{"lab": {"uuid": "b2c2deeb-e883-4ac0-b9e2-906e598884d6", "@type": ["Lab", "Item"], "title": "Andrew Belmont, ILLINOIS", "correspondence": [{"contact_email": "YXNiZWxAaWxsaW5vaXMuZWR1", "@id": "/users/92f90aed-7df1-4bd9-9e74-a472cb50d663/", "display_title": "Andrew Belmont"}], "@id": "/labs/andrew-belmont-lab/", "status": "current", "display_title": "Andrew Belmont, ILLINOIS", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b2c2deeb-e883-4ac0-b9e2-906e598884d6"]}}, "award": {"project": "4DN", "uuid": "ef637c2d-7e48-4e26-aad2-eac1f680d4e8", "display_title": "IDENTIFICATION OF THE ACTIVE NUCLEAR NICHE(S) USING NOVEL PROTEOMIC, GENOMIC, TRANSGENIC, AND LIVE-CELL MICROSCOPY TECHNOLOGIES", "@id": "/awards/1U01DK127422-01/", "status": "current", "@type": ["Award", "Item"], "name": "1U01DK127422-01", "center_title": "Belmont", "description": "RT-CDF: The study of gene expression and possible role of condensates in regulating gene expression havelargely ignored known nuclear structures. This proposal is significant because we propose a novel model forthe role of nuclear organization in regulating gene expression: 1) Nuclear speckles and still unknown nuclearcompartments/bodies help organize other phase-separated condensates to modulate gene expression; 2)Nuclear speckles together with surrounding nuclear compartments/bodies and associated phase-separatedcondensates together represent active nuclear niches which may have different functional properties; 3) Smalldistances matter: gene movements of only a few hundred nm between repressive and these different activenuclear niches may differentially regulate gene expression; 4) Action-at-a distance: component flux into andout of these nuclear compartments will have global effects on gene expression; 5) These same nuclearcompartments/bodies may similarly modulate RNA processing and organize nuclear export. Here we propose to: 1) Identify multiple components of known and still unknown nuclear \u201cactiveniches\u201d; 2) Map genome-wide the positions and predicted movements of genes relative to these active nichesduring physiological transitions; 3) Visualize nuclear body/compartment dynamics and fluxes of proteinsbetween nuclear bodies in steady-state and through physiological transitions; 4) Visualize movements ofreporter transgenes, endogenous genes, and rewired chromosome loci relative to these nuclearbodies/compartments and temporally correlate changes in gene expression with their dynamic movements andcompartment associations; 5) Visualize movements of pre-mRNAs and nuclear mRNAs during RNAprocessing and export; 6) Measure fluxes of nuclear body components to and from adjacent transcribingchromatin. Additionally, we propose developing relatively low-cost, novel microscope platforms and softwarespecifically designed to facilitate these live-cell imaging goals in our laboratories as well as others. Our Aims will be to: 1. Map proteins, genes, RNAs relative to active nuclear compartment(s) usingiterative rounds of TSA-MS-Ratio, validation by light microscopy, and TSA-Seq; 2. Measure dynamics ofbodies, components of nuclear bodies using live-cell imaging; 3. Measure temporal correlation betweenchanges in gene expression and gene movement relative to nuclear bodies and visualize the export path ofexpressed transcripts; 4. Design and deliver two novel microscopes designed to facilitate Aims 1-3 at amodest cost. Successful completion of these Aims should significantly change our current understanding of therole of nuclear organization in regulating gene expression with impact across a wide range of research fields.\"", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "pi": {"error": "no view permissions"}}, "badges": [{"badge": {"status": "released", "@id": "/badges/biosample-metadata-incomplete/", "warning": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "@type": ["Badge", "Item"], "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "display_title": "Biosample Metadata Incomplete", "badge_classification": "Warning", "badge_icon": "/static/img/badges/biosample-icon.svg", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Biosample missing morphology_image", "Tiered cell line cultured after 2022-05-10 missing 4DN specified FBS vendor and lot info"]}], "status": "released", "aliases": ["belmont-lab:biosample_hct116-son-srrm2-auxin-KD-rna-seq_B2"], "accession": "4DNBSHJIHF5R", "biosource": [{"lab": {"display_title": "4DN DCIC, HMS", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "award": {"@id": "/awards/1U01CA200059-01/", "status": "current", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@type": ["Award", "Item"], "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"synonyms": ["large bowel", "posterior intestine"], "@type": ["OntologyTerm", "Item"], "term_id": "UBERON:0001155", "status": "released", "term_url": "http://purl.obolibrary.org/obo/UBERON_0001155", "term_name": "colon", "uuid": "3e39f551-bc0b-4bee-b932-29d71956fb94", "@id": "/ontology-terms/UBERON:0001155/", "display_title": "colon", "preferred_name": "colon", "slim_terms": [{"status": "released", "synonyms": ["intestinum crassum", "Entire large intestine"], "@id": "/ontology-terms/UBERON:0000059/", "uuid": "111174bc-8535-4448-903e-854af460a233", "display_title": "large intestine", "term_url": "http://purl.obolibrary.org/obo/UBERON_0000059", "term_id": "UBERON:0000059", "preferred_name": "large intestine", "@type": ["OntologyTerm", "Item"], "term_name": "large intestine", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "synonyms": ["alimentary