{"lab": {"uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "display_title": "David Gilbert, SDBRI", "correspondence": [{"contact_email": "Z2lsYmVydEBzZGJyaS5vcmc=", "@id": "/users/1dbb8e49-38e4-4154-a97c-af8176a58c44/", "display_title": "David Gilbert"}], "@id": "/labs/david-gilbert-lab/", "title": "David Gilbert, SDBRI", "@type": ["Lab", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}, "pi": {"error": "no view permissions"}}, "award": {"status": "current", "center_title": "CDIMV - Ma", "uuid": "9f6d9e4a-9542-49c7-8a54-c6c9a1862d90", "@type": ["Award", "Item"], "project": "4DN", "@id": "/awards/1UM1HG011593-01/", "display_title": "MULTISCALE ANALYSES OF 4D NUCLEOME STRUCTURE AND FUNCTION BY COMPREHENSIVE MULTIMODAL DATA INTEGRATION", "description": "CDIMV: The cell nucleus is a heterogeneous organelle that consists of nuclear bodies such as nuclear lamina, speckles, nucleoli and PML bodies. These structures continuously tether and tug chromatin at the small and large scales to synergistically orchestrate dynamic functions in distinct spatio-temporal compartments. A major obstacle to the production of navigable 4D reference maps and relating structure to function in the nucleus remains understanding how these different scales of organization influence each other. In particular, we have a poor understanding of the large-scale genome organization. Growing evidence suggests that such nuclear compartmentalization is causally connected with vital genome functions in human health and disease. However, the principles of this nuclear compartmentalization, its dynamics during changes in cell conditions, and its functional relevance are poorly understood. One lesson from Phase 1 4DN was the huge gap in throughput between imaging methods, that directly measure large-scale multi-landmark relationships, and genomic methods, that aim for whole genome high-resolution maps but are indirect measurements and provide limited information about large-scale compartments. For this 4DN UM1 Center application, we propose to meet these needs through the following Aims: (1) Generate multi-modal imaging and genomic datasets to reveal the structure, dynamics, and function of nuclear compartmentalization; (2) Develop and apply computational tools for data-driven genome structure modeling and integrative analysis of nuclear compartmentalization; (3) Develop an integrative analysis and visualization platform with navigable 4D reference maps of nuclear organization. The combined datasets and results of our proposed approaches will advance our understanding of nuclear compartmentalization, the interwoven connections among different nuclear components, and their functional significance. Our new integrative analysis tools and data-driven predictive models will produce more complete nuclear organization reference maps that integrate large-scale chromosome structure data from live and super-resolution microscopy with multi-modal genomic data including smaller scale chromatin interaction maps and predict functional relationships and dynamic responses. Our navigable reference maps will be publicly accessible through an analysis platform that provides interactive visualization of multiple data types, thus enabling investigators with diverse expertise to simultaneously explore their own data and related datasets/tools and promoting collaborations that will open new horizons into the role of the 4D nucleome in human health and disease.", "name": "1UM1HG011593-01", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "45c602097b213d89f003e64c24e9715e", "status": "released", "aliases": ["gilbert-lab:HCT116-Rad21-KD-IZ"], "filename": "HCT116_Rad21KD_mito_norm.txt", "accession": "4DNFIGOMS9G7", "file_size": 40643, "file_type": "initiation zones", "description": "Group 3 Initiation zones called from HCT116 Rad21 KD read depth normalized down sampled array", "file_format": {"file_format": "txt", "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "display_title": "txt", "status": "released", "@id": "/file-formats/txt/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2021-11-02T08:15:14.867311+00:00", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-03-09T22:05:24.394522+00:00"}, "produced_from": ["gilbert-lab:HCT116-Rad21-KD-mitochondrial-normalised-repli-seq-array"], "content_md5sum": "45c602097b213d89f003e64c24e9715e", "public_release": "2021-11-10", "schema_version": "3", "genome_assembly": "GRCh38", "project_release": "2021-11-10", "override_dataset": "Multi-fraction Repliseq on HCT116", "contributing_labs": [{"@type": ["Lab", "Item"], "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "correspondence": [{"contact_email": "amNyZW1pbnNAc2Vhcy51cGVubi5lZHU=", "@id": "/users/8773d50c-1716-4153-9a18-d0f5ff2aa5ee/", "display_title": "Jennifer Phillips-Cremins"}], "display_title": "Jennifer Cremins, UPENN", "status": "current", "@id": "/labs/jennifer-cremins-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}, "pi": {"error": "no view permissions"}}], "override_condition": "CTCF depletion", "file_classification": "processed file", "override_biosource_name": "HCT116 with Crispr generated mClover and AID-tagged RAD21", "override_experiment_type": "Multi-stage Repli-seq", "@id": "/files-processed/4DNFIGOMS9G7/", "@type": ["FileProcessed", "File", "Item"], "uuid": "97de1968-f2b1-4a2d-b897-3f321d7b41a0", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIGOMS9G7.txt", "external_references": [], "experiments": [], "file_type_detailed": "initiation zones (txt)", "track_and_facet_info": {"experiment_type": "Multi-stage Repli-seq", "dataset": "Multi-fraction Repliseq on HCT116", "condition": "CTCF depletion", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged RAD21", "lab_name": "David Gilbert, SDBRI"}, "title": "4DNFIGOMS9G7", "href": "/files-processed/4DNFIGOMS9G7/@@download/4DNFIGOMS9G7.txt", "upload_key": "97de1968-f2b1-4a2d-b897-3f321d7b41a0/4DNFIGOMS9G7.txt", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/97de1968-f2b1-4a2d-b897-3f321d7b41a0/4DNFIGOMS9G7.txt", "tsv_notes": "This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available.", "workflow_run_inputs": [{"error": "no view permissions"}], "workflow_run_outputs": [], "experiment_sets": [{"display_title": "4DNES92AU9JR", "status": "released", "@id": "/experiment-sets/4DNES92AU9JR/", "uuid": "12403dc8-614f-4ff5-82f7-fd9def786894", "@type": ["ExperimentSet", "Item"], "accession": "4DNES92AU9JR", "last_modified": {"date_modified": "2023-10-04T20:04:37.285130+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "source_experiment_sets": [{"status": "released", "uuid": "12403dc8-614f-4ff5-82f7-fd9def786894", "@id": "/experiment-sets/4DNES92AU9JR/", "@type": ["ExperimentSet", "Item"], "display_title": "4DNES92AU9JR", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiment-sets/4DNES92AU9JR/", "embedded_path": "experiment_sets.last_modified", "item": {"date_modified": "2023-10-04T20:04:37.285130+00:00"}}, {"parent": "/files-processed/4DNFIGOMS9G7/", "embedded_path": "last_modified", "item": {"date_modified": "2022-03-09T22:05:24.394522+00:00"}}]}, "validation-errors": []}