{"lab": {"title": "Alistair Boettiger, STANFORD", "@type": ["Lab", "Item"], "status": "current", "correspondence": [{"contact_email": "YWJvZXR0aWdAc3RhbmZvcmQuZWR1", "@id": "/users/b8835c78-05e3-4173-a6c5-1ab93b4d12cc/", "display_title": "Alistair Boettiger"}], "display_title": "Alistair Boettiger, STANFORD", "@id": "/labs/alistair-boettiger-lab/", "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": {"center_title": "External", "center": "External", "display_title": "EXTERNAL AWARD", "description": "Funding source is from outside 4DN.", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "status": "current", "name": "external-award", "@id": "/awards/external-award/", "project": "External", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "badges": [{"badge": {"@type": ["Badge", "Item"], "display_title": "Replicate Numbers", "description": "Issues with replicate numbers", "@id": "/badges/replicate-numbers/", "warning": "Replicate Numbers", "badge_classification": "Warning", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "status": "released", "title": "Replicate Numbers", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Replicate set contains only a single biological replicate"]}], "status": "released", "aliases": ["alistair-boettiger-lab:A549_2-Mb_28-30"], "accession": "4DNESL619Z5V", "condition": "Chr21:28-30 Mb in A549 cells", "description": "Chromatin tracing of a 2-Mb region on chromosome 21 (Chr21:28Mb-30Mb) in A549 cells", "date_created": "2022-09-02T10:49:16.915666+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "Chromatin tracing of 2-Mb on chr21", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-06-26T16:41:32.735127+00:00"}, "public_release": "2022-10-20", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-mic/4DNEX46ABFUV/", "@type": ["ExperimentMic", "Experiment", "Item"], "display_title": "multiplexed FISH on A549 - 4DNEX46ABFUV", "uuid": "c7ece6b4-cf03-4717-9e85-490ffd4cc0e0", "status": "released", "accession": "4DNEX46ABFUV", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"award": {"uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@type": ["Award", "Item"], "display_title": "EXTERNAL AWARD", "@id": "/awards/external-award/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "bintu_data_github", "uuid": "1f991c02-ed0c-40bf-9e48-7d9238183823", "@id": "/static-sections/1f991c02-ed0c-40bf-9e48-7d9238183823/", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "uuid": "eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb", "display_title": "Xiaowei Zhuang, HARVARD", "status": "current", "@id": "/labs/xiaowei-zhuang-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb"]}}], "content_as_html": "<div class=\"markdown-container\"><p>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 <a href=\"https://fish-omics-format.readthedocs.io/en/latest/\" rel=\"noopener noreferrer\" target=\"_blank\">FOF-CT</a>.</p></div>", "lab": {"@type": ["Lab", "Item"], "uuid": "312cb909-76a6-405d-a96c-c3292abf08a1", "status": "current", "@id": "/labs/alistair-boettiger-lab/", "display_title": "Alistair Boettiger, STANFORD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.312cb909-76a6-405d-a96c-c3292abf08a1"]}}, "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/).", "@type": ["StaticSection", "UserContent", "Item"], "filetype": "md", "options": {"filetype": "md", "collapsible": false, "default_open": true}, "name": "bintu_data_github", "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", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "The experiments associated with this study are derived from either [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 ", "name": "microscope_note_bintu_et_al_2018", "award": {"@id": "/awards/2U01CA200059-06/", "@type": ["Award", "Item"], "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Microscope configuration - Bintu et al 2018", "status": "released", "aliases": ["4dn-dcic-lab:microscope_note_bintu_et_al_2018"], "options": {"filetype": "md", "collapsible": true, "default_open": true, "convert_ext_links": true}, "date_created": "2025-06-24T17:16:55.834655+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-06-24T17:54:50.616249+00:00"}, "schema_version": "2", "@id": "/static-sections/5ad41494-d5cf-4b56-80a6-35cf100c2c26/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "5ad41494-d5cf-4b56-80a6-35cf100c2c26", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.6f9809b1-b9b4-4f2f-8e6d-0762bce320ef"]}, "display_title": "Microscope