{"lab": {"status": "current", "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/", "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": {"status": "current", "project": "4DN", "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.\"", "@id": "/awards/1U01DK127422-01/", "uuid": "ef637c2d-7e48-4e26-aad2-eac1f680d4e8", "name": "1U01DK127422-01", "@type": ["Award", "Item"], "display_title": "IDENTIFICATION OF THE ACTIVE NUCLEAR NICHE(S) USING NOVEL PROTEOMIC, GENOMIC, TRANSGENIC, AND LIVE-CELL MICROSCOPY TECHNOLOGIES", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "faf21085058fec0c82e83e732632cc45", "status": "released", "aliases": ["belmont-lab:HCT116_1216_2XDTT_IAA_DDX39B_Pulldown_bio1_AGTTCC_L002_R1_001.fastq"], "filename": "HCT116_1216_2XDTT_IAA_DDX39B_Pulldown_bio1_AGTTCC_L002_R1_001.fastq.gz", "accession": "4DNFIWWY8GNU", "file_size": 3060258933, "file_type": "reads", "instrument": "NovaSeq6000", "file_format": {"status": "released", "display_title": "fastq", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "read_length": 100, "date_created": "2024-12-19T19:27:47.704077+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-09-05T17:24:29.871829+00:00"}, "content_md5sum": "fa261f8c3d29572a103195999c619a0e", "public_release": "2025-08-27", "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIWWY8GNU/fastqc_report.html", "Total Sequences": 71752921, "@id": "/quality-metrics-fastqc/75ff1a51-a228-46ac-8f08-6f583dc63a3b/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "75ff1a51-a228-46ac-8f08-6f583dc63a3b", "display_title": "QualityMetricFastqc from 2024-12-23", "status": "released", "Sequence length": "100", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "2", "file_first_line": "@LH00285:109:22N322LT3:2:1101:3025:1016 1:N:0:AGTTCC", "project_release": "2025-08-27", "flowcell_details": [{"barcode": "AGTTCC", "machine": "NovaSeq6000"}], "file_classification": "raw file", "@id": "/files-fastq/4DNFIWWY8GNU/", "@type": ["FileFastq", "File", "Item"], "uuid": "8c4a2515-5c03-45dd-af3e-d6969d44ae9f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIWWY8GNU.fastq.gz", "external_references": [], "experiments": [{"@type": ["ExperimentTsaseq", "Experiment", "Item"], "display_title": "TSA-seq against DDX39B protein on HCT116 (Tier 2) - 4DNEXK1UBWZO", "status": "released", "@id": "/experiments-tsaseq/4DNEXK1UBWZO/", "uuid": "5fb79b0c-fe5b-4bcd-8d1b-19c66e475cf8", "accession": "4DNEXK1UBWZO", "biosample": {"display_title": "4DNBSPK4WZYH", "@id": "/biosamples/4DNBSPK4WZYH/", "@type": ["Biosample", "Item"], "status": "released", "biosource_summary": "HCT116 (Tier 2)", "accession": "4DNBSPK4WZYH", "treatments_summary": "5PhIAA treatment (5.0 \u03bcM, 4.0h at 37.0\u00b0C)", "uuid": "4f2f75a2-e1ba-409c-851c-a3c5f47d2504", "modifications_summary": "Crispr insertion for SON gene and Crispr insertion for SRRM2 gene", "biosource": [{"cell_line_tier": "Tier 2", "@id": "/biosources/4DNSRMYUIVGD/", "display_title": "HCT116 (Tier 2) - 4DNSRMYUIVGD", "uuid": "393880ea-f928-406d-a4bf-78435b8975ef", "biosource_type": "immortalized cell line", "@type": ["Biosource", "Item"], "status": "released", "cell_line": {"@type": ["OntologyTerm", "Item"], "uuid": "49d090b2-5326-40ce-9c19-7a214c682272", "display_title": "HCT116", "@id": "/ontology-terms/EFO:0002824/", "term_id": "EFO:0002824", "preferred_name": "HCT116", "term_name": "HCT116", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "modifications": [], "tissue": {"@type": ["OntologyTerm", "Item"], "preferred_name": "colon", "term_name": "colon", "uuid": "3e39f551-bc0b-4bee-b932-29d71956fb94", "display_title": "colon", "term_id": "UBERON:0001155", "status": "released", "@id": "/ontology-terms/UBERON:0001155/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"scientific_name": "Homo sapiens", "@id": "/organisms/9606/", "@type": ["Organism", "Item"], "name": "human", "status": "released", "display_title": "H. sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@id": "/individuals-human/4DNINJ6WV6L1/", "@type": ["IndividualHuman", "Individual", "Item"], "status": "released", "display_title": "4DNINJ6WV6L1", "protected_data": false, "uuid": "1f0f0999-c5b4-430e-8650-8ebb3491d699", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "cell_culture_details": [{"status": "released", "@type": ["BiosampleCellCulture", "Item"], "uuid": "e0467db5-8966-4180-9db2-ff215fe4c9a7", "@id": "/biosample-cell-cultures/e0467db5-8966-4180-9db2-ff215fe4c9a7/", "display_title": "BiosampleCellCulture from 