{"lab": {"@type": ["Lab", "Item"], "uuid": "312cb909-76a6-405d-a96c-c3292abf08a1", "status": "current", "@id": "/labs/alistair-boettiger-lab/", "correspondence": [{"contact_email": "YWJvZXR0aWdAc3RhbmZvcmQuZWR1", "@id": "/users/b8835c78-05e3-4173-a6c5-1ab93b4d12cc/", "display_title": "Alistair Boettiger"}], "title": "Alistair Boettiger, STANFORD", "display_title": "Alistair Boettiger, STANFORD", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.312cb909-76a6-405d-a96c-c3292abf08a1"]}}, "award": {"project": "External", "description": "Funding source is from outside 4DN.", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "display_title": "EXTERNAL AWARD", "name": "external-award", "center": "External", "status": "current", "@type": ["Award", "Item"], "center_title": "External", "@id": "/awards/external-award/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "51915218ce73494f6524902cff671354", "status": "released", "aliases": ["alistair-boettiger-lab:fileproc_A549_2-Mb_28-30_B1_T1_f1"], "filename": "coreTable_A549_chr21_28_30Mb.csv", "accession": "4DNFIGLYJRQJ", "file_size": 12858977, "file_type": "FOF-CT - DNA-spot/trace core", "file_format": {"file_format": "csv", "@id": "/file-formats/csv/", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "display_title": "csv", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2022-09-02T10:47:56.882079+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-01-03T21:45:45.224976+00:00"}, "content_md5sum": "51915218ce73494f6524902cff671354", "public_release": "2022-10-20", "schema_version": "3", "static_headers": [{"lab": {"status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "Processed files in this dataset are provided in the 4DN standard FISH-Omics Format - Chromatin Tracing (FOF-CT).\n\nThis is a collection of tabular files, consisting of several tables.\nThe DNA-spot/trace core table is organized around individual DNA bright Spots that are spatially linked together in a three-dimensional (3D) polymeric Trace.\nAdditional optional tables can complement this information and vary according to the specific dataset. \n\nThe full documentation is available here: https://fish-omics-format.readthedocs.io/", "name": "fof-ct.note", "award": {"status": "current", "@id": "/awards/2U01CA200059-06/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "@type": ["Award", "Item"], "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Note on FOF-CT file format", "status": "released", "aliases": ["4dn-dcic-lab:fof_ct_note"], "options": {"filetype": "md", "collapsible": true, "default_open": false}, "date_created": "2022-03-07T18:23:27.469177+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-03-08T14:28:37.893086+00:00"}, "schema_version": "2", "@id": "/static-sections/a09a2833-b56b-4e81-8eff-bb8ae6aaa596/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "a09a2833-b56b-4e81-8eff-bb8ae6aaa596", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.e4a22298-1da4-4e59-8a65-9e661f47fb48"]}, "display_title": "Note on FOF-CT file format", "external_references": [], "content": "Processed files in this dataset are provided in the 4DN standard FISH-Omics Format - Chromatin Tracing (FOF-CT).\n\nThis is a collection of tabular files, consisting of several tables.\nThe DNA-spot/trace core table is organized around individual DNA bright Spots that are spatially linked together in a three-dimensional (3D) polymeric Trace.\nAdditional optional tables can complement this information and vary according to the specific dataset. \n\nThe full documentation is available here: https://fish-omics-format.readthedocs.io/", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p>Processed files in this dataset are provided in the 4DN standard FISH-Omics Format - Chromatin Tracing (FOF-CT).</p>\n<p>This is a collection of tabular files, consisting of several tables.\nThe DNA-spot/trace core table is organized around individual DNA bright Spots that are spatially linked together in a three-dimensional (3D) polymeric Trace.\nAdditional optional tables can complement this information and vary according to the specific dataset. </p>\n<p>The full documentation is available here: https://fish-omics-format.readthedocs.io/</p></div>"}], "genome_assembly": "GRCh38", "project_release": "2022-10-20", "contributing_labs": [{"@type": ["Lab", "Item"], "uuid": "eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb", "correspondence": [{"contact_email": "emh1YW5nQGNoZW1pc3RyeS5oYXJ2YXJkLmVkdQ==", "@id": "/users/acfc5a08-19ff-47ef-9261-75e6134dc0fe/", "display_title": "Xiaowei Zhuang"}], "@id": "/labs/xiaowei-zhuang-lab/", "display_title": "Xiaowei Zhuang, HARVARD", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb"]}}], "file_classification": "processed file", "@id": "/files-processed/4DNFIGLYJRQJ/", "@type": ["FileProcessed", "File", "Item"], "uuid": "0593b358-23b4-4320-ad7e-e8c26783f612", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIGLYJRQJ.csv", "external_references": [], "experiments": [{"accession": "4DNEX46ABFUV", "@id": "/experiments-mic/4DNEX46ABFUV/", "@type": ["ExperimentMic", "Experiment", "Item"], "uuid": "c7ece6b4-cf03-4717-9e85-490ffd4cc0e0", "status": "released", "display_title": "multiplexed