{"lab": {"display_title": "Alistair Boettiger, STANFORD", "@type": ["Lab", "Item"], "correspondence": [{"contact_email": "YWJvZXR0aWdAc3RhbmZvcmQuZWR1", "@id": "/users/b8835c78-05e3-4173-a6c5-1ab93b4d12cc/", "display_title": "Alistair Boettiger"}], "title": "Alistair Boettiger, STANFORD", "status": "current", "@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": {"name": "external-award", "project": "External", "@type": ["Award", "Item"], "center_title": "External", "@id": "/awards/external-award/", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "center": "External", "description": "Funding source is from outside 4DN.", "status": "current", "display_title": "EXTERNAL AWARD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "badges": [{"badge": {"title": "Replicate Numbers", "badge_classification": "Warning", "status": "released", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "@id": "/badges/replicate-numbers/", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "description": "Issues with replicate numbers", "display_title": "Replicate Numbers", "warning": "Replicate Numbers", "@type": ["Badge", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Replicate set contains only a single biological replicate"]}], "status": "released", "aliases": ["alistair-boettiger-lab:Fab7"], "accession": "4DNESRHE38D8", "condition": "Fab-7 mutant, 2-kb resolution", "description": "Optical Reconstruction of Chromatin Architecture (ORCA) of a 130-kb regulatory region of the bithorax complex (BX-C) spanning abd-A to Abd-B at 2-kb steps in Fab-7 mutant fly embryos. Additionally, 29 mRNA and nascent RNA species are detected by sequential RNA FISH.", "date_created": "2022-05-20T08:51:59.588862+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "Chromatin tracing of BX-C in Drosophila", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-06-26T16:47:31.686117+00:00"}, "public_release": "2023-03-15", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"display_title": "multiplexed FISH on embryo - 4DNEX2QK6G63", "accession": "4DNEX2QK6G63", "@id": "/experiments-mic/4DNEX2QK6G63/", "uuid": "2ecfa688-994c-4a75-9805-ad587f9b98b4", "@type": ["ExperimentMic", "Experiment", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_headers": [{"lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "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 [84d52890-7e46-4cf8-810c-071ed0673ce8](https://data.4dnucleome.org/microscope-configurations/84d52890-7e46-4cf8-810c-071ed0673ce8) or [a2b6ca4e-7de9-484f-b8c3-c868b68f929e](https://data.4dnucleome.org/microscope-configurations/a2b6ca4e-7de9-484f-b8c3-c868b68f929e) microscopes.", "name": "microscope_note_mateo_2019", "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": "Microscope configuration - Mateo et al. 2019", "status": "released", "aliases": ["4dn-dcic-lab:4dn-dcic-lab:microscope_note_mateo_2019"], "options": {"filetype": "md", "collapsible": true, "default_open": true, "convert_ext_links": true}, "date_created": "2025-06-24T17:21:22.763623+00:00", "section_type": "Page Section", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-06-24T17:53:33.255560+00:00"}, "schema_version": "2", "@id": "/static-sections/297ecba1-56bc-4758-8aa6-831d0d286dd4/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "297ecba1-56bc-4758-8aa6-831d0d286dd4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.6f9809b1-b9b4-4f2f-8e6d-0762bce320ef"]}, "display_title": "Microscope configuration - Mateo et al. 2019", "external_references": [], "content": "The experiments associated with this study are derived from either [84d52890-7e46-4cf8-810c-071ed0673ce8](https://data.4dnucleome.org/microscope-configurations/84d52890-7e46-4cf8-810c-071ed0673ce8) 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/84d52890-7e46-4cf8-810c-071ed0673ce8\" rel=\"noopener noreferrer\" target=\"_blank\">84d52890-7e46-4cf8-810c-071ed0673ce8</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": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "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": {"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 