{"lab": {"uuid": "8932f234-660e-4fad-b0a3-342dcc799438", "correspondence": [{"contact_email": "dHd1QGdlbmV0aWNzLm1lZC5oYXJ2YXJkLmVkdQ==", "@id": "/users/af7beabd-7452-4b15-bc84-3ba5f72521d5/", "display_title": "Chao-Ting Wu"}], "title": "Chao-Ting Wu, HARVARD", "display_title": "Chao-Ting Wu, HARVARD", "@type": ["Lab", "Item"], "status": "current", "@id": "/labs/chao-ting-wu-lab/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8932f234-660e-4fad-b0a3-342dcc799438"]}}, "award": {"center_title": "External", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "name": "external-award", "@id": "/awards/external-award/", "status": "current", "description": "Funding source is from outside 4DN.", "@type": ["Award", "Item"], "project": "External", "display_title": "EXTERNAL AWARD", "center": "External", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "496cedeb98987f0ce8505e087c5f9d70", "status": "released", "aliases": ["chao-ting-wu-lab:fileproc_oligostorm_B1_T1_f1"], "filename": "2017-08-03-19-34-25_Location-01.csv", "accession": "4DNFICP54S3V", "file_size": 27163226, "file_type": "localizations", "description": "The csv file contains a list of particle localizations from 1 nucleus, after drift correction, clustering and filtering were applied.", "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@id": "/file-formats/csv/", "display_title": "csv", "@type": ["FileFormat", "Item"], "file_format": "csv", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2021-07-15T16:07:45.133212+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-10-12T23:32:22.859233+00:00"}, "content_md5sum": "496cedeb98987f0ce8505e087c5f9d70", "public_release": "2021-07-28", "schema_version": "3", "static_headers": [{"lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "Particle localizations for the OligoSTORM dataset from Nir et al. 2018 are in csv format, as produced by the Vutara SRX software from Bruker.\nA detailed description of all the columns is provided in [this extract](/documents/107a9f91-f97b-4581-a52e-c46e4072473e/@@download/attachment/Understanding%20Vutara%20Particles.csv%20File.pdf) from the software manual.", "name": "oligostorm.particles-format", "award": {"display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "@id": "/awards/2U01CA200059-06/", "@type": ["Award", "Item"], "status": "current", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Note on file format for particle localization from Vutara", "status": "released", "aliases": ["4dn-dcic-lab:note_particles_csv_vutara_format"], "options": {"filetype": "md", "collapsible": true, "default_open": true}, "date_created": "2021-07-15T18:46:48.069572+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-07-15T18:47:13.573746+00:00"}, "schema_version": "2", "@id": "/static-sections/8ecacdd9-3ad5-4a0b-b4df-a2a6fb4e4f64/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "8ecacdd9-3ad5-4a0b-b4df-a2a6fb4e4f64", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.e4a22298-1da4-4e59-8a65-9e661f47fb48"]}, "display_title": "Note on file format for particle localization from Vutara", "external_references": [], "content": "Particle localizations for the OligoSTORM dataset from Nir et al. 2018 are in csv format, as produced by the Vutara SRX software from Bruker.\nA detailed description of all the columns is provided in [this extract](/documents/107a9f91-f97b-4581-a52e-c46e4072473e/@@download/attachment/Understanding%20Vutara%20Particles.csv%20File.pdf) from the software manual.", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p>Particle localizations for the OligoSTORM dataset from Nir et al. 2018 are in csv format, as produced by the Vutara SRX software from Bruker.\nA detailed description of all the columns is provided in <a href=\"/documents/107a9f91-f97b-4581-a52e-c46e4072473e/@@download/attachment/Understanding%20Vutara%20Particles.csv%20File.pdf\">this extract</a> from the software manual.</p></div>"}], "project_release": "2021-07-28", "file_classification": "processed file", "@id": "/files-processed/4DNFICP54S3V/", "@type": ["FileProcessed", "File", "Item"], "uuid": "6b7c5e3c-a318-471c-af52-f5ffe35b6062", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFICP54S3V.csv", "external_references": [], "experiments": [{"status": "released", "display_title": "multiplexed FISH on GM23248 - 4DNEXP1ZWBGC", "@id": "/experiments-mic/4DNEXP1ZWBGC/", "@type": ["ExperimentMic", "Experiment", "Item"], "uuid": "d1c44c89-0c39-45ed-8251-4e5e51d79f56", "accession": "4DNEXP1ZWBGC", "biosample": {"biosource_summary": "GM23248", "display_title": "4DNBSTRDP43G", "@type": ["Biosample", "Item"], "@id": "/biosamples/4DNBSTRDP43G/", "treatments_summary": "None", "accession": "4DNBSTRDP43G", "status": "released", "uuid": "59a88960-a19d-4570-bdf4-b78790cc1076", "modifications_summary": "None", "biosource": [{"@type": ["Biosource", "Item"], "status": "released", "@id": "/biosources/4DNSRGX8QYMD/", "display_title": "GM23248 - 4DNSRGX8QYMD", "cell_line_tier": "Unclassified", "biosource_type": "primary cell line", "uuid": "4ece180e-4283-46a0-9b12-972fb8e0b2a6", "tissue": {"status": "released", "term_name": "skin fibroblast", "@type": ["OntologyTerm", "Item"], "uuid": "1a658f38-8dee-4ed2-92ca-c694b5cef902", "preferred_name": "skin fibroblast", "@id": "/ontology-terms/CL:0002620/", "display_title": "skin fibroblast", "term_id": "CL:0002620", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"status": "released", "term_id": "EFO:0005723", "term_name": "GM23248", "display_title": "GM23248", "preferred_name": "GM23248", "@id": "/ontology-terms/EFO:0005723/", "@type": ["OntologyTerm", "Item"], "uuid": "13ca9fbc-9f8a-4df8-a79e-c6647696fb30", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"display_title": "4DNINPD2TEHV", "uuid": "06ba86f8-aef5-4f8b-b773-92c9819b6279", "@id": "/individuals-human/4DNINPD2TEHV/", "@type": ["IndividualHuman", "Individual", "Item"], "status": "released", "protected_data": false, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"status": "released", "@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@type": ["Organism", "Item"], "name": "human", "scientific_name": "Homo sapiens", "display_title": "H. sapiens", "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_sets": [{"accession": "4DNESQN4JCAS", "@id": "/experiment-set-replicates/4DNESQN4JCAS/", "display_title": "4DNESQN4JCAS", "status": "released", "experimentset_type": "replicate", "uuid": "5fd10b48-5ccc-45c7-8753-f41fbd213566", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_type": {"display_title": "multiplexed FISH", "status": "released", "title": "multiplexed FISH", "uuid": "bcdda46a-489d-4d22-be80-c9c21552c915", "@id": "/experiment-types/multiplexed-fish/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-05-17T14:59:37.334797+00:00"}}], "file_type_detailed": "localizations (csv)", "track_and_facet_info": {"experimental_lab": "Chao-Ting Wu, HARVARD", "experiment_type": "multiplexed FISH", "experiment_bucket": "processed file", "assay_info": "22 genomic regions", "dataset": "Super-resolution imaging of chromosome walks", "condition": "8 Mb walks on chr19", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "GM23248", "lab_name": "Chao-Ting Wu, HARVARD"}, "title": "4DNFICP54S3V", "href": "/files-processed/4DNFICP54S3V/@@download/4DNFICP54S3V.csv", "upload_key": "6b7c5e3c-a318-471c-af52-f5ffe35b6062/4DNFICP54S3V.csv", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/6b7c5e3c-a318-471c-af52-f5ffe35b6062/4DNFICP54S3V.csv", "tsv_notes": "", "workflow_run_inputs": [{"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "status": "released", "@id": "/workflow-runs-awsem/73e557f7-9d9f-49a0-be01-d7ad23326672/", "display_title": "md5 0.2.6 run 2021-07-15 16:27:06.839468", "uuid": "73e557f7-9d9f-49a0-be01-d7ad23326672", "input_files": [{"workflow_argument_name": "input_file", "value": {"@id": "/files-processed/4DNFICP54S3V/", "@type": ["FileProcessed", "File", "Item"], "filename": "2017-08-03-19-34-25_Location-01.csv", "status": "released", "uuid": "6b7c5e3c-a318-471c-af52-f5ffe35b6062", "display_title": "4DNFICP54S3V.csv", "accession": "4DNFICP54S3V", "file_format": {"status": "released", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "file_format": "csv", "@id": "/file-formats/csv/", "display_title": "csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "output_files": [{"workflow_argument_name": "report"}], "workflow": {"@id": "/workflows/4DNWF2HFF82B/", "title": "md5 0.2.6", "uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "display_title": "md5 0.2.6 - 4DNWF2HFF82B", "@type": ["Workflow", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [], "experiment_sets": [], "source_experiment_sets": [{"status": "released", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "5fd10b48-5ccc-45c7-8753-f41fbd213566", "@id": "/experiment-set-replicates/4DNESQN4JCAS/", "display_title": "4DNESQN4JCAS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-mic/4DNEXP1ZWBGC/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2023-05-17T14:59:37.334797+00:00"}}, {"parent": "/static-sections/8ecacdd9-3ad5-4a0b-b4df-a2a6fb4e4f64/", "embedded_path": "static_headers.last_modified", "item": {"date_modified": "2021-07-15T18:47:13.573746+00:00"}}, {"parent": "/files-processed/4DNFICP54S3V/", "embedded_path": "last_modified", "item": {"date_modified": "2021-10-12T23:32:22.859233+00:00"}}]}, "validation-errors": []}