{"lab": {"correspondence": [{"contact_email": "YXNiZWxAaWxsaW5vaXMuZWR1", "@id": "/users/92f90aed-7df1-4bd9-9e74-a472cb50d663/", "display_title": "Andrew Belmont"}], "uuid": "b2c2deeb-e883-4ac0-b9e2-906e598884d6", "@id": "/labs/andrew-belmont-lab/", "@type": ["Lab", "Item"], "status": "current", "title": "Andrew Belmont, ILLINOIS", "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": {"center_title": "Belmont", "@type": ["Award", "Item"], "name": "1U01DK127422-01", "@id": "/awards/1U01DK127422-01/", "display_title": "IDENTIFICATION OF THE ACTIVE NUCLEAR NICHE(S) USING NOVEL PROTEOMIC, GENOMIC, TRANSGENIC, AND LIVE-CELL MICROSCOPY TECHNOLOGIES", "uuid": "ef637c2d-7e48-4e26-aad2-eac1f680d4e8", "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.\"", "status": "current", "project": "4DN", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "pi": {"error": "no view permissions"}}, "md5sum": "f35e32c1d96fdd6982bbc6875efa4626", "status": "released", "aliases": ["belmont-lab:HCT116_DDX39B_2xDTT_bio2_hg38.bw"], "filename": "HCT116_DDX39B_2xDTT_bio2_hg38.bw", "accession": "4DNFIHNOAO4X", "file_size": 1131239, "file_type": "normalized counts", "description": "20kb bin (read normalized) count track", "file_format": {"@type": ["FileFormat", "Item"], "file_format": "bw", "display_title": "bw", "@id": "/file-formats/bw/", "status": "released", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "higlass_uid": "656db0d5-2b1d-4c8c-932a-62cf071371ad", "date_created": "2025-07-21T18:53:53.163605+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-09-05T17:46:40.998268+00:00"}, "produced_from": ["belmont-lab:HCT116_2XDTT_DDX39B_Pulldown_bio2_19_GTGAAA_L004_R1_001.fastq", "belmont-lab:HCT116_2XDTT_DDX39B_Input_bio2_18_GTCCGC_L004_R1_001.fastq"], "content_md5sum": "f35e32c1d96fdd6982bbc6875efa4626", "public_release": "2025-08-27", "schema_version": "3", "static_content": [{"content": {"status": "released", "uuid": "cea2469d-81fb-4bb5-8079-6919cc45e23d", "description": "", "lab": {"@type": ["Lab", "Item"], "status": "current", "uuid": "b2c2deeb-e883-4ac0-b9e2-906e598884d6", "display_title": "Andrew Belmont, ILLINOIS", "@id": "/labs/andrew-belmont-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b2c2deeb-e883-4ac0-b9e2-906e598884d6"]}}, "title": "4DNFIHNOAO4X - normalized counts for HCT116 (Tier 2) TSA-seq DDX39B protein", "award": {"@id": "/awards/1U01DK127422-01/", "display_title": "IDENTIFICATION OF THE ACTIVE NUCLEAR NICHE(S) USING NOVEL PROTEOMIC, GENOMIC, TRANSGENIC, AND LIVE-CELL MICROSCOPY TECHNOLOGIES", "@type": ["Award", "Item"], "status": "current", "uuid": "ef637c2d-7e48-4e26-aad2-eac1f680d4e8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "name": "cea2469d-81fb-4bb5-8079-6919cc45e23d", "filetype": "HiglassViewConfig", "@id": "/higlass-view-configs/cea2469d-81fb-4bb5-8079-6919cc45e23d/", "display_title": "4DNFIHNOAO4X - normalized counts for HCT116 (Tier 2) TSA-seq DDX39B protein", "@type": ["HiglassViewConfig", "UserContent", "Item"], "contributing_labs": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}, "location": "tab:higlass", "description": "auto_generated_higlass_view_config"}], "genome_assembly": "GRCh38", "project_release": "2025-08-27", "file_classification": "processed file", "@id": "/files-processed/4DNFIHNOAO4X/", "@type": ["FileProcessed", "File", "Item"], "uuid": "ca28edd9-1d95-4ebd-9d48-d8139919e440", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIHNOAO4X.bw", "external_references": [], "experiments": [{"uuid": "19003687-6491-471d-976f-39509aeb36f0", "accession": "4DNEXAIACHR8", "@id": "/experiments-tsaseq/4DNEXAIACHR8/", "display_title": "TSA-seq against DDX39B protein on HCT116 (Tier 2) - 4DNEXAIACHR8", "@type": ["ExperimentTsaseq", "Experiment", "Item"], "status": "released", "biosample": {"@id": "/biosamples/4DNBSU2F64A2/", "@type": ["Biosample", "Item"], "biosource_summary": "HCT116 (Tier 2)", "uuid": "90152aa4-14c0-49c9-a2fc-9f764aa3dd3b", "accession": "4DNBSU2F64A2", "treatments_summary": "None", "status": "released", "display_title": "4DNBSU2F64A2", "modifications_summary": "None", "cell_culture_details": [{"@id": "/biosample-cell-cultures/a399e053-1786-421b-9afd-24bb73ff2e6b/", "@type": ["BiosampleCellCulture", "Item"], "display_title": "BiosampleCellCulture from 