tract", "alimentary system", "Entire digestive system", "gut", "gastrointestinal system"], "@id": "/ontology-terms/UBERON:0001007/", "uuid": "111129bc-8535-4448-903e-854af460a233", "display_title": "digestive system", "term_url": "http://purl.obolibrary.org/obo/UBERON_0001007", "term_id": "UBERON:0001007", "preferred_name": "digestive system", "@type": ["OntologyTerm", "Item"], "term_name": "digestive system", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["dcic:HCT116T2", "4dn-dcic-lab:HCT116T2"], "accession": "4DNSRMYUIVGD", "cell_line": {"term_id": "EFO:0002824", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/EFO:0002824/", "display_title": "HCT116", "term_url": "http://www.ebi.ac.uk/efo/EFO_0002824", "uuid": "49d090b2-5326-40ce-9c19-7a214c682272", "term_name": "HCT116", "preferred_name": "HCT116", "status": "released", "synonyms": ["HCT-116 cell", "HCT116 cell"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"sex": "male", "display_title": "4DNINJ6WV6L1", "@type": ["IndividualHuman", "Individual", "Item"], "status": "released", "@id": "/individuals-human/4DNINJ6WV6L1/", "uuid": "1f0f0999-c5b4-430e-8650-8ebb3491d699", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "references": [], "description": "HCT116 Human colon carcinoma cell line", "date_created": "2017-05-10T19:39:40.478821+00:00", "submitted_by": {"error": "no view permissions"}, "SOP_cell_line": {"display_title": "4DN_HCT116_SOP_220120.pdf", "@id": "/protocols/fa2db8dd-2b46-474d-ab56-9f19b630ac99/", "status": "released", "@type": ["Protocol", "Item"], "uuid": "fa2db8dd-2b46-474d-ab56-9f19b630ac99", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-01-20T14:44:31.031352+00:00"}, "modifications": [], "biosource_type": "immortalized cell line", "cell_line_tier": "Tier 2", "public_release": "2017-09-05", "schema_version": "2", 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["Modification", "Item"], "display_title": "Crispr insertion for SON gene", "target_of_mod": [{"@type": ["BioFeature", "Item"], "status": "released", "uuid": "e575fc6a-5f83-4c5f-a0ee-3cde3ceede33", "display_title": "SON gene", "organism_name": "human", "@id": "/bio-features/e575fc6a-5f83-4c5f-a0ee-3cde3ceede33/", "relevant_genes": [{"preferred_symbol": "SON", "display_title": "SON", "@type": ["Gene", "Item"], "status": "released", "@id": "/genes/6651/", "uuid": "8c8bcbc3-ef7f-443a-9b14-628f941b37ae", "geneid": "6651", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "feature_type": {"@type": ["OntologyTerm", "Item"], "display_title": "gene", "term_url": "http://purl.obolibrary.org/obo/SO_0000704", "term_name": "gene", "preferred_name": "gene", "term_id": "SO:0000704", "status": "released", "@id": "/ontology-terms/SO:0000704/", "uuid": "0231da78-1adc-4b8a-89b9-4f91908412a3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, 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{"@type": ["OntologyTerm", "Item"], "display_title": "gene", "term_url": "http://purl.obolibrary.org/obo/SO_0000704", "term_name": "gene", "preferred_name": "gene", "term_id": "SO:0000704", "status": "released", "@id": "/ontology-terms/SO:0000704/", "uuid": "0231da78-1adc-4b8a-89b9-4f91908412a3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "public_release": "2025-08-27", "schema_version": "2", "project_release": "2025-08-27", "cell_culture_details": [{"lab": {"status": "current", "@id": "/labs/andrew-belmont-lab/", "@type": ["Lab", "Item"], "display_title": "Andrew Belmont, ILLINOIS", "uuid": "b2c2deeb-e883-4ac0-b9e2-906e598884d6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b2c2deeb-e883-4ac0-b9e2-906e598884d6"]}}, "award": {"uuid": "ef637c2d-7e48-4e26-aad2-eac1f680d4e8", "@type": ["Award", "Item"], "display_title": "IDENTIFICATION OF THE ACTIVE NUCLEAR NICHE(S) USING NOVEL PROTEOMIC, GENOMIC, TRANSGENIC, AND LIVE-CELL MICROSCOPY TECHNOLOGIES", "status": "current", "@id": "/awards/1U01DK127422-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["belmont-lab:bcc_hct116-son-srrm2-auxin-KD-rna-seq_B2"], "karyotype": "NA", "description": "Cultured in McCoy\u2019s 5A medium supplemented with 10% fetal bovine serum (FBS) as per 4DN SOP", "date_created": "2025-07-23T21:11:31.169027+00:00", "submitted_by": {"error": "no view permissions"}, "doubling_time": "1 day", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-08-27T14:21:10.493961+00:00"}, "passage_number": 5, "public_release": "2025-08-27", "schema_version": "2", "doubling_number": "NA", "project_release": "2025-08-27", "culture_duration": 22.0, "culture_start_date": "2024-05-30", "culture_harvest_date": "2024-06-21", "in_vitro_differentiated": "No", "@id": "/biosample-cell-cultures/b20de0b8-9ad2-4584-a0c0-bc9594274a9e/", "@type": ["BiosampleCellCulture", "Item"], "uuid": "b20de0b8-9ad2-4584-a0c0-bc9594274a9e", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "BiosampleCellCulture from 2025-07-23", "external_references": []}], "@id": "/biosamples/4DNBSHJIHF5R/", "@type": ["Biosample", "Item"], "uuid": "24506d39-05ad-430b-a5f5-33109da60a5f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNBSHJIHF5R", "external_references": [], "modifications_summary": "Crispr insertion for SON gene and Crispr insertion for SRRM2 gene", "modifications_summary_short": "SON insertion", "treatments_summary": " 5PhIAA treatment (5 \u03bcM, 16h at 37\u00b0C)", "tissue_organ_info": {"tissue_source": "colon", "organ_system": ["large intestine", "digestive 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