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": "2023-03-15", "experiments_in_set": [{"status": "released", "accession": "4DNEX2QK6G63", "@type": ["ExperimentMic", "Experiment", "Item"], "@id": "/experiments-mic/4DNEX2QK6G63/", "uuid": "2ecfa688-994c-4a75-9805-ad587f9b98b4", "display_title": "multiplexed FISH on embryo - 4DNEX2QK6G63", "processed_files": [{"file_size": 39981844, "file_format": {"status": "released", "display_title": "csv", "@id": "/file-formats/csv/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "md5sum": "b8d12861e159a22b3ad77bc66d905729", "uuid": "8038f43a-1178-4149-80e2-3f221dc1be3d", "accession": "4DNFI33S94RO", "file_type_detailed": "FOF-CT - DNA-spot/trace core (csv)", "@id": "/files-processed/4DNFI33S94RO/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8038f43a-1178-4149-80e2-3f221dc1be3d/4DNFI33S94RO.csv", "genome_assembly": "dm6", "@type": ["FileProcessed", "File", "Item"], "upload_key": "8038f43a-1178-4149-80e2-3f221dc1be3d/4DNFI33S94RO.csv", "file_classification": "processed file", "display_title": "4DNFI33S94RO.csv", "file_type": "FOF-CT - DNA-spot/trace core", "href": "/files-processed/4DNFI33S94RO/@@download/4DNFI33S94RO.csv", "lab": {"@type": ["Lab", "Item"], "@id": "/labs/alistair-boettiger-lab/", "status": "current", "uuid": "312cb909-76a6-405d-a96c-c3292abf08a1", "display_title": "Alistair Boettiger, STANFORD", "name": "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": "52 consecutive 2-kb loci in the BX-C region (fruit fly)", "dataset": "Chromatin tracing of BX-C in Drosophila", "condition": "Fab-7 mutant, 2-kb resolution", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "embryo", "lab_name": "Alistair Boettiger, STANFORD"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "last_modified": {"date_modified": "2023-06-21T18:46:52.799007+00:00"}}, {"file_size": 5721731, "file_format": {"status": "released", "display_title": "csv", "@id": "/file-formats/csv/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "md5sum": "3f85ff0699b0ebc09084bf85582531ed", "uuid": "b085c7d2-f434-4ca3-a1b4-f5270c799061", "accession": "4DNFIDX6D81X", "file_type_detailed": "FOF-CT - spot quality (csv)", "@id": "/files-processed/4DNFIDX6D81X/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/b085c7d2-f434-4ca3-a1b4-f5270c799061/4DNFIDX6D81X.csv", "genome_assembly": "dm6", "@type": ["FileProcessed", "File", "Item"], "upload_key": "b085c7d2-f434-4ca3-a1b4-f5270c799061/4DNFIDX6D81X.csv", "file_classification": "processed file", "display_title": "4DNFIDX6D81X.csv", "file_type": "FOF-CT - spot quality", "href": "/files-processed/4DNFIDX6D81X/@@download/4DNFIDX6D81X.csv", "lab": {"@type": ["Lab", "Item"], "@id": "/labs/alistair-boettiger-lab/", "status": "current", "uuid": "312cb909-76a6-405d-a96c-c3292abf08a1", "display_title": "Alistair Boettiger, STANFORD", "name": "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": "52 consecutive 2-kb loci in the BX-C region (fruit fly)", "dataset": "Chromatin tracing of BX-C in Drosophila", "condition": "Fab-7 mutant, 2-kb resolution", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "embryo", "lab_name": "Alistair Boettiger, STANFORD"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "last_modified": {"date_modified": "2023-06-21T18:46:49.422780+00:00"}}, {"file_size": 2321517, "file_format": {"status": "released", "display_title": "csv", "@id": "/file-formats/csv/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "md5sum": "f6040fd2ac0ad72be51dedec96cdef61", "uuid": "00d16456-6a54-4872-b2ee-8a4a4fe95831", "accession": "4DNFIX7ZLPU4", "file_type_detailed": "FOF-CT - cell data (csv)", "@id": "/files-processed/4DNFIX7ZLPU4/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/00d16456-6a54-4872-b2ee-8a4a4fe95831/4DNFIX7ZLPU4.csv", "genome_assembly": "dm6", "@type": ["FileProcessed", "File", "Item"], "upload_key": "00d16456-6a54-4872-b2ee-8a4a4fe95831/4DNFIX7ZLPU4.csv", "file_classification": "processed file", "display_title": "4DNFIX7ZLPU4.csv", "file_type": "FOF-CT - cell