2024-12-18", "uuid": "a399e053-1786-421b-9afd-24bb73ff2e6b", "status": "released", "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosource": [{"status": "released", "biosource_type": "immortalized cell line", "uuid": "393880ea-f928-406d-a4bf-78435b8975ef", "display_title": "HCT116 (Tier 2) - 4DNSRMYUIVGD", "cell_line_tier": "Tier 2", "@id": "/biosources/4DNSRMYUIVGD/", "@type": ["Biosource", "Item"], "modifications": [], "cell_line": {"term_name": "HCT116", "@id": "/ontology-terms/EFO:0002824/", "uuid": "49d090b2-5326-40ce-9c19-7a214c682272", "term_id": "EFO:0002824", "@type": ["OntologyTerm", "Item"], "display_title": "HCT116", "status": "released", "preferred_name": "HCT116", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"display_title": "H. sapiens", "@id": "/organisms/9606/", "@type": ["Organism", "Item"], "name": "human", "status": "released", "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"uuid": "1f0f0999-c5b4-430e-8650-8ebb3491d699", "display_title": "4DNINJ6WV6L1", "@type": ["IndividualHuman", "Individual", "Item"], "status": "released", "@id": "/individuals-human/4DNINJ6WV6L1/", "protected_data": false, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0001155/", "preferred_name": "colon", "display_title": "colon", "status": "released", "uuid": "3e39f551-bc0b-4bee-b932-29d71956fb94", "term_name": "colon", "term_id": "UBERON:0001155", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"uuid": "75d7181c-e329-463e-b776-a467433aa4db", "status": "released", "title": "TSA-seq", "@id": "/experiment-types/tsa-seq/", "display_title": "TSA-seq", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNESR7SW5G9", "uuid": "57aa1091-dae1-46c3-954e-124befdc9500", "accession": "4DNESR7SW5G9", "status": "released", "@id": "/experiment-set-replicates/4DNESR7SW5G9/", "experimentset_type": "replicate", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2025-08-27T19:28:50.284503+00:00"}}], "file_type_detailed": "normalized counts (bw)", "track_and_facet_info": {"experimental_lab": "Andrew Belmont, ILLINOIS", "experiment_type": "TSA-seq", "experiment_bucket": "processed file", "assay_info": "DDX39B protein", "dataset": "TSA-seq v2 DDX39B in HCT116", "condition": "condition3enhancementG - anti-DDX39B", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Andrew Belmont, ILLINOIS", "track_title": "normalized counts for HCT116 (Tier 2) TSA-seq DDX39B protein"}, "title": "4DNFIHNOAO4X", "href": "/files-processed/4DNFIHNOAO4X/@@download/4DNFIHNOAO4X.bw", "upload_key": "ca28edd9-1d95-4ebd-9d48-d8139919e440/4DNFIHNOAO4X.bw", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ca28edd9-1d95-4ebd-9d48-d8139919e440/4DNFIHNOAO4X.bw", "tsv_notes": "", "workflow_run_inputs": [{"uuid": "5f186de9-7883-43a2-b068-ef7329463c11", "@id": "/workflow-runs-awsem/5f186de9-7883-43a2-b068-ef7329463c11/", "status": "released", "display_title": "md5 0.2.6 run 2025-07-21 19:28:03.805489", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "workflow": {"@type": ["Workflow", "Item"], "title": "md5 0.2.6", "status": "released", "@id": "/workflows/4DNWF2HFF82B/", "uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "display_title": "md5 0.2.6 - 4DNWF2HFF82B", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "report"}], "input_files": [{"workflow_argument_name": "input_file", "value": {"filename": "HCT116_DDX39B_2xDTT_bio2_hg38.bw", "@id": "/files-processed/4DNFIHNOAO4X/", "accession": "4DNFIHNOAO4X", "display_title": "4DNFIHNOAO4X.bw", "status": "released", "@type": ["FileProcessed", "File", "Item"], "uuid": "ca28edd9-1d95-4ebd-9d48-d8139919e440", "file_format": {"uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bw/", "status": "released", "display_title": "bw", "@type": ["FileFormat", "Item"], "file_format": "bw", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [], "experiment_sets": [], "source_experiment_sets": [{"status": "released", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNESR7SW5G9/", "uuid": "57aa1091-dae1-46c3-954e-124befdc9500", "display_title": "4DNESR7SW5G9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-tsaseq/4DNEXAIACHR8/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2025-08-27T19:28:50.284503+00:00"}}, {"parent": "/files-processed/4DNFIHNOAO4X/", "embedded_path": "last_modified", "item": {"date_modified": "2025-09-05T17:46:40.998268+00:00"}}]}, "validation-errors": []}