2024-12-19", "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "experiment_sets": [{"display_title": "4DNESKJXCQMF", "status": "released", "@id": "/experiment-set-replicates/4DNESKJXCQMF/", "experimentset_type": "replicate", "uuid": "415b5916-7a96-4411-99ed-ddd7e6afd91d", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "accession": "4DNESKJXCQMF", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "last_modified": {"date_modified": "2025-08-27T18:27:52.477759+00:00"}, "experiment_type": {"uuid": "75d7181c-e329-463e-b776-a467433aa4db", "@id": "/experiment-types/tsa-seq/", "title": "TSA-seq", "status": "released", "display_title": "TSA-seq", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "file_type_detailed": "reads (fastq)", "track_and_facet_info": {"experimental_lab": "Andrew Belmont, ILLINOIS", "experiment_type": "TSA-seq", "experiment_bucket": "raw file", "assay_info": "DDX39B protein", "dataset": "TSA-seq v2 DDX39B in HCT116 SON SRRM2 double degron cells", "condition": "condition3primeenhancementG-anti-DDX39B_Auxin", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Andrew Belmont, ILLINOIS"}, "title": "4DNFIWWY8GNU", "href": "/files-fastq/4DNFIWWY8GNU/@@download/4DNFIWWY8GNU.fastq.gz", "upload_key": "8c4a2515-5c03-45dd-af3e-d6969d44ae9f/4DNFIWWY8GNU.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/8c4a2515-5c03-45dd-af3e-d6969d44ae9f/4DNFIWWY8GNU.fastq.gz", "tsv_notes": "", "workflow_run_inputs": [{"@id": "/workflow-runs-awsem/a97f7964-b104-4449-8532-0f711e4df6fa/", "display_title": "md5 0.2.6 run 2024-12-23 17:28:19.942664", "status": "released", "uuid": "a97f7964-b104-4449-8532-0f711e4df6fa", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "report"}], "input_files": [{"workflow_argument_name": "input_file", "value": {"uuid": "8c4a2515-5c03-45dd-af3e-d6969d44ae9f", "@id": "/files-fastq/4DNFIWWY8GNU/", "accession": "4DNFIWWY8GNU", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIWWY8GNU.fastq.gz", "status": "released", "filename": "HCT116_1216_2XDTT_IAA_DDX39B_Pulldown_bio1_AGTTCC_L002_R1_001.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "workflow": {"uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "display_title": "md5 0.2.6 - 4DNWF2HFF82B", "@type": ["Workflow", "Item"], "@id": "/workflows/4DNWF2HFF82B/", "title": "md5 0.2.6", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/workflow-runs-awsem/b89bc349-9bc2-49b8-848c-ed8d0ed43a88/", "display_title": "fastq-first-line v2 run 2024-12-23 17:46:38.385816", "status": "released", "uuid": "b89bc349-9bc2-49b8-848c-ed8d0ed43a88", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "first_line"}], "input_files": [{"workflow_argument_name": "fastq", "value": {"uuid": "8c4a2515-5c03-45dd-af3e-d6969d44ae9f", "@id": "/files-fastq/4DNFIWWY8GNU/", "accession": "4DNFIWWY8GNU", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIWWY8GNU.fastq.gz", "status": "released", "filename": "HCT116_1216_2XDTT_IAA_DDX39B_Pulldown_bio1_AGTTCC_L002_R1_001.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "workflow": {"uuid": "93a1a931-d55d-4623-adfb-0fa735daf6ae", "display_title": "Getting first line of fastq file - 4DNWFASTQFO1", "@type": ["Workflow", "Item"], "@id": "/workflows/4DNWFASTQFO1/", "title": "Getting first line of fastq file", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/workflow-runs-awsem/2470e22a-3364-4648-8760-364f4bba8b19/", "display_title": "fastqc v2 run 2024-12-23 18:07:05.336901", "status": "released", "uuid": "2470e22a-3364-4648-8760-364f4bba8b19", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "report_zip", "value_qc": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/75ff1a51-a228-46ac-8f08-6f583dc63a3b/", "uuid": "75ff1a51-a228-46ac-8f08-6f583dc63a3b", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIWWY8GNU/fastqc_report.html", "display_title": "QualityMetricFastqc from 2024-12-23", "overall_quality_status": "PASS", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "input_fastq", "value": {"uuid": "8c4a2515-5c03-45dd-af3e-d6969d44ae9f", "@id": "/files-fastq/4DNFIWWY8GNU/", "accession": "4DNFIWWY8GNU", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIWWY8GNU.fastq.gz", "status": "released", "filename": "HCT116_1216_2XDTT_IAA_DDX39B_Pulldown_bio1_AGTTCC_L002_R1_001.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "workflow": {"uuid": "49e96b51-ed6c-4418-a693-d0e9f79adfa5", "display_title": "FastQC v2 - 4DNWFAEU2GB7", "@type": ["Workflow", "Item"], "@id": "/workflows/4DNWFAEU2GB7/", "title": "FastQC v2", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"error": "no view permissions"}], "workflow_run_outputs": [], "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}