data", "href": "/files-processed/4DNFIX7ZLPU4/@@download/4DNFIX7ZLPU4.csv", "lab": {"@type": ["Lab", "Item"], "@id": "/labs/alistair-boettiger-lab/", "status": "current", "uuid": "312cb909-76a6-405d-a96c-c3292abf08a1", "display_title": "Alistair Boettiger, STANFORD", "name": "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": "52 consecutive 2-kb loci in the BX-C region (fruit fly)", "dataset": "Chromatin tracing of BX-C in Drosophila", "condition": "Fab-7 mutant, 2-kb resolution", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "embryo", "lab_name": "Alistair Boettiger, STANFORD"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "last_modified": {"date_modified": "2023-06-21T18:46:46.880090+00:00"}}], "biosample": {"@type": ["Biosample", "Item"], "biosource_summary": "embryo", "modifications_summary": "None", "uuid": "f94e6844-2e97-4b2b-9ef9-febc21377f47", "biosample_category": ["Multicellular Tissue"], "accession": "4DNBSEX5ZSCZ", "biosample_type": "tissue", "display_title": "4DNBSEX5ZSCZ", "treatments_summary": "None", "@id": "/biosamples/4DNBSEX5ZSCZ/", "status": "released", "biosource": [{"cell_line_tier": "Unclassified", "uuid": "9a60dbc8-3421-43a4-bf3a-b0c6b577f3a2", "display_title": "embryo - 4DNSRIJMG1TH", "biosource_type": "tissue", "@id": "/biosources/4DNSRIJMG1TH/", "@type": ["Biosource", "Item"], "accession": "4DNSRIJMG1TH", "status": "released", "tissue": {"preferred_name": "embryo", "term_id": "UBERON:0000922", "status": "released", "display_title": "embryo", "@type": ["OntologyTerm", "Item"], "synonyms": ["embryonic organism"], "uuid": "94a7d7e3-b38e-462a-91e6-55df4a2c120f", "term_name": "embryo", "@id": "/ontology-terms/UBERON:0000922/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/7227/", "display_title": "D. melanogaster", "@type": ["Organism", "Item"], "name": "fruit fly", "status": "released", "scientific_name": "Drosophila melanogaster", "uuid": "b3911449-1b28-44cf-af23-084ae4eff147", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"tissue_source": "embryo"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "reference_files": [{"file_type_detailed": "target regions (bed)", "href": "/files-reference/4DNFI9HYOM6I/@@download/4DNFI9HYOM6I.bed.gz", "accession": "4DNFI9HYOM6I", "file_classification": "ancillary file", "file_type": "target regions", "uuid": "b5fa0a90-0e82-4fd1-91b6-37a9b3d1a471", "@type": ["FileReference", "File", "Item"], "status": "released", "@id": "/files-reference/4DNFI9HYOM6I/", "file_size": 812, "display_title": "4DNFI9HYOM6I.bed.gz", "md5sum": "048358580d175e19567db97932d85eda", "lab": {"@type": ["Lab", "Item"], "status": "current", "uuid": "312cb909-76a6-405d-a96c-c3292abf08a1", "display_title": "Alistair Boettiger, STANFORD", "@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"]}}, "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFI9HYOM6I", "uuid": "f73d5d91-7fc5-47a3-8f0e-2cfaf5a52062", "@id": "/higlass-view-configs/f73d5d91-7fc5-47a3-8f0e-2cfaf5a52062/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "file_format": {"@type": ["FileFormat", "Item"], "file_format": "bed", "display_title": "bed", "status": "released", "@id": "/file-formats/bed/", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "oligo sequences (zip)", "href": "/files-reference/4DNFIK62FTWO/@@download/4DNFIK62FTWO.zip", "accession": "4DNFIK62FTWO", "file_classification": "ancillary file", "file_type": "oligo sequences", "uuid": "956eca8a-e546-4462-a75b-2a9e47ae3e0d", "@type": ["FileReference", "File", "Item"], "status": "released", "@id": "/files-reference/4DNFIK62FTWO/", "file_size": 1853410, "display_title": "4DNFIK62FTWO.zip", "md5sum": "f6cf6451f365137716e353a4708b901a", "lab": {"@type": ["Lab", "Item"], "status": "current", "uuid": "312cb909-76a6-405d-a96c-c3292abf08a1", "display_title": "Alistair Boettiger, STANFORD", "@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"]}}, "file_format": {"@type": ["FileFormat", "Item"], "file_format": "zip", "display_title": "zip", "status": "released", "@id": "/file-formats/zip/", "uuid": "d13d06cf-218e-4f61-44f0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"value": "52 consecutive 2-kb loci in the BX-C region (fruit fly)", "field": "Target", "combined": "Target: 52 consecutive 2-kb