{"lab": {"uuid": "795847de-20b6-4f8c-ba8d-185215469cbf", "@type": ["Lab", "Item"], "status": "current", "correspondence": [{"contact_email": "YmlyZW5AdWNzZC5lZHU=", "@id": "/users/e3159ffc-a5a9-43a1-8cfa-90b776c39788/", "display_title": "Bing Ren"}], "display_title": "Bing Ren, UCSD", "@id": "/labs/bing-ren-lab/", "title": "Bing Ren, UCSD", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.795847de-20b6-4f8c-ba8d-185215469cbf"]}}, "award": {"name": "1UM1HG011585-01", "description": "CDIMV: The transcriptional regulatory sequences communicate with each other dynamically in the 3D nuclear space to direct cell type specific gene expression. Currently, a major barrier to understanding the transcriptional regulatory programs is the lack of tools, models and maps to explore the chromatin architecture in diverse cell types and physiological contexts. We will address this pressing need by deploying transformative technologies to study the chromatin architecture in mammalian cells at an unprecedented resolution and scale. Specifically, we will generate navigable, cell-type-specific reference maps of chromatin architecture in the mouse, macaque and human brains by integrating high resolution and high throughput imaging and orthogonal single-cell-based genomic methods. We will also dissect the role of chromatin architecture in gene regulation through a set of controlled perturbation experiments in the mouse ES cells (ESC) and ESC-derived neural progenitor cells (NPC). We will develop structural models of chromatin organization with advanced polymer physics and statistical learning methods, and validate their predictive power in embryonic stem cells and in ex vivo brain slices. Finally, we will make the reference maps, analytical tools, visualization methods and structural models available to the broader community. The proposed research project will dramatically transform our ability to analyze the 4D Nucleome of complex tissues, and produce the much-needed maps, tools and models for understanding the gene regulatory programs encoded in the linear genome sequences.", "@id": "/awards/1UM1HG011585-01/", "display_title": "CENTER FOR INTEGRATED MULTI-MODAL AND MULTI-SCALE NUCLEOME RESEARCH", "status": "current", "uuid": "ee89349a-1d43-4048-9142-bc750f0f3b32", "project": "4DN", "center_title": "CDIMV - Ren", "@type": ["Award", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "a873bb24b61f9546cc0e41a364cbf97f", "status": "released", "aliases": ["bing-ren-lab:fileproc_chromtracing_reanalysis_brain_B1_T1_core_1mb_f1"], "filename": "mbrain_1_Ex_1mb_spaligned_FINAL.csv", "accession": "4DNFIYNWVJEP", "file_size": 28940727, "file_type": "FOF-CT - DNA-spot/trace core", "description": "DNA-Spot/Trace Data core table obtained form Bing Ren's lab by re-processing with a spatial genome aligner the previously published whole-genome chromosome tracing data at 1-Mb resolution in mouse brain (replicate 1) from Long Cai's lab - NOTE: This analysis includes only fully-segmented excitatory neurons, discarding all other cells", "file_format": {"file_format": "csv", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "csv", "@id": "/file-formats/csv/", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2022-09-01T13:58:11.326396+00:00", "notes_to_tsv": ["This file includes only fully-segmented excitatory neurons. ", "Only Trace_ID is changed (FOV_cell_chrom_tracenumber), all other columns are retained from original dataset"], "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-01-03T21:58:51.206496+00:00"}, "produced_from": ["4DNFI4JGAIHP"], "content_md5sum": "a873bb24b61f9546cc0e41a364cbf97f", "public_release": "2022-09-20", "schema_version": "3", "genome_assembly": "GRCm38", "project_release": "2022-09-20", "contributing_labs": [{"correspondence": [{"contact_email": "bGNhaUBjYWx0ZWNoLmVkdQ==", "@id": "/users/5b7ed4cb-4848-4eee-9dd5-75edde523b0f/", "display_title": "Long Cai"}], "uuid": "6384bbb3-d82f-4584-8a6a-4b4e7c988d14", "display_title": "Long Cai, CALTECH", "@type": ["Lab", "Item"], "status": "current", "@id": "/labs/long-cai-lab/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6384bbb3-d82f-4584-8a6a-4b4e7c988d14"]}}], "file_classification": "processed file", "@id": "/files-processed/4DNFIYNWVJEP/", "@type": ["FileProcessed", "File", "Item"], "uuid": "fbc6c480-96a1-479c-a038-ffe5d11604a0", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIYNWVJEP.csv", "external_references": [], "experiments": [{"status": "released", "uuid": "59fa8ecd-0748-451b-976b-911cf7928de4", "@type": ["ExperimentMic", "Experiment", "Item"], "accession": "4DNEXWI45RB4", "@id": "/experiments-mic/4DNEXWI45RB4/", "display_title": "multiplexed FISH on cerebral cortex - 4DNEXWI45RB4", "biosample": {"uuid": "3d17adea-b3a2-42b7-9fcc-15410e2dddda", "display_title": "4DNBSTWADCJS", "treatments_summary": "None", "accession": "4DNBSTWADCJS", "status": "released", "modifications_summary": "None", "biosource_summary": "cerebral cortex", "@id": "/biosamples/4DNBSTWADCJS/", "@type": ["Biosample", "Item"], "biosource": [{"display_title": "cerebral cortex - 4DNSR9Q964EF", "@id": "/biosources/4DNSR9Q964EF/", "cell_line_tier": "Unclassified", "uuid": "224cf207-98a5-4b28-b541-5a99b479a392", "biosource_type": "tissue", "status": "released", "@type": ["Biosource", "Item"], "tissue": {"uuid": "ca9e9160-1aaf-41ec-94da-3070e14a7a46", "term_name": "cerebral