{"lab": {"@type": ["Lab", "Item"], "@id": "/labs/alistair-boettiger-lab/", "status": "current", "display_title": "Alistair Boettiger, STANFORD", "title": "Alistair Boettiger, STANFORD", "correspondence": [{"contact_email": "YWJvZXR0aWdAc3RhbmZvcmQuZWR1", "@id": "/users/b8835c78-05e3-4173-a6c5-1ab93b4d12cc/", "display_title": "Alistair Boettiger"}], "uuid": "312cb909-76a6-405d-a96c-c3292abf08a1", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.312cb909-76a6-405d-a96c-c3292abf08a1"]}}, "award": {"@type": ["Award", "Item"], "display_title": "EXTERNAL AWARD", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "name": "external-award", "center_title": "External", "status": "current", "project": "External", "@id": "/awards/external-award/", "description": "Funding source is from outside 4DN.", "center": "External", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "badges": [{"badge": {"uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "title": "Replicate Numbers", "@id": "/badges/replicate-numbers/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "description": "Issues with replicate numbers", "warning": "Replicate Numbers", "display_title": "Replicate Numbers", "status": "released", "badge_classification": "Warning", "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_28-30_cell_cycle"], "accession": "4DNESSXNNJUB", "condition": "Chr21:28-30 Mb in IMR90 cells across cell cycle", "description": "Chromatin tracing of a 2-Mb region on chromosome 21 (Chr21:28Mb-30Mb) in IMR90 cells across G1, S and G2 stages of the cell cycle", "date_created": "2022-09-02T10:49:14.610693+00:00", "submitted_by": {"error": "no view permissions"}, 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href=\"https://fish-omics-format.readthedocs.io/en/latest/\" rel=\"noopener noreferrer\" target=\"_blank\">FOF-CT</a>.</p></div>", "filetype": "md", "award": {"@id": "/awards/external-award/", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "status": "current", "@type": ["Award", "Item"], "display_title": "EXTERNAL AWARD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["StaticSection", "UserContent", "Item"], "status": "released", "display_title": "bintu_data_github", "@id": "/static-sections/1f991c02-ed0c-40bf-9e48-7d9238183823/", "content": "This dataset was initially published on GitHub https://github.com/BoettigerLab/ChromatinImaging/tree/master/Data in a lab-specified format.\nData in the 4DN portal is derived from the same experiments, but has been formatted according to the 4DN standard [FOF-CT](https://fish-omics-format.readthedocs.io/en/latest/).", "options": {"filetype": "md", "collapsible": false, "default_open": true}, "name": "bintu_data_github", "lab": {"@type": ["Lab", "Item"], "display_title": "Alistair Boettiger, STANFORD", "@id": "/labs/alistair-boettiger-lab/", "uuid": "312cb909-76a6-405d-a96c-c3292abf08a1", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.312cb909-76a6-405d-a96c-c3292abf08a1"]}}, "contributing_labs": [{"display_title": "Xiaowei Zhuang, HARVARD", "uuid": "eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb", "status": "current", "@id": "/labs/xiaowei-zhuang-lab/", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb"]}}], "uuid": "1f991c02-ed0c-40bf-9e48-7d9238183823", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.e4a22298-1da4-4e59-8a65-9e661f47fb48"]}}, "location": "tab:attribution"}], "static_headers": [{"lab": {"display_title": "4DN DCIC, HMS", 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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": {"display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", 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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 available here: https://fish-omics-format.readthedocs.io/</p></div>"}], "project_release": "2022-10-20", "contributing_labs": [{"@id": "/labs/xiaowei-zhuang-lab/", "status": "current", "display_title": "Xiaowei Zhuang, HARVARD", "correspondence": [{"contact_email": "emh1YW5nQGNoZW1pc3RyeS5oYXJ2YXJkLmVkdQ==", "@id": "/users/acfc5a08-19ff-47ef-9261-75e6134dc0fe/", "display_title": "Xiaowei Zhuang"}], "@type": ["Lab", "Item"], "uuid": "eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb"]}}], "experiments_in_set": [{"@type": ["ExperimentMic", "Experiment", "Item"], "@id": "/experiments-mic/4DNEXXQVNRK6/", "status": "released", "display_title": "multiplexed FISH on IMR-90 - 4DNEXXQVNRK6", "accession": "4DNEXXQVNRK6", "uuid": "737aee11-ec30-4987-bf82-746bc2645a5f", "biosample": {"biosample_type": "primary cells", 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"@id": "/ontology-terms/UBERON:0002048/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111128bc-8535-4448-903e-854af460a233", "display_title": "respiratory system", "@id": "/ontology-terms/UBERON:0001004/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "badges": [{"messages": ["Biosample missing Cell Culture Details"], "badge": {"description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "title": "Biosample Metadata Incomplete", "badge_icon": "/static/img/badges/biosample-icon.svg", "badge_classification": "Warning", "@type": ["Badge", "Item"], "status": "released", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "display_title": "Biosample Metadata Incomplete", "warning": "Biosample Metadata Incomplete", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"organ_system": ["endoderm", "lung", "respiratory system"], "tissue_source": "fibroblast of lung"}}, "processed_files": [{"md5sum": "bd5e2604a5d915118749ebbae637c8fb", "file_type": "FOF-CT - DNA-spot/trace core", "@id": "/files-processed/4DNFIORVNYGB/", "upload_key": "135a2d39-6352-4a92-8e9b-dd5d9548ff0b/4DNFIORVNYGB.csv", "file_size": 5289103, "uuid": "135a2d39-6352-4a92-8e9b-dd5d9548ff0b", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/135a2d39-6352-4a92-8e9b-dd5d9548ff0b/4DNFIORVNYGB.csv", "file_type_detailed": "FOF-CT - DNA-spot/trace core (csv)", "file_format": 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"alistair-boettiger-lab", "status": "current", "uuid": "312cb909-76a6-405d-a96c-c3292abf08a1", "@type": ["Lab", "Item"], "display_title": "Alistair Boettiger, STANFORD", "@id": "/labs/alistair-boettiger-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.312cb909-76a6-405d-a96c-c3292abf08a1"]}}, "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, Geminin, Chromosomes", "dataset": "Chromatin tracing of 2-Mb on chr21", "condition": "Chr21:28-30 Mb in IMR90 cells across cell cycle", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "IMR-90", "lab_name": "Alistair Boettiger, STANFORD"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "953de37a5062dc55225242ee39ca6369", "file_type": "FOF-CT - trace 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