{"lab": {"uuid": "312cb909-76a6-405d-a96c-c3292abf08a1", "title": "Alistair Boettiger, STANFORD", "@id": "/labs/alistair-boettiger-lab/", "@type": ["Lab", "Item"], "display_title": "Alistair Boettiger, STANFORD", "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": {"project": "External", "display_title": "EXTERNAL AWARD", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "center_title": "External", "name": "external-award", "@type": ["Award", "Item"], "center": "External", "description": "Funding source is from outside 4DN.", "@id": "/awards/external-award/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "badges": [{"badge": {"display_title": "Replicate Numbers", "@type": ["Badge", "Item"], "description": "Issues with replicate numbers", "@id": "/badges/replicate-numbers/", "badge_classification": "Warning", "title": "Replicate Numbers", "warning": "Replicate Numbers", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "status": "released", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Replicate set contains only a single biological replicate"]}], "status": "released", "aliases": ["alistair-boettiger-lab:IMR90_2-Mb_18-20"], "accession": "4DNES97DWLA6", "condition": "Chr21:18-20 Mb (no TADs) in IMR90 cells", "description": "Chromatin tracing of a 2-Mb region lacking TAD boundaries on chromosome 21 (Chr21:18.6Mb-20.6Mb) in IMR90 cells", "date_created": "2022-09-02T10:49:12.299260+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "Chromatin tracing of 2-Mb 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experiments, but has been formatted according to the 4DN standard <a href=\"https://fish-omics-format.readthedocs.io/en/latest/\" rel=\"noopener noreferrer\" target=\"_blank\">FOF-CT</a>.</p></div>", "status": "released", "name": "bintu_data_github", "uuid": "1f991c02-ed0c-40bf-9e48-7d9238183823", "lab": {"uuid": "312cb909-76a6-405d-a96c-c3292abf08a1", "@id": "/labs/alistair-boettiger-lab/", "@type": ["Lab", "Item"], "display_title": "Alistair Boettiger, STANFORD", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.312cb909-76a6-405d-a96c-c3292abf08a1"]}}, "display_title": "bintu_data_github", "@type": ["StaticSection", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.e4a22298-1da4-4e59-8a65-9e661f47fb48"]}}, "location": "tab:attribution"}], "static_headers": [{"lab": {"status": "current", "uuid": 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[c8e8a284-c6d0-4b97-9670-822ae7a8296f](https://data.4dnucleome.org/microscope-configurations/c8e8a284-c6d0-4b97-9670-822ae7a8296f) or [a2b6ca4e-7de9-484f-b8c3-c868b68f929e](https://data.4dnucleome.org/microscope-configurations/a2b6ca4e-7de9-484f-b8c3-c868b68f929e) microscopes ", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p>The experiments associated with this study are derived from either <a href=\"https://data.4dnucleome.org/microscope-configurations/c8e8a284-c6d0-4b97-9670-822ae7a8296f\" rel=\"noopener noreferrer\" target=\"_blank\">c8e8a284-c6d0-4b97-9670-822ae7a8296f</a> or <a href=\"https://data.4dnucleome.org/microscope-configurations/a2b6ca4e-7de9-484f-b8c3-c868b68f929e\" rel=\"noopener noreferrer\" target=\"_blank\">a2b6ca4e-7de9-484f-b8c3-c868b68f929e</a> microscopes </p></div>"}, {"lab": {"status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], 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(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 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DNA-spot/trace core", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/729fd2b6-d927-499e-a2bd-ff82c32a4eed/4DNFII2E9PV7.csv", "file_size": 4292404, "uuid": "729fd2b6-d927-499e-a2bd-ff82c32a4eed", "upload_key": "729fd2b6-d927-499e-a2bd-ff82c32a4eed/4DNFII2E9PV7.csv", "file_classification": "processed file", "file_format": {"@id": "/file-formats/csv/", "display_title": "csv", "status": "released", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFII2E9PV7.csv", "file_type_detailed": "FOF-CT - DNA-spot/trace core (csv)", "md5sum": "8be6ee33054debb435a50539aa003d85", "href": "/files-processed/4DNFII2E9PV7/@@download/4DNFII2E9PV7.csv", "genome_assembly": "GRCh38", "@id": "/files-processed/4DNFII2E9PV7/", "status": "released", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFII2E9PV7", "contributing_labs": 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FISH", "experiment_bucket": "processed file", "assay_info": "65 consecutive 30-kb loci in a region without TADs on chr21", "dataset": "Chromatin tracing of 2-Mb on chr21", "condition": "Chr21:18-20 Mb (no TADs) in IMR90 cells", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "IMR-90", "lab_name": "Alistair Boettiger, STANFORD"}, "external_references": []}], "biosample": {"biosample_category": ["IMR-90"], "biosource_summary": "IMR-90", "biosample_type": "primary cells", "@id": "/biosamples/4DNBSEW9BLPR/", "status": "released", "display_title": "4DNBSEW9BLPR", "uuid": "654e615f-522f-47b3-94f7-07f105040f3e", "treatments_summary": "None", "@type": ["Biosample", "Item"], "accession": "4DNBSEW9BLPR", "modifications_summary": "None", "biosource": [{"display_title": "IMR-90 - 4DNSRXXGU3CH", "cell_line_tier": "Unclassified", "accession": "4DNSRXXGU3CH", "@type": ["Biosource", "Item"], "uuid": "26ebb2b1-2902-4446-a25f-9fc6523ed5cf", "@id": "/biosources/4DNSRXXGU3CH/", "status": "released", "biosource_type": "primary cell line", "cell_line": {"term_id": "EFO:0001196", "uuid": "c45d70f2-980b-4a6c-b762-bb48fdd7913a", "status": "released", "display_title": "IMR-90", "preferred_name": "IMR-90", "term_name": "IMR-90", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/EFO:0001196/", "synonyms": ["IMR90"], "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"display_title": "fibroblast of lung", "@type": ["OntologyTerm", "Item"], "uuid": "999f1c8c-f02b-4a2b-b269-53ec1234b26f", "term_id": "CL:0002553", "@id": "/ontology-terms/CL:0002553/", "status": "released", "synonyms": ["NHLF", "fibroblast of lung"], "term_name": "fibroblast of lung", "preferred_name": "fibroblast of lung", "slim_terms": [{"uuid": "111121bc-8535-4448-903e-854af460a233", "display_title": "endoderm", "status": "released", "@id": "/ontology-terms/UBERON:0000925/", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "status": "current", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "status": "released", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": 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"edit": ["group.admin"]}}], "tissue_organ_info": {"tissue_source": "fibroblast of lung", "organ_system": ["endoderm", "lung", "respiratory system"]}, "badges": [{"messages": ["Biosample missing Cell Culture Details"], "badge": {"warning": "Biosample Metadata Incomplete", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "badge_icon": "/static/img/badges/biosample-icon.svg", "status": "released", "@type": ["Badge", "Item"], "title": "Biosample Metadata Incomplete", "display_title": "Biosample Metadata Incomplete", "badge_classification": "Warning", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "reference_files": [{"file_size": 725, "file_type_detailed": "target regions (bed)", 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