configuration - Bintu et al 2018", "external_references": [], "content": "The experiments associated with this study are derived from either [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", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "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": {"@id": "/awards/2U01CA200059-06/", "@type": ["Award", "Item"], "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "status": "current", "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>"}], "project_release": "2022-10-20", "contributing_labs": [{"correspondence": [{"contact_email": "emh1YW5nQGNoZW1pc3RyeS5oYXJ2YXJkLmVkdQ==", "@id": "/users/acfc5a08-19ff-47ef-9261-75e6134dc0fe/", "display_title": "Xiaowei Zhuang"}], "@type": ["Lab", "Item"], "@id": "/labs/xiaowei-zhuang-lab/", "status": "current", "display_title": "Xiaowei Zhuang, HARVARD", "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"], "status": "released", "accession": "4DNEX46ABFUV", "uuid": "c7ece6b4-cf03-4717-9e85-490ffd4cc0e0", "@id": "/experiments-mic/4DNEX46ABFUV/", "display_title": "multiplexed FISH on A549 - 4DNEX46ABFUV", "processed_files": [{"file_type_detailed": "FOF-CT - DNA-spot/trace core (csv)", "genome_assembly": "GRCh38", "md5sum": "51915218ce73494f6524902cff671354", "display_title": "4DNFIGLYJRQJ.csv", "@type": ["FileProcessed", "File", "Item"], "file_size": 12858977, "href": "/files-processed/4DNFIGLYJRQJ/@@download/4DNFIGLYJRQJ.csv", "@id": "/files-processed/4DNFIGLYJRQJ/", "upload_key": "0593b358-23b4-4320-ad7e-e8c26783f612/4DNFIGLYJRQJ.csv", "file_type": "FOF-CT - DNA-spot/trace core", "status": "released", "file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@id": "/file-formats/csv/", "status": "released", "display_title": "csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFIGLYJRQJ", "uuid": "0593b358-23b4-4320-ad7e-e8c26783f612", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/0593b358-23b4-4320-ad7e-e8c26783f612/4DNFIGLYJRQJ.csv", "file_classification": "processed file", "lab": {"display_title": "Alistair Boettiger, STANFORD", "@type": ["Lab", "Item"], "uuid": "312cb909-76a6-405d-a96c-c3292abf08a1", "status": "current", "@id": "/labs/alistair-boettiger-lab/", "name": "alistair-boettiger-lab", "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", "@type": ["Lab", "Item"], "@id": "/labs/xiaowei-zhuang-lab/", "name": "xiaowei-zhuang-lab", "status": "current", "uuid": "eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb"]}}], "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", "dataset": "Chromatin tracing of 2-Mb on chr21", "condition": "Chr21:28-30 Mb in A549 cells", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "A549", "lab_name": "Alistair Boettiger, STANFORD"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-01-03T21:45:45.224976+00:00"}}], "biosample": {"accession": "4DNBST1RIXZA", "status": "released", "@id": "/biosamples/4DNBST1RIXZA/", "biosample_type": "immortalized cells", "display_title": "4DNBST1RIXZA", "treatments_summary": "None", "biosample_category": ["Other"], "@type": ["Biosample", "Item"], "uuid": "c8c14269-6d8d-46c5-9fc5-abca37b468f5", "modifications_summary": "None", "biosource_summary": "A549", "badges": [{"messages": ["Biosample missing Cell Culture Details"], "badge": {"badge_classification": "Warning", "@type": ["Badge", "Item"], "@id": "/badges/biosample-metadata-incomplete/", "warning": "Biosample Metadata Incomplete", "badge_icon": "/static/img/badges/biosample-icon.svg", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "status": "released", "display_title": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "biosource": [{"biosource_type": "immortalized cell line", "@id": "/biosources/4DNSRFLY6T15/", "status": "released", "accession": "4DNSRFLY6T15", "uuid": "044733e7-db6c-412c-b1c3-eb77c811dd3e", "cell_line_tier": "Unclassified", "display_title": "A549 - 4DNSRFLY6T15", "@type": ["Biosource", "Item"], "tissue": {"status": "released", "display_title": "lung", "preferred_name": "lung", "synonyms": ["pulmo"], "@type": ["OntologyTerm", "Item"], "uuid": "111186bc-8535-4448-903e-854af460a233", "term_name": "lung", "@id": "/ontology-terms/UBERON:0002048/", "term_id": "UBERON:0002048", "slim_terms": [{"uuid": "111128bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0001004/", "status": "released", "display_title": "respiratory system", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111186bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0002048/", "status": "released", "display_title": "lung", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111121bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0000925/", "status": "released", "display_title": "endoderm", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"@type": ["OntologyTerm", "Item"], "display_title": "A549", "status": "released", "term_name": "A549", "@id": "/ontology-terms/EFO:0001086/", "synonyms": ["A-549", "A549 cell"], "term_id": "EFO:0001086", "preferred_name": "A549", "uuid": "2fea36d1-69bd-4039-8c58-a5d9bf6bcdad", "slim_terms": [{"@id": "/ontology-terms/UBERON:0000925/", "@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "endoderm", "uuid": "111121bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "@type": ["Organism", "Item"], "status": "released", "@id": "/organisms/9606/", "name": "human", "scientific_name": "Homo sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"tissue_source": "lung", "organ_system": ["respiratory system", "lung", "endoderm"]}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "reference_files": [{"file_size": 713, "href": "/files-reference/4DNFIANU6Y4T/@@download/4DNFIANU6Y4T.bed.gz", "@id": "/files-reference/4DNFIANU6Y4T/", "status": "released", "file_type_detailed": "target regions (bed)", "md5sum": "f93ae18149b7a3575fb47ba0b4b21358", "accession": "4DNFIANU6Y4T", "display_title": "4DNFIANU6Y4T.bed.gz", "file_type": "target regions", "@type": ["FileReference", "File", "Item"], "uuid": "0a4f4ea0-9897-4dd6-936b-e51e7546b701", "file_classification": "ancillary file", "contributing_labs": [{"status": "current", "@type": ["Lab", "Item"], "display_title": "Xiaowei Zhuang, HARVARD", "name": "xiaowei-zhuang-lab", "@id": "/labs/xiaowei-zhuang-lab/", "uuid": "eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb"]}}], "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"uuid": "325a1412-01d7-4c25-a91c-85a3857f1678", "@id": "/higlass-view-configs/325a1412-01d7-4c25-a91c-85a3857f1678/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "display_title": "4DNFIANU6Y4T", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "file_format": {"file_format": "bed", "status": "released", "display_title": "bed", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "@id": "/file-formats/bed/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "alistair-boettiger-lab", "@type": ["Lab", "Item"], "display_title": "Alistair Boettiger, STANFORD", "uuid": "312cb909-76a6-405d-a96c-c3292abf08a1", "@id": "/labs/alistair-boettiger-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.312cb909-76a6-405d-a96c-c3292abf08a1"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 2484641, "href": "/files-reference/4DNFILBDMLUL/@@download/4DNFILBDMLUL.zip", "@id": "/files-reference/4DNFILBDMLUL/", "status": "released", "file_type_detailed": "oligo sequences (zip)", "md5sum": "7090747795347ad742308b92d7aa98a0", "accession": "4DNFILBDMLUL", "display_title": "4DNFILBDMLUL.zip", "file_type": "oligo sequences", "@type": ["FileReference", "File", "Item"], "uuid": "e3068b80-9959-42ee-aad8-991a2db3aeab", "file_classification": "ancillary file", "contributing_labs": [{"status": "current", "@type": ["Lab", "Item"], "display_title": "Xiaowei Zhuang, HARVARD", "name": "xiaowei-zhuang-lab", "@id": "/labs/xiaowei-zhuang-lab/", "uuid": "eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb"]}}], "file_format": {"file_format": "zip", "status": "released", "display_title": "zip", "uuid": "d13d06cf-218e-4f61-44f0-91f226248b2c", "@id": "/file-formats/zip/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "alistair-boettiger-lab", "@type": ["Lab", "Item"], "display_title": "Alistair Boettiger, STANFORD", "uuid": "312cb909-76a6-405d-a96c-c3292abf08a1", "@id": "/labs/alistair-boettiger-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.312cb909-76a6-405d-a96c-c3292abf08a1"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_type": {"@id": "/experiment-types/multiplexed-fish/", "title": "multiplexed