{"lab": {"status": "current", "uuid": "eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb", "title": "Xiaowei Zhuang, HARVARD", "@id": "/labs/xiaowei-zhuang-lab/", "correspondence": [{"contact_email": "emh1YW5nQGNoZW1pc3RyeS5oYXJ2YXJkLmVkdQ==", "@id": "/users/acfc5a08-19ff-47ef-9261-75e6134dc0fe/", "display_title": "Xiaowei Zhuang"}], "@type": ["Lab", "Item"], "display_title": "Xiaowei Zhuang, HARVARD", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb"]}}, "award": {"@type": ["Award", "Item"], "name": "1UM1HG011585-01", "@id": "/awards/1UM1HG011585-01/", "project": "4DN", "status": "current", "description": "CDIMV: The transcriptional regulatory sequences communicate with each other dynamically in the 3D nuclear space to direct cell type specific gene expression. Currently, a major barrier to understanding the transcriptional regulatory programs is the lack of tools, models and maps to explore the chromatin architecture in diverse cell types and physiological contexts. We will address this pressing need by deploying transformative technologies to study the chromatin architecture in mammalian cells at an unprecedented resolution and scale. Specifically, we will generate navigable, cell-type-specific reference maps of chromatin architecture in the mouse, macaque and human brains by integrating high resolution and high throughput imaging and orthogonal single-cell-based genomic methods. We will also dissect the role of chromatin architecture in gene regulation through a set of controlled perturbation experiments in the mouse ES cells (ESC) and ESC-derived neural progenitor cells (NPC). We will develop structural models of chromatin organization with advanced polymer physics and statistical learning methods, and validate their predictive power in embryonic stem cells and in ex vivo brain slices. Finally, we will make the reference maps, analytical tools, visualization methods and structural models available to the broader community. The proposed research project will dramatically transform our ability to analyze the 4D Nucleome of complex tissues, and produce the much-needed maps, tools and models for understanding the gene regulatory programs encoded in the linear genome sequences.", "uuid": "ee89349a-1d43-4048-9142-bc750f0f3b32", "display_title": "CENTER FOR INTEGRATED MULTI-MODAL AND MULTI-SCALE NUCLEOME RESEARCH", "center_title": "CDIMV - Ren", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["xiaowei-zhuang-lab:experiment_dna-merfish_combined_rna-merfish_B1_T1"], "protocol": {"uuid": "d39ddb61-5d16-4e13-833d-4c8349382466", "display_title": "Experimental protocol", "@type": ["Protocol", "Item"], "@id": "/protocols/d39ddb61-5d16-4e13-833d-4c8349382466/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEXCWE7KU7", "biosample": {"@id": "/biosamples/4DNBSUH1CEQ3/", "biosample_type": "primary cