c-098612876bd9", "@id": "/bio-features/dc6a4e96-eb3d-4225-8d3c-098612876bd9/", "preferred_label": "Total 473 TADs spanning between Chr1-Chr19", "feature_type": {"uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "display_title": "region", "preferred_name": "region", "@id": "/ontology-terms/SO:0000001/", "term_name": "region", "@type": ["OntologyTerm", "Item"], "status": "released", "term_id": "SO:0000001", "term_url": "http://purl.obolibrary.org/obo/SO_0000001", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch02"}, {"path": {"@type": ["ImagingPath", "Item"], "imaging_rounds": "1-50", "display_title": "~60kb feature-containing or central region of each of 473 TADs spanning from Chr1 to Ch19 targeted by ATTO 565-labelled imaging oligos", "@id": "/imaging-paths/a158da46-0ac2-45fb-a2de-4071c0845313/", "override_display_title": "~60kb feature-containing or central region of each of 473 TADs spanning from Chr1 to Ch19 targeted by ATTO 565-labelled imaging oligos", "uuid": "a158da46-0ac2-45fb-a2de-4071c0845313", "status": "released", "target": [{"display_title": "Total 473 TADs spanning between Chr1-Chr19 (mouse)", "status": "released", "@type": ["BioFeature", "Item"], "organism_name": "mouse", "uuid": "dc6a4e96-eb3d-4225-8d3c-098612876bd9", "@id": "/bio-features/dc6a4e96-eb3d-4225-8d3c-098612876bd9/", "preferred_label": "Total 473 TADs spanning between Chr1-Chr19", "feature_type": {"uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "display_title": "region", "preferred_name": "region", "@id": "/ontology-terms/SO:0000001/", "term_name": "region", "@type": ["OntologyTerm", "Item"], "status": "released", "term_id": "SO:0000001", "term_url": "http://purl.obolibrary.org/obo/SO_0000001", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch03"}], "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-06-12T16:08:30.368674+00:00"}, "public_release": "2025-06-12", "schema_version": "3", "experiment_type": {"@id": "/experiment-types/multiplexed-fish/", "assay_subclass_short": "FISH", "experiment_category": "Microscopy", "uuid": "bcdda46a-489d-4d22-be80-c9c21552c915", "display_title": "multiplexed FISH", "@type": ["ExperimentType", "Item"], "status": "released", "title": "multiplexed FISH", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/csv/", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "file_format": "csv", "display_title": "csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFIU7X8FJJ", "file_size": 218824111, "@id": "/files-processed/4DNFIU7X8FJJ/", "file_type_detailed": "FOF-CT - DNA-spot/trace core (csv)", "file_classification": "processed file", "uuid": "a21b73af-2ba3-42b3-9a57-e90f989668a1", "status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIU7X8FJJ.csv", "href": "/files-processed/4DNFIU7X8FJJ/@@download/4DNFIU7X8FJJ.csv", "upload_key": "a21b73af-2ba3-42b3-9a57-e90f989668a1/4DNFIU7X8FJJ.csv", "file_type": "FOF-CT - DNA-spot/trace core", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a21b73af-2ba3-42b3-9a57-e90f989668a1/4DNFIU7X8FJJ.csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Siyuan Wang, YALE", "experiment_type": "multiplexed FISH", "experiment_bucket": "processed file", "assay_info": "Chromosomes, Total 473 TADs spanning between Chr1-Chr19 (mouse)", "dataset": "Multiplexed FISH in lung tissue", "condition": "LUAD (GFP+)", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "LUAD from mouse SA3440 and LUAD cells from mouse MM1433 and LUAD cells from mouse MM2030 and LUAD cells from mouse SA3501 and LUAD cells from mouse MM1690", "lab_name": "Siyuan Wang, YALE"}}], "project_release": "2025-06-12", "reference_files": [{"file_type_detailed": "target regions (bed)", "uuid": "70f49cbc-cfec-43c6-921a-64289cf18cca", "accession": "4DNFI72VKAWO", "@type": ["FileReference", "File", "Item"], "status": "released", "display_title": "4DNFI72VKAWO.bed.gz", "file_type": "target regions", "file_size": 3886, "file_classification": "ancillary file", "@id": "/files-reference/4DNFI72VKAWO/", "file_format": {"status": "released", "file_format": "bed", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "display_title": "bed", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bed/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"uuid": "a8fa67c9-425e-4624-a3df-241d8e050b05", "@id": "/higlass-view-configs/a8fa67c9-425e-4624-a3df-241d8e050b05/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFI72VKAWO", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "oligo sequences (zip)", "uuid": "a5d86981-51d9-486a-afca-a42b5ba3f327", "accession": "4DNFID52LWSC", "@type": ["FileReference", "File", "Item"], "status": "released", "display_title": "4DNFID52LWSC.zip", "file_type": "oligo sequences", "file_size": 55257, "file_classification": "ancillary file", "@id": "/files-reference/4DNFID52LWSC/", "file_format": {"status": "released", "file_format": "zip", "uuid": "d13d06cf-218e-4f61-44f0-91f226248b2c", "display_title": "zip", "@type": ["FileFormat", "Item"], "@id": "/file-formats/zip/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "oligo sequences (zip)", "uuid": "d160d051-c1b7-41bd-84fa-b465244f2ac7", "accession": "4DNFIJNKTWQA", "@type": ["FileReference", "File", "Item"], "status": "released", "display_title": "4DNFIJNKTWQA.zip", "file_type": "oligo sequences", "file_size": 10948018, "file_classification": "ancillary file", "@id": "/files-reference/4DNFIJNKTWQA/", "file_format": {"status": "released", "file_format": "zip", "uuid": "d13d06cf-218e-4f61-44f0-91f226248b2c", "display_title": "zip", "@type": ["FileFormat", "Item"], "@id": "/file-formats/zip/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "oligo sequences (zip)", "uuid": "93c51831-2c37-4819-9129-9aa4c6568456", "accession": "4DNFIFGA7PCI", "@type": ["FileReference", "File", "Item"], "status": "released", "display_title": "4DNFIFGA7PCI.zip", "file_type": "oligo sequences", "file_size": 16511, "file_classification": "ancillary file", "@id": "/files-reference/4DNFIFGA7PCI/", "file_format": {"status": "released", "file_format": "zip", "uuid": "d13d06cf-218e-4f61-44f0-91f226248b2c", "display_title": "zip", "@type": ["FileFormat", "Item"], "@id": "/file-formats/zip/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "extinguishing_method": "photobleaching", "@id": "/experiments-mic/4DNEX4F82R7B/", "@type": ["ExperimentMic", "Experiment", "Item"], "uuid": "4b95a309-37f5-422d-97c6-19fef98629c2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "multiplexed FISH on LUAD from mouse SA3440 and LUAD cells from mouse MM1433 and LUAD cells from mouse MM2030 and LUAD cells from mouse SA3501 and LUAD cells from mouse MM1690 - 4DNEX4F82R7B", "external_references": [], "experiment_sets": [{"experimentset_type": "replicate", "display_title": "4DNESX1I17ZA", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "accession": "4DNESX1I17ZA", "uuid": "49554ffc-2ca3-4fab-b97d-24682b9921b4", "@id": "/experiment-set-replicates/4DNESX1I17ZA/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"@type": ["Publication", "Item"], "ID": "doi:10.1101/2023.07.23.550157", "date_published": "2024-09-09", "abstract": "Although three-dimensional (3D) genome structures are altered in cancer cells,  little is known about how these changes evolve and diversify during cancer  progression. Leveraging genome-wide chromatin tracing to visualize 3D genome  folding directly in tissues, we generated 3D genome cancer atlases of murine lung  and pancreatic adenocarcinoma. Our data reveal stereotypical, non-monotonic, and  stage-specific alterations in 3D genome folding heterogeneity, compaction, and  compartmentalization as cancers progress from normal to preinvasive and  ultimately to