FISH", "experiment_category": "Microscopy", "status": "released", "assay_subclass_short": "FISH", "assay_subclassification": "Chromatin Tracing", "@type": ["ExperimentType", "Item"], "assay_classification": "Fluorescence Localization", "other_tags": ["Single Cell"], "display_title": "multiplexed FISH", "uuid": "bcdda46a-489d-4d22-be80-c9c21552c915", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2025-06-16T18:43:43.854844+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "experiment_categorizer": {"field": "Target", "value": "65 consecutive 30-kb loci on chr21", "combined": "Target: 65 consecutive 30-kb loci on chr21"}}], "experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESL619Z5V/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "3415c620-9789-47f6-9c88-5cb2648748e8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESL619Z5V", "external_references": [], "produced_in_pub": {"display_title": "Bintu B et al. (2018) PMID:30361340", "@id": "/publications/e6451832-8312-4e74-bd74-742801f726e1/", "status": "current", "uuid": "e6451832-8312-4e74-bd74-742801f726e1", "journal": "Science (New York, N.Y.)", "abstract": "The spatial organization of chromatin is pivotal for regulating genome functions. We report an imaging method for tracing chromatin organization with kilobase- and nanometer-scale resolution, unveiling chromatin conformation across topologically associating domains (TADs) in thousands of individual cells. Our imaging data revealed TAD-like structures with globular conformation and sharp domain boundaries in single cells. The boundaries varied from cell to cell, occurring with nonzero probabilities at all genomic positions but preferentially at CCCTC-binding factor (CTCF)- and cohesin-binding sites. Notably, cohesin depletion, which abolished TADs at the population-average level, did not diminish TAD-like structures in single cells but eliminated preferential domain boundary positions. Moreover, we observed widespread, cooperative, multiway chromatin interactions, which remained after cohesin depletion. These results provide critical insight into the mechanisms underlying chromatin domain and hub formation.", "url": "https://www.ncbi.nlm.nih.gov/pubmed/30361340", "short_attribution": "Bintu B et al. (2018)", "ID": "PMID:30361340", "date_published": "2018-10-26", "authors": ["Bintu B", "Mateo LJ", "Su JH", "Sinnott-Armstrong NA", "Parker M", "Kinrot S", "Yamaya K", "Boettiger AN", "Zhuang X"], "title": "Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells.", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"authors": ["Bintu B", "Mateo LJ", "Su JH", "Sinnott-Armstrong NA", "Parker M", "Kinrot S", "Yamaya K", "Boettiger AN", "Zhuang X"], "@type": ["Publication", "Item"], "abstract": "The spatial organization of chromatin is pivotal for regulating genome functions. We report an imaging method for tracing chromatin organization with kilobase- and nanometer-scale resolution, unveiling chromatin conformation across topologically associating domains (TADs) in thousands of individual cells. Our imaging data revealed TAD-like structures with globular conformation and sharp domain boundaries in single cells. The boundaries varied from cell to cell, occurring with nonzero probabilities at all genomic positions but preferentially at CCCTC-binding factor (CTCF)- and cohesin-binding sites. Notably, cohesin depletion, which abolished TADs at the population-average level, did not diminish TAD-like structures in single cells but eliminated preferential domain boundary positions. Moreover, we observed widespread, cooperative, multiway chromatin interactions, which remained after cohesin depletion. These results provide critical insight into the mechanisms underlying chromatin domain and hub formation.", "title": "Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells.", "date_published": "2018-10-26", "uuid": "e6451832-8312-4e74-bd74-742801f726e1", "status": "current", "display_title": "Bintu B et al. (2018) PMID:30361340", "ID": "PMID:30361340", "@id": "/publications/e6451832-8312-4e74-bd74-742801f726e1/", "journal": "Science (New York, N.Y.)