loci in the BX-C region (fruit fly)"}, "experiment_type": {"assay_subclass_short": "FISH", "experiment_category": "Microscopy", "@type": ["ExperimentType", "Item"], "other_tags": ["Single Cell"], "assay_classification": "Fluorescence Localization", "assay_subclassification": "Chromatin Tracing", "@id": "/experiment-types/multiplexed-fish/", "uuid": "bcdda46a-489d-4d22-be80-c9c21552c915", "display_title": "multiplexed FISH", "title": "multiplexed FISH", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "last_modified": {"date_modified": "2023-03-15T15:22:25.759419+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESRHE38D8/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "255bb785-2e3d-4ab9-82aa-652faf5181bb", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESRHE38D8", "external_references": [], "produced_in_pub": {"abstract": "The establishment of cell types during development requires precise interactions  between genes and distal regulatory sequences. We have a limited understanding of  how these interactions look in three dimensions, vary across cell types in  complex tissue, and relate to transcription. Here we describe optical  reconstruction of chromatin architecture (ORCA), a method that can trace the DNA  path in single cells with nanoscale accuracy and genomic resolution reaching two  kilobases. We used ORCA to study a Hox gene cluster in cryosectioned Drosophila  embryos and labelled around 30 RNA species in parallel. We identified  cell-type-specific physical borders between active and Polycomb-repressed DNA,  and unexpected Polycomb-independent borders. Deletion of Polycomb-independent  borders led to ectopic enhancer-promoter contacts, aberrant gene expression, and  developmental defects. Together, these results illustrate an approach for  high-resolution, single-cell DNA domain analysis in vivo, identify domain  structures that change with cell identity, and show that border elements  contribute to the formation of physical domains in Drosophila.", "uuid": "6c007db6-3eba-41d8-9d50-cb7e7c05841f", "short_attribution": "Mateo LJ et al. (2019)", "journal": "Nature", "authors": ["Mateo LJ", "Murphy SE", "Hafner A", "Cinquini IS", "Walker CA", "Boettiger AN"], "ID": "PMID:30886393", "@id": "/publications/6c007db6-3eba-41d8-9d50-cb7e7c05841f/", "date_published": "2019-04", "url": "https://www.ncbi.nlm.nih.gov/pubmed/30886393", "display_title": "Mateo LJ et al. (2019) PMID:30886393", "title": "Visualizing DNA folding and RNA in embryos at single-cell resolution.", "status": "current", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"title": "Visualizing DNA folding and RNA in embryos at single-cell resolution.", "uuid": "6c007db6-3eba-41d8-9d50-cb7e7c05841f", "display_title": "Mateo LJ et al. (2019) PMID:30886393", "@id": "/publications/6c007db6-3eba-41d8-9d50-cb7e7c05841f/", "status": "current", "ID": "PMID:30886393", "date_published": "2019-04", "abstract": "The establishment of cell types during development requires precise interactions  between genes and distal regulatory sequences. We have a limited understanding of  how these interactions look in three dimensions, vary across cell types in  complex tissue, and relate to transcription. Here we describe optical  reconstruction of chromatin architecture (ORCA), a method that can trace the DNA  path in single cells with nanoscale accuracy and genomic resolution reaching two  kilobases. We used ORCA to study a Hox gene cluster in cryosectioned Drosophila  embryos and labelled around 30 RNA species in parallel. We identified  cell-type-specific physical borders between active and Polycomb-repressed DNA,  and unexpected Polycomb-independent borders. Deletion of Polycomb-independent  borders led to ectopic enhancer-promoter contacts, aberrant gene expression, and  developmental defects. Together, these results illustrate an approach for  high-resolution, single-cell DNA domain analysis in vivo, identify domain  structures that change with cell identity, and show that border elements  contribute to the formation of physical domains in Drosophila.", "@type": ["Publication", "Item"], "journal": "Nature", "authors": ["Mateo