{"lab": {"display_title": "Alistair Boettiger, STANFORD", "title": "Alistair Boettiger, STANFORD", "uuid": "312cb909-76a6-405d-a96c-c3292abf08a1", "@type": ["Lab", "Item"], "@id": "/labs/alistair-boettiger-lab/", "status": "current", "correspondence": [{"contact_email": "YWJvZXR0aWdAc3RhbmZvcmQuZWR1", "@id": "/users/b8835c78-05e3-4173-a6c5-1ab93b4d12cc/", "display_title": "Alistair Boettiger"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.312cb909-76a6-405d-a96c-c3292abf08a1"]}}, "award": {"uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "center_title": "External", "@id": "/awards/external-award/", "@type": ["Award", "Item"], "name": "external-award", "project": "External", "center": "External", "description": "Funding source is from outside 4DN.", "display_title": "EXTERNAL AWARD", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "95277465bbe083a22cb7362ee8264874", "status": "released", "aliases": ["alistair-boettiger-lab:fileproc_BXC3kb_B1_T1_quality_f1"], "filename": "BXC3kb_dm6_rep1_qualityTable.csv", "accession": "4DNFIX2T16SV", "file_size": 10103782, "file_type": "FOF-CT - spot quality", "file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "display_title": "csv", "status": "released", "file_format": "csv", "@id": "/file-formats/csv/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2022-05-20T08:50:31.239637+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-06-21T18:53:43.343294+00:00"}, "content_md5sum": "95277465bbe083a22cb7362ee8264874", "public_release": "2023-03-15", "schema_version": "3", "static_headers": [{"lab": {"@id": "/labs/4dn-dcic-lab/", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "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": {"display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "@id": "/awards/2U01CA200059-06/", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "status": "current", "@type": ["Award", "Item"], "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": "dm6", "project_release": "2023-03-15", "file_classification": "processed file", "@id": "/files-processed/4DNFIX2T16SV/", "@type": ["FileProcessed", "File", "Item"], "uuid": "0b8d974e-9ca5-491b-9039-fd07103e01a4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIX2T16SV.csv", "external_references": [], "experiments": [{"@type": ["ExperimentMic", "Experiment", "Item"], "uuid": "2bfbf2a4-4d78-4de5-bc26-b19f8b3916e6", "accession": "4DNEXCHTPTO2", "@id": "/experiments-mic/4DNEXCHTPTO2/", "display_title": "multiplexed FISH on embryo - 4DNEXCHTPTO2", "status": "released", "biosample": {"modifications_summary": "None", "@type": ["Biosample", "Item"], "status": "released", "display_title": "4DNBSA3C6NUK", "treatments_summary": "None", "uuid": "333c1618-b3ce-4e90-929a-ac0d4a761120", "biosource_summary": "embryo", "@id": "/biosamples/4DNBSA3C6NUK/", "accession": "4DNBSA3C6NUK", "biosource": [{"uuid": "742ef336-6e8c-4e91-bb21-83aa49508180", "display_title": "embryo - 4DNSR13C9VV1", "@type": ["Biosource", "Item"], "biosource_type": "tissue", "cell_line_tier": "Unclassified", "status": "released", "@id": "/biosources/4DNSR13C9VV1/", "tissue": {"@id": "/ontology-terms/UBERON:0000922/", "preferred_name": "embryo", "term_id": "UBERON:0000922", "term_name": "embryo", "uuid": "94a7d7e3-b38e-462a-91e6-55df4a2c120f", "display_title": "embryo", "status": "released", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/7227/", "name": "fruit fly", "scientific_name": "Drosophila melanogaster", "uuid": "b3911449-1b28-44cf-af23-084ae4eff147", "status": "released", "@type": ["Organism", "Item"], "display_title": "D. melanogaster", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"display_title": "4DNIN5IU82K5", "@type": ["IndividualFly", "Individual", "Item"], "status": "released", "uuid": "f7f60690-0ad2-435a-9cd3-a0bd9de4cd96", "@id": "/individuals-fly/4DNIN5IU82K5/", "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", "status": "released", "@id": "/experiment-types/multiplexed-fish/", "uuid": "bcdda46a-489d-4d22-be80-c9c21552c915", "@type": ["ExperimentType", "Item"], "title": "multiplexed FISH", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"experimentset_type": "replicate", "uuid": "9ebc668e-95db-4dbf-8468-dbd81a364fce", "status": "released", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNESMH5QM1S/", "display_title": "4DNESMH5QM1S", "accession": "4DNESMH5QM1S", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-03-15T15:22:26.311710+00:00"}}], "file_type_detailed": "FOF-CT - spot quality (csv)", "track_and_facet_info": {"experimental_lab": "Alistair Boettiger, STANFORD", "experiment_type": "multiplexed FISH", "experiment_bucket": "processed file", "assay_info": "29 mRNAs and nascent RNAs (fruit fly), 52 consecutive 3-kb loci in the BX-C region (fruit fly)", "dataset": "Chromatin tracing of BX-C in Drosophila", "condition": "Wild type, 3-kb resolution", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "embryo", "lab_name": "Alistair Boettiger, STANFORD"}, "title": "4DNFIX2T16SV", "href": "/files-processed/4DNFIX2T16SV/@@download/4DNFIX2T16SV.csv", "upload_key": "0b8d974e-9ca5-491b-9039-fd07103e01a4/4DNFIX2T16SV.csv", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/0b8d974e-9ca5-491b-9039-fd07103e01a4/4DNFIX2T16SV.csv", "tsv_notes": "", "workflow_run_inputs": [{"@id": "/workflow-runs-awsem/2caeb15e-d9be-4b0c-8bb8-7aef968ed79e/", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "status": "released", "display_title": "md5 0.2.6 run 2023-03-14 18:28:38.118245", "uuid": "2caeb15e-d9be-4b0c-8bb8-7aef968ed79e", "output_files": [{"workflow_argument_name": "report"}], "workflow": {"uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "display_title": "md5 0.2.6 - 4DNWF2HFF82B", "title": "md5 0.2.6", "@type": ["Workflow", "Item"], "status": "released", "@id": "/workflows/4DNWF2HFF82B/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "input_files": [{"workflow_argument_name": "input_file", "value": {"@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIX2T16SV", "status": "released", "@id": "/files-processed/4DNFIX2T16SV/", "uuid": "0b8d974e-9ca5-491b-9039-fd07103e01a4", "display_title": "4DNFIX2T16SV.csv", "filename": "BXC3kb_dm6_rep1_qualityTable.csv", "file_format": {"display_title": "csv", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "file_format": "csv", "@id": "/file-formats/csv/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [], "experiment_sets": [], "source_experiment_sets": [{"@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNESMH5QM1S", "@id": "/experiment-set-replicates/4DNESMH5QM1S/", "status": "released", "uuid": "9ebc668e-95db-4dbf-8468-dbd81a364fce", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-mic/4DNEXCHTPTO2/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2023-03-15T15:22:26.311710+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"}}, {"parent": "/files-processed/4DNFIX2T16SV/", "embedded_path": "last_modified", "item": {"date_modified": "2023-06-21T18:53:43.343294+00:00"}}]}, "validation-errors": []}