{"lab": {"@id": "/labs/andrew-belmont-lab/", "correspondence": [{"contact_email": "YXNiZWxAaWxsaW5vaXMuZWR1", "@id": "/users/92f90aed-7df1-4bd9-9e74-a472cb50d663/", "display_title": "Andrew Belmont"}], "display_title": "Andrew Belmont, ILLINOIS", "@type": ["Lab", "Item"], "title": "Andrew Belmont, ILLINOIS", "status": "current", "uuid": "b2c2deeb-e883-4ac0-b9e2-906e598884d6", "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", "name": "1U01DK127422-01", "status": "current", "display_title": "IDENTIFICATION OF THE ACTIVE NUCLEAR NICHE(S) USING NOVEL PROTEOMIC, GENOMIC, TRANSGENIC, AND LIVE-CELL MICROSCOPY TECHNOLOGIES", "@type": ["Award", "Item"], "project": "4DN", "@id": "/awards/1U01DK127422-01/", "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.\"", "uuid": "ef637c2d-7e48-4e26-aad2-eac1f680d4e8", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "6a60d6a975323f1e9baa0441a7f6a63c", "status": "released", "aliases": ["belmont-lab:U2OS_DDX39B_2xDTT_bio2_rep2_hg38.bw"], "filename": "U2OS_DDX39B_2xDTT_bio2_rep2_hg38.bw", "accession": "4DNFIJO9UN3Y", "file_size": 1114801, "file_type": "normalized counts", "description": "20kb bin (read normalized) count track", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/bw/", "file_format": "bw", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "higlass_uid": "aaa8fd58-cd45-4b68-af32-46dc764bd395", "date_created": "2025-07-21T18:53:40.152160+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-09-05T17:46:51.380383+00:00"}, "produced_from": ["belmont-lab:U2OS_2xDTT_DDX39B_PULLDOWN_bio2_rep2_CTTGTAAT-AGATCTCG_L002_R1_001.fastq", "belmont-lab:U2OS_2xDTT_DDX39B_INPUT_bio2_rep2_CAGATCAT-AGATCTCG_L002_R1_001.fastq"], "content_md5sum": "6a60d6a975323f1e9baa0441a7f6a63c", "public_release": "2025-08-27", "schema_version": "3", "static_content": [{"content": {"description": "", "uuid": "a10fc19a-cbf6-4105-af25-58af87a803bc", "status": "released", "lab": {"@id": "/labs/andrew-belmont-lab/", "status": "current", "@type": ["Lab", "Item"], "uuid": "b2c2deeb-e883-4ac0-b9e2-906e598884d6", "display_title": "Andrew Belmont, ILLINOIS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b2c2deeb-e883-4ac0-b9e2-906e598884d6"]}}, "title": "4DNFIJO9UN3Y - normalized counts for U2OS (Tier 2) TSA-seq DDX39B protein", "filetype": "HiglassViewConfig", "@type": ["HiglassViewConfig", "UserContent", "Item"], "name": "a10fc19a-cbf6-4105-af25-58af87a803bc", "contributing_labs": [], "award": {"status": "current", "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", "@type": ["Award", "Item"], "@id": "/awards/1U01DK127422-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFIJO9UN3Y - normalized counts for U2OS (Tier 2) TSA-seq DDX39B protein", "@id": "/higlass-view-configs/a10fc19a-cbf6-4105-af25-58af87a803bc/", "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/4DNFIJO9UN3Y/", "@type": ["FileProcessed", "File", "Item"], "uuid": "04716e98-2885-4cf8-9d8e-86b955e073ff", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIJO9UN3Y.bw", "external_references": [], "experiments": [{"@type": ["ExperimentTsaseq", "Experiment", "Item"], "status": "released", "@id": "/experiments-tsaseq/4DNEXK4ZYUBM/", "accession": "4DNEXK4ZYUBM", "uuid": "43a8983b-c7b9-4bbf-8cdb-b6d3ee99a43a", "display_title": "TSA-seq against DDX39B protein on U2OS (Tier 2) - 4DNEXK4ZYUBM", "biosample": {"accession": "4DNBS5PTAHOL", "modifications_summary": "None", "biosource_summary": "U2OS (Tier 2)", "display_title": "4DNBS5PTAHOL", "treatments_summary": "None", "@type": ["Biosample", "Item"], "status": "released", "uuid": "2f848014-0d2b-4765-bc14-5aae5efc3a6f", "@id": "/biosamples/4DNBS5PTAHOL/", "biosource": [{"cell_line_tier": "Tier 2", "display_title": "U2OS (Tier 2) - 4DNSR3V9ST6H", "@id": "/biosources/4DNSR3V9ST6H/", "biosource_type": "immortalized cell line", "@type": ["Biosource", "Item"], "status": "released", "uuid": "c60f7cf5-a3d6-4946-8f75-5170a36482b0", "modifications": [], "tissue": {"uuid": "01b91fc0-6552-4a09-ad79-c7766cd4cfea", "@type": ["OntologyTerm", "Item"], "term_id": "UBERON:0002481", "status": "released", "display_title": "bone tissue", "term_name": "bone tissue", "preferred_name": "bone tissue", "@id": "/ontology-terms/UBERON:0002481/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "organism": {"@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@type": ["Organism", "Item"], "display_title": "H. sapiens", "status": "released", "scientific_name": "Homo sapiens", "name": "human", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"uuid": "a72dc763-e53a-4429-9137-64ba424c0d41", "status": "released", "term_name": "U2OS", "display_title": "U2OS", "preferred_name": "U2OS", "@type": ["OntologyTerm", "Item"], "term_id": "EFO:0002869", "@id": "/ontology-terms/EFO:0002869/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@id": "/individuals-human/4DNINPN9UG9G/", "display_title": "4DNINPN9UG9G", "uuid": "b7d5e27d-e831-4f99-a72f-426f95422e3f", "@type": ["IndividualHuman", "Individual", "Item"], "status": "released", "protected_data": false, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "cell_culture_details": [{"in_vitro_differentiated": "No", "display_title": "BiosampleCellCulture from 2024-12-19", "@id": "/biosample-cell-cultures/e00114d2-1601-4087-9aff-bb8e43ddbe7b/", "status": "released", "uuid": "e00114d2-1601-4087-9aff-bb8e43ddbe7b", "@type": ["BiosampleCellCulture", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "e81e78f4-189b-42e4-9c2a-b3a67d043c99", "experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESMCHASAW/", "status": "released", "display_title": "4DNESMCHASAW", "accession": "4DNESMCHASAW", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_type": {"@id": "/experiment-types/tsa-seq/", "@type": ["ExperimentType", "Item"], "title": "TSA-seq", "display_title": "TSA-seq", "status": "released", "uuid": "75d7181c-e329-463e-b776-a467433aa4db", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2025-08-27T17:29:06.200044+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "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 U2OS", "condition": "condition3enhancementG - anti-DDX39B", "replicate_info": "Biorep 2, Techrep 2", "biosource_name": "U2OS (Tier 2)", "lab_name": "Andrew Belmont, ILLINOIS", "track_title": "normalized counts for U2OS (Tier 2) TSA-seq DDX39B protein"}, "title": "4DNFIJO9UN3Y", "href": "/files-processed/4DNFIJO9UN3Y/@@download/4DNFIJO9UN3Y.bw", "upload_key": "04716e98-2885-4cf8-9d8e-86b955e073ff/4DNFIJO9UN3Y.bw", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/04716e98-2885-4cf8-9d8e-86b955e073ff/4DNFIJO9UN3Y.bw", "tsv_notes": "", "workflow_run_inputs": [{"uuid": "70d7e2aa-abcd-4e35-929b-4bff95776a89", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "display_title": "md5 0.2.6 run 2025-07-21 19:28:27.770530", "status": "released", "@id": "/workflow-runs-awsem/70d7e2aa-abcd-4e35-929b-4bff95776a89/", "workflow": {"status": "released", "@type": ["Workflow", "Item"], "title": "md5 0.2.6", "display_title": "md5 0.2.6 - 4DNWF2HFF82B", "uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "@id": "/workflows/4DNWF2HFF82B/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "report"}], "input_files": [{"workflow_argument_name": "input_file", "value": {"display_title": "4DNFIJO9UN3Y.bw", "uuid": "04716e98-2885-4cf8-9d8e-86b955e073ff", "status": "released", "filename": "U2OS_DDX39B_2xDTT_bio2_rep2_hg38.bw", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIJO9UN3Y", "@id": "/files-processed/4DNFIJO9UN3Y/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bw/", "file_format": "bw", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [], "experiment_sets": [], "source_experiment_sets": [{"uuid": "e81e78f4-189b-42e4-9c2a-b3a67d043c99", "status": "released", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNESMCHASAW", "@id": "/experiment-set-replicates/4DNESMCHASAW/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-tsaseq/4DNEXK4ZYUBM/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2025-08-27T17:29:06.200044+00:00"}}, {"parent": "/files-processed/4DNFIJO9UN3Y/", "embedded_path": "last_modified", "item": {"date_modified": "2025-09-05T17:46:51.380383+00:00"}}]}, "validation-errors": []}