LJ", "Murphy SE", "Hafner A", "Cinquini IS", "Walker CA", "Boettiger AN"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 1, "imaging_paths": [{"path": {"@id": "/imaging-paths/f26bd2ff-1322-4c34-a80c-cc88c747c845/", "uuid": "f26bd2ff-1322-4c34-a80c-cc88c747c845", "@type": ["ImagingPath", "Item"], "status": "released", "display_title": "52 consecutive 2-kb loci in the BX-C region (fruit fly) targeted by oligo probe library (with Cy3-labeled fiducial oligo probes)", "labeled_probe": "fiducial oligo probes", "other_probes": ["oligo probe library"], "target": [{"status": "released", "preferred_label": "52 consecutive 2-kb loci in the BX-C region", "@id": "/bio-features/761fd245-d348-4d24-8d96-673279539166/", "uuid": "761fd245-d348-4d24-8d96-673279539166", "organism_name": "fruit fly", "@type": ["BioFeature", "Item"], "display_title": "52 consecutive 2-kb loci in the BX-C region (fruit fly)", "feature_type": {"@id": "/ontology-terms/SO:0000001/", "@type": ["OntologyTerm", "Item"], "uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "term_id": "SO:0000001", "preferred_name": "region", "term_name": "region", "term_url": "http://purl.obolibrary.org/obo/SO_0000001", "display_title": "region", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "genome_location": [{"location_description": "a 130-kb regulatory region of the bithorax complex (BX-C) spanning abd-A to Abd-B on chromosome 3R", "uuid": "889156f9-1c5d-4b65-8d34-c7ced619947d", "start_coordinate": 16809260, "display_title": "dm6:3R:16809260-16939263", "status": "released", "@id": "/genomic-regions/889156f9-1c5d-4b65-8d34-c7ced619947d/", "genome_assembly": "dm6", "chromosome": "3R", "end_coordinate": 16939263, "@type": ["GenomicRegion", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_type": {"@type": ["ExperimentType", "Item"], "status": "released", "@id": "/experiment-types/dna-fish/", "title": "DNA FISH", "display_title": "DNA FISH", "uuid": "5761d0ec-35b0-4aa8-8b81-aac94def59b8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch00"}, {"path": {"@id": "/imaging-paths/65af0a21-c044-4a03-8690-7021698668d7/", "uuid": "65af0a21-c044-4a03-8690-7021698668d7", "@type": ["ImagingPath", "Item"], "status": "released", "display_title": "52 consecutive 2-kb loci in the BX-C region (fruit fly) targeted by oligo probe library, readout oligo library (with Cy5-labeled imaging oligos)", "labeled_probe": "imaging oligos", "other_probes": ["oligo probe library", "readout oligo library"], "target": [{"status": "released", "preferred_label": "52 consecutive 2-kb loci in the BX-C region", "@id": "/bio-features/761fd245-d348-4d24-8d96-673279539166/", "uuid": "761fd245-d348-4d24-8d96-673279539166", "organism_name": "fruit fly", "@type": ["BioFeature", "Item"], "display_title": "52 consecutive 2-kb loci in the BX-C region (fruit fly)", "feature_type": {"@id": "/ontology-terms/SO:0000001/", "@type": ["OntologyTerm", "Item"], "uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "term_id": "SO:0000001", "preferred_name": "region", "term_name": "region", "term_url": "http://purl.obolibrary.org/obo/SO_0000001", "display_title": "region", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "genome_location": [{"location_description": "a 130-kb regulatory region of the bithorax complex (BX-C) spanning abd-A to Abd-B on chromosome 3R", "uuid": "889156f9-1c5d-4b65-8d34-c7ced619947d", "start_coordinate": 16809260, "display_title": "dm6:3R:16809260-16939263", "status": "released", "@id": "/genomic-regions/889156f9-1c5d-4b65-8d34-c7ced619947d/", "genome_assembly": "dm6", "chromosome": "3R", "end_coordinate": 16939263, "@type": ["GenomicRegion", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_type": {"@type": ["ExperimentType", "Item"], "status": "released", "@id": "/experiment-types/dna-fish/", "title": "DNA FISH", "display_title": "DNA FISH", "uuid": "5761d0ec-35b0-4aa8-8b81-aac94def59b8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch01"}], "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/experiment-set-replicates/4DNESRHE38D8/", "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": []}