invasive tumors, discovering a potential structural bottleneck in  early tumor progression. Remarkably, 3D genome architectures distinguish  histologic cancer states in single cells, despite considerable cell-to-cell  heterogeneity. Gene-level analyses of evolutionary changes in 3D genome  compartmentalization not only showed compartment-associated genes are more  homogeneously regulated, but also elucidated prognostic and dependency genes in  lung adenocarcinoma and a previously unappreciated role for polycomb-group  protein Rnf2 in 3D genome regulation. Our results demonstrate the utility of  mapping the single-cell cancer 3D genome in tissues and illuminate its potential  to identify new diagnostic, prognostic, and therapeutic biomarkers in cancer.", "title": "Tracing the evolution of single-cell cancer 3D genomes: an atlas for cancer gene  discovery.", "short_attribution": "Liu M et al. (2024)", "status": "current", "authors": ["Liu M", "Jin S", "Agabiti SS", "Jensen TB", "Yang T", "Radda JSD", "Ruiz CF", "Baldissera G", "Rajaei M", "Townsend JP", "Muzumdar MD", "Wang S"], "uuid": "e83173f7-95e4-40ad-9748-e13b2a518fc6", "display_title": "Liu M et al. (2024) doi:10.1101/2023.07.23.550157", "journal": "bioRxiv : the preprint server for biology", "@id": "/publications/e83173f7-95e4-40ad-9748-e13b2a518fc6/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"date_published": "2024-09-09", "authors": ["Liu M", "Jin S", "Agabiti SS", "Jensen TB", "Yang T", "Radda JSD", "Ruiz CF", "Baldissera G", "Rajaei M", "Townsend JP", "Muzumdar MD", "Wang S"], "title": "Tracing the evolution of single-cell cancer 3D genomes: an atlas for cancer gene  discovery.", "@id": "/publications/e83173f7-95e4-40ad-9748-e13b2a518fc6/", "short_attribution": "Liu M et al. (2024)", "display_title": "Liu M et al. (2024) doi:10.1101/2023.07.23.550157", "abstract": "Although three-dimensional (3D) genome structures are altered in cancer cells,  little is known about how these changes evolve and diversify during cancer  progression. Leveraging genome-wide chromatin tracing to visualize 3D genome  folding directly in tissues, we generated 3D genome cancer atlases of murine lung  and pancreatic adenocarcinoma. Our data reveal stereotypical, non-monotonic, and  stage-specific alterations in 3D genome folding heterogeneity, compaction, and  compartmentalization as cancers progress from normal to preinvasive and  ultimately to invasive tumors, discovering a potential structural bottleneck in  early tumor progression. Remarkably, 3D genome architectures distinguish  histologic cancer states in single cells, despite considerable cell-to-cell  heterogeneity. Gene-level analyses of evolutionary changes in 3D genome  compartmentalization not only showed compartment-associated genes are more  homogeneously regulated, but also elucidated prognostic and dependency genes in  lung adenocarcinoma and a previously unappreciated role for polycomb-group  protein Rnf2 in 3D genome regulation. Our results demonstrate the utility of  mapping the single-cell cancer 3D genome in tissues and illuminate its potential  to identify new diagnostic, prognostic, and therapeutic biomarkers in cancer.", "journal": "bioRxiv : the preprint server for biology", "uuid": "e83173f7-95e4-40ad-9748-e13b2a518fc6", "@type": ["Publication", "Item"], "ID": "doi:10.1101/2023.07.23.550157", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "value": "Chromosomes, Total 473 TADs spanning between Chr1-Chr19 (mouse)", "combined": "Target: Chromosomes, Total 473 TADs spanning between Chr1-Chr19 (mouse)"}, "experiment_summary": "multiplexed FISH on LUAD from mouse SA3440 and LUAD cells from mouse MM1433 and LUAD cells from mouse MM2030 and LUAD cells from mouse SA3501 and LUAD cells from mouse MM1690", "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}