cortex", "preferred_name": "cerebral cortex", "term_id": "UBERON:0000956", "@id": "/ontology-terms/UBERON:0000956/", "@type": ["OntologyTerm", "Item"], "display_title": "cerebral cortex", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@type": ["IndividualMouse", "Individual", "Item"], "uuid": "69fd64a1-191b-4ba9-8a68-4b401374deee", "@id": "/individuals-mouse/4DNINZFHQKIV/", "display_title": "4DNINZFHQKIV", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"status": "released", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "display_title": "M. musculus", "scientific_name": "Mus musculus", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "name": "mouse", "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": {"display_title": "multiplexed FISH", "@type": ["ExperimentType", "Item"], "uuid": "bcdda46a-489d-4d22-be80-c9c21552c915", "status": "released", "@id": "/experiment-types/multiplexed-fish/", "title": "multiplexed FISH", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"accession": "4DNES53WJMNL", "display_title": "4DNES53WJMNL", "@id": "/experiment-set-replicates/4DNES53WJMNL/", "experimentset_type": "replicate", "uuid": "497d7102-4fcd-4788-b41d-f3577c74ab59", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2025-06-16T18:58:47.674260+00:00"}}], "file_type_detailed": "FOF-CT - DNA-spot/trace core (csv)", "track_and_facet_info": {"experimental_lab": "Long Cai, CALTECH", "experiment_type": "multiplexed FISH", "experiment_bucket": "Data re-processed with spatial genome aligner (Ren lab)", "assay_info": "78 RNAs (mouse), 8 genomic regions, 8 proteins, Chromosomes", "dataset": "Chromatin tracing in mouse brain", "condition": "Mouse cerebral cortex", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "cerebral cortex", "lab_name": "Bing Ren, UCSD"}, "title": "4DNFIYNWVJEP", "href": "/files-processed/4DNFIYNWVJEP/@@download/4DNFIYNWVJEP.csv", "upload_key": "fbc6c480-96a1-479c-a038-ffe5d11604a0/4DNFIYNWVJEP.csv", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/fbc6c480-96a1-479c-a038-ffe5d11604a0/4DNFIYNWVJEP.csv", "tsv_notes": "This file includes only fully-segmented excitatory neurons. ,Only Trace_ID is changed (FOV_cell_chrom_tracenumber), all other columns are retained from original dataset", "workflow_run_inputs": [{"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "status": "released", "display_title": "md5 0.2.6 run 2022-09-01 14:26:53.816451", "uuid": "1af3b6d8-8833-46b3-ba7d-481d3ae2a367", "@id": "/workflow-runs-awsem/1af3b6d8-8833-46b3-ba7d-481d3ae2a367/", "output_files": [{"workflow_argument_name": "report"}], "input_files": [{"workflow_argument_name": "input_file", "value": {"uuid": "fbc6c480-96a1-479c-a038-ffe5d11604a0", "accession": "4DNFIYNWVJEP", "display_title": "4DNFIYNWVJEP.csv", "@id": "/files-processed/4DNFIYNWVJEP/", "filename": "mbrain_1_Ex_1mb_spaligned_FINAL.csv", "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "file_format": "csv", "@id": "/file-formats/csv/", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@id": "/workflows/4DNWF2HFF82B/", "display_title": "md5 0.2.6 - 4DNWF2HFF82B", "status": "released", "uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "title": "md5 0.2.6", "@type": ["Workflow", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [{"display_title": "File Provenance Tracking Workflow run on 2022-09-05 10:51:57.914996", "status": "released", "uuid": "9e13c510-ce43-45ed-aecb-1e1fbf7da1be", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/9e13c510-ce43-45ed-aecb-1e1fbf7da1be/", "output_files": [{"workflow_argument_name": "outputs", "value": {"@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIYNWVJEP.csv", "accession": "4DNFIYNWVJEP", "@id": "/files-processed/4DNFIYNWVJEP/", "uuid": "fbc6c480-96a1-479c-a038-ffe5d11604a0", "status": "released", "file_format": {"file_format": "csv", "display_title": "csv", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/csv/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "inputs", "value": {"@id": "/files-processed/4DNFI4JGAIHP/", "display_title": "4DNFI4JGAIHP.csv", "status": "released", "uuid": "af67b4c4-449a-45ca-a782-eafaa6686597", "filename": "4dn_FOF-CT_core_brain_replicate1_1Mb.csv", "accession": "4DNFI4JGAIHP", "@type": ["FileProcessed", "File", "Item"], "file_format": {"status": "released", "display_title": "csv", "@type": ["FileFormat", "Item"], "@id": "/file-formats/csv/", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "file_format": "csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"title": "File Provenance Tracking Workflow", "uuid": "bef50397-4d72-4ed1-9c78-100e14e5c47f", "@id": "/workflows/4DNWFBFZYHIE/", "display_title": "File Provenance Tracking Workflow - 4DNWFBFZYHIE", "@type": ["Workflow", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_sets": [], "source_experiment_sets": [{"display_title": "4DNES53WJMNL", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "status": "released", "uuid": "497d7102-4fcd-4788-b41d-f3577c74ab59", "@id": "/experiment-set-replicates/4DNES53WJMNL/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-mic/4DNEXWI45RB4/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2025-06-16T18:58:47.674260+00:00"}}, {"parent": "/files-processed/4DNFIYNWVJEP/", "embedded_path": "last_modified", "item": {"date_modified": "2023-01-03T21:58:51.206496+00:00"}}]}, "validation-errors": []}