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 1, "imaging_paths": [{"path": {"@id": "/imaging-paths/858d19ee-b17b-4096-ba08-392dee91e907/", "display_title": "65 consecutive 30-kb loci on chr21 targeted by oligo probe library (with Alexa Fluor 647-labeled readout oligos)", "other_probes": ["oligo probe library"], "status": "released", "labeled_probe": "readout oligos", "@type": ["ImagingPath", "Item"], "imaging_rounds": "1-41", "uuid": "858d19ee-b17b-4096-ba08-392dee91e907", "target": [{"preferred_label": "65 consecutive 30-kb loci on chr21", "status": "released", "@id": "/bio-features/230debc7-5598-4abb-9b58-8e70ca124a08/", "uuid": "230debc7-5598-4abb-9b58-8e70ca124a08", "@type": ["BioFeature", "Item"], "display_title": "65 consecutive 30-kb loci on chr21", "organism_name": "human", "genome_location": [{"@id": "/genomic-regions/79a17046-c35b-4564-8176-62b810a2f0e6/", "chromosome": "21", "end_coordinate": 30300000, "genome_assembly": "GRCh38", "@type": ["GenomicRegion", "Item"], "display_title": "GRCh38:21:28000001-30300000", "status": "released", "uuid": "79a17046-c35b-4564-8176-62b810a2f0e6", "start_coordinate": 28000001, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "feature_type": {"term_id": "SO:0000001", "term_name": "region", "uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "region", "preferred_name": "region", "@id": "/ontology-terms/SO:0000001/", "term_url": "http://purl.obolibrary.org/obo/SO_0000001", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_type": {"title": "DNA FISH", "status": "released", "@type": ["ExperimentType", "Item"], "uuid": "5761d0ec-35b0-4aa8-8b81-aac94def59b8", "display_title": "DNA FISH", "@id": "/experiment-types/dna-fish/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch03"}, {"path": {"@id": "/imaging-paths/e1cda834-4c1f-4d4a-814e-363a4f320b7a/", "display_title": "65 consecutive 30-kb loci on chr21 targeted by oligo probe library, readout oligo library (with Alexa Fluor 647-labeled imaging oligos)", "other_probes": ["oligo probe library", "readout oligo library"], "status": "released", "labeled_probe": "imaging oligos", "@type": ["ImagingPath", "Item"], "imaging_rounds": "42-65", "uuid": "e1cda834-4c1f-4d4a-814e-363a4f320b7a", "target": [{"preferred_label": "65 consecutive 30-kb loci on chr21", "status": "released", "@id": "/bio-features/230debc7-5598-4abb-9b58-8e70ca124a08/", "uuid": "230debc7-5598-4abb-9b58-8e70ca124a08", "@type": ["BioFeature", "Item"], "display_title": "65 consecutive 30-kb loci on chr21", "organism_name": "human", "genome_location": [{"@id": "/genomic-regions/79a17046-c35b-4564-8176-62b810a2f0e6/", "chromosome": "21", "end_coordinate": 30300000, "genome_assembly": "GRCh38", "@type": ["GenomicRegion", "Item"], "display_title": "GRCh38:21:28000001-30300000", "status": "released", "uuid": "79a17046-c35b-4564-8176-62b810a2f0e6", "start_coordinate": 28000001, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "feature_type": {"term_id": "SO:0000001", "term_name": "region", "uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "region", "preferred_name": "region", "@id": "/ontology-terms/SO:0000001/", "term_url": "http://purl.obolibrary.org/obo/SO_0000001", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_type": {"title": "DNA FISH", "status": "released", "@type": ["ExperimentType", "Item"], "uuid": "5761d0ec-35b0-4aa8-8b81-aac94def59b8", "display_title": "DNA FISH", "@id": "/experiment-types/dna-fish/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch03"}, {"path": {"@id": "/imaging-paths/d826c3b0-125a-4ceb-a7ce-829cd74b2b23/", "display_title": "540/560nm fiducial beads", "status": "released", "labeled_probe": "540/560nm fiducial beads", "@type": ["ImagingPath", "Item"], "uuid": "d826c3b0-125a-4ceb-a7ce-829cd74b2b23", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch02"}], "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBST1RIXZA/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing Cell Culture Details"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}, {"parent": "/experiment-set-replicates/4DNESL619Z5V/", "embedded_path": "badges", "item": {"messages": ["Replicate set contains only a single biological replicate"], "badge": {"commendation": null, "warning": "Replicate Numbers", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "@id": "/badges/replicate-numbers/", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "description": "Issues with replicate numbers"}}}]}, "validation-errors": []}