FISH on A549 - 4DNEX46ABFUV", "experiment_sets": [{"experimentset_type": "replicate", "display_title": "4DNESL619Z5V", "accession": "4DNESL619Z5V", "status": "released", "uuid": "3415c620-9789-47f6-9c88-5cb2648748e8", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNESL619Z5V/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosample": {"accession": "4DNBST1RIXZA", "modifications_summary": "None", "@id": "/biosamples/4DNBST1RIXZA/", "status": "released", "uuid": "c8c14269-6d8d-46c5-9fc5-abca37b468f5", "@type": ["Biosample", "Item"], "treatments_summary": "None", "biosource_summary": "A549", "display_title": "4DNBST1RIXZA", "biosource": [{"cell_line_tier": "Unclassified", "biosource_type": "immortalized cell line", "display_title": "A549 - 4DNSRFLY6T15", "@type": ["Biosource", "Item"], "status": "released", "uuid": "044733e7-db6c-412c-b1c3-eb77c811dd3e", "@id": "/biosources/4DNSRFLY6T15/", "cell_line": {"@id": "/ontology-terms/EFO:0001086/", "term_name": "A549", "preferred_name": "A549", "term_id": "EFO:0001086", "@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "A549", "uuid": "2fea36d1-69bd-4039-8c58-a5d9bf6bcdad", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "modifications": [], "organism": {"name": "human", "scientific_name": "Homo sapiens", "@type": ["Organism", "Item"], "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "status": "released", "display_title": "H. sapiens", "@id": "/organisms/9606/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"protected_data": false, "@type": ["IndividualHuman", "Individual", "Item"], "display_title": "4DNINRY29RK2", "status": "released", "uuid": "6db764c0-14fd-4ffb-966a-3f0e3412207f", "@id": "/individuals-human/4DNINRY29RK2/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"display_title": "lung", "@id": "/ontology-terms/UBERON:0002048/", "preferred_name": "lung", "status": "released", "term_name": "lung", "uuid": "111186bc-8535-4448-903e-854af460a233", "term_id": "UBERON:0002048", "@type": ["OntologyTerm", "Item"], "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": "bcdda46a-489d-4d22-be80-c9c21552c915", "@type": ["ExperimentType", "Item"], "@id": "/experiment-types/multiplexed-fish/", "title": "multiplexed FISH", "status": "released", "display_title": "multiplexed FISH", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2025-06-16T18:43:43.854844+00:00"}}], "file_type_detailed": "FOF-CT - DNA-spot/trace core (csv)", "track_and_facet_info": {"experimental_lab": "Alistair Boettiger, STANFORD", "experiment_type": "multiplexed FISH", "experiment_bucket": "processed file", "assay_info": "65 consecutive 30-kb loci on chr21", "dataset": "Chromatin tracing of 2-Mb on chr21", "condition": "Chr21:28-30 Mb in A549 cells", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "A549", "lab_name": "Alistair Boettiger, STANFORD"}, "title": "4DNFIGLYJRQJ", "href": "/files-processed/4DNFIGLYJRQJ/@@download/4DNFIGLYJRQJ.csv", "upload_key": "0593b358-23b4-4320-ad7e-e8c26783f612/4DNFIGLYJRQJ.csv", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/0593b358-23b4-4320-ad7e-e8c26783f612/4DNFIGLYJRQJ.csv", "tsv_notes": "", "workflow_run_inputs": [{"status": "released", "@id": "/workflow-runs-awsem/3b2f0503-8b12-49db-8b00-88bd8445cbe4/", "uuid": "3b2f0503-8b12-49db-8b00-88bd8445cbe4", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "display_title": "md5 0.2.6 run 2022-10-03 07:26:36.204388", "output_files": [{"workflow_argument_name": "report"}], "input_files": [{"workflow_argument_name": "input_file", "value": {"accession": "4DNFIGLYJRQJ", "status": "released", "uuid": "0593b358-23b4-4320-ad7e-e8c26783f612", "display_title": "4DNFIGLYJRQJ.csv", "filename": "coreTable_A549_chr21_28_30Mb.csv", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIGLYJRQJ/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "csv", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@id": "/file-formats/csv/", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "workflow": {"status": "released", "@id": "/workflows/4DNWF2HFF82B/", "uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "display_title": "md5 0.2.6 - 4DNWF2HFF82B", "@type": ["Workflow", "Item"], "title": "md5 0.2.6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [], "experiment_sets": [], "source_experiment_sets": [{"display_title": "4DNESL619Z5V", "@id": "/experiment-set-replicates/4DNESL619Z5V/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "3415c620-9789-47f6-9c88-5cb2648748e8", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-mic/4DNEX46ABFUV/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2025-06-16T18:43:43.854844+00:00"}}, {"parent": "/files-processed/4DNFIGLYJRQJ/", "embedded_path": "last_modified", "item": {"date_modified": "2023-01-03T21:45:45.224976+00:00"}}, {"parent": "/static-sections/a09a2833-b56b-4e81-8eff-bb8ae6aaa596/", "embedded_path": "static_headers.last_modified", "item": {"date_modified": "2022-03-08T14:28:37.893086+00:00"}}]}, "validation-errors": []}