{"lab": {"title": "Chao-Ting Wu, HARVARD", "uuid": "8932f234-660e-4fad-b0a3-342dcc799438", "correspondence": [{"contact_email": "dHd1QGdlbmV0aWNzLm1lZC5oYXJ2YXJkLmVkdQ==", "@id": "/users/af7beabd-7452-4b15-bc84-3ba5f72521d5/", "display_title": "Chao-Ting Wu"}], "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/chao-ting-wu-lab/", "display_title": "Chao-Ting Wu, HARVARD", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8932f234-660e-4fad-b0a3-342dcc799438"]}}, "award": {"project": "External", "description": "Funding source is from outside 4DN.", "center_title": "External", "center": "External", "@id": "/awards/external-award/", "name": "external-award", "status": "current", "display_title": "EXTERNAL AWARD", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "0930e04f44e24d67d54eb37c4f1b2028", "status": "released", "aliases": ["chao-ting-wu-lab:fileproc_oligostorm_B6_T1_f3"], "filename": "2018-01-11-09-35-19_Location-04.csv", "accession": "4DNFI1RY2DY8", "file_size": 3232814, "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": {"@type": ["FileFormat", "Item"], "display_title": "csv", "status": "released", "file_format": "csv", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@id": "/file-formats/csv/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2021-07-15T16:12:49.425161+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-10-12T23:28:49.644075+00:00"}, "content_md5sum": "0930e04f44e24d67d54eb37c4f1b2028", "public_release": "2021-07-28", "schema_version": "3", "static_headers": [{"lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "status": "current", "@type": ["Lab", "Item"], "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", "@type": ["Award", "Item"], "status": "current", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "@id": "/awards/2U01CA200059-06/", "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": "
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 from the software manual.
"}], "project_release": "2021-07-28", "file_classification": "processed file", "@id": "/files-processed/4DNFI1RY2DY8/", "@type": ["FileProcessed", "File", "Item"], "uuid": "e0e9fe28-2e9f-4905-b31a-ef7e5eb15945", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFI1RY2DY8.csv", "external_references": [], "experiments": [{"status": "released", "accession": "4DNEX3K9EZJ4", "@type": ["ExperimentMic", "Experiment", "Item"], "@id": "/experiments-mic/4DNEX3K9EZJ4/", "uuid": "eb6a253f-21cf-4141-9a8d-003f9872506d", "display_title": "multiplexed FISH on GM23248 - 4DNEX3K9EZJ4", "biosample": {"modifications_summary": "None", "@id": "/biosamples/4DNBSC2ZEGBF/", "@type": ["Biosample", "Item"], "biosource_summary": "GM23248", "treatments_summary": "None", "accession": "4DNBSC2ZEGBF", "uuid": "b0ac1706-9cb1-42a4-8a06-67f2deb4e7cd", "status": "released", "display_title": "4DNBSC2ZEGBF", "biosource": [{"biosource_type": "primary cell line", "status": "released", "@id": "/biosources/4DNSRGX8QYMD/", "cell_line_tier": "Unclassified", "uuid": "4ece180e-4283-46a0-9b12-972fb8e0b2a6", "display_title": "GM23248 - 4DNSRGX8QYMD", "@type": ["Biosource", "Item"], "individual": {"protected_data": false, "display_title": "4DNINPD2TEHV", "status": "released", "@id": "/individuals-human/4DNINPD2TEHV/", "@type": ["IndividualHuman", "Individual", "Item"], "uuid": "06ba86f8-aef5-4f8b-b773-92c9819b6279", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"display_title": "H. sapiens", "@type": ["Organism", "Item"], "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "name": "human", "status": "released", "scientific_name": "Homo sapiens", "@id": "/organisms/9606/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"@type": ["OntologyTerm", "Item"], "display_title": "GM23248", "status": "released", "@id": "/ontology-terms/EFO:0005723/", "preferred_name": "GM23248", "term_id": "EFO:0005723", "term_name": "GM23248", "uuid": "13ca9fbc-9f8a-4df8-a79e-c6647696fb30", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@id": "/ontology-terms/CL:0002620/", "preferred_name": "skin fibroblast", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "skin fibroblast", "uuid": "1a658f38-8dee-4ed2-92ca-c694b5cef902", "term_id": "CL:0002620", "term_name": "skin fibroblast", "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", "uuid": "bcdda46a-489d-4d22-be80-c9c21552c915", "@type": ["ExperimentType", "Item"], "title": "multiplexed FISH", "@id": "/experiment-types/multiplexed-fish/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"uuid": "5fd10b48-5ccc-45c7-8753-f41fbd213566", "display_title": "4DNESQN4JCAS", "accession": "4DNESQN4JCAS", "experimentset_type": "replicate", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "status": "released", "@id": "/experiment-set-replicates/4DNESQN4JCAS/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "last_modified": {"date_modified": "2023-05-17T14:59:46.466271+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "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": "Chromosome segment CS1 on chr19, Chromosome segment CS2 on chr19, Chromosome segment CS3 on chr19, Chromosome segment CS4 on chr19, Chromosome segment CS5 on chr19, Chromosome segment CS6 on chr19, Chromosome segment CS7 on chr19, Chromosome segment CS8 on chr19, Chromosome segment CS9 on chr19, Sub-region 1 of CS7, Sub-region 2 of CS7, Sub-region 3 of CS7, Sub-region 4 of CS7, Loop anchor I, within CS6, Loop body, within CS6, Loop anchor II, within CS6, Loop flanking region (downstream), within CS6, Loop flanking region (upstream), within CS6, DNMT1 gene region, Differentially methylated region (DMR) of DNMT1 gene, CS_1C on chr19, CS0 on chr19", "dataset": "Super-resolution imaging of chromosome walks", "condition": "8 Mb walks on chr19", "replicate_info": "Biorep 6, Techrep 1", "biosource_name": "GM23248", "lab_name": "Chao-Ting Wu, HARVARD"}, "title": "4DNFI1RY2DY8", "href": "/files-processed/4DNFI1RY2DY8/@@download/4DNFI1RY2DY8.csv", "upload_key": "e0e9fe28-2e9f-4905-b31a-ef7e5eb15945/4DNFI1RY2DY8.csv", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e0e9fe28-2e9f-4905-b31a-ef7e5eb15945/4DNFI1RY2DY8.csv", "tsv_notes": "", "workflow_run_inputs": [{"display_title": "md5 0.2.6 run 2021-07-15 16:26:25.367929", "@id": "/workflow-runs-awsem/723a407e-876e-4ae8-89c1-7c120930fa0e/", "status": "released", "uuid": "723a407e-876e-4ae8-89c1-7c120930fa0e", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "workflow": {"@type": ["Workflow", "Item"], "@id": "/workflows/4DNWF2HFF82B/", "uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "title": "md5 0.2.6", "display_title": "md5 0.2.6 - 4DNWF2HFF82B", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "input_files": [{"workflow_argument_name": "input_file", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "e0e9fe28-2e9f-4905-b31a-ef7e5eb15945", "@id": "/files-processed/4DNFI1RY2DY8/", "display_title": "4DNFI1RY2DY8.csv", "status": "released", "filename": "2018-01-11-09-35-19_Location-04.csv", "accession": "4DNFI1RY2DY8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "csv", "@id": "/file-formats/csv/", "file_format": "csv", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "output_files": [{"workflow_argument_name": "report"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [], "experiment_sets": [], "source_experiment_sets": [{"display_title": "4DNESQN4JCAS", "uuid": "5fd10b48-5ccc-45c7-8753-f41fbd213566", "status": "released", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNESQN4JCAS/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"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": "/experiments-mic/4DNEX3K9EZJ4/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2023-05-17T14:59:46.466271+00:00"}}, {"parent": "/files-processed/4DNFI1RY2DY8/", "embedded_path": "last_modified", "item": {"date_modified": "2021-10-12T23:28:49.644075+00:00"}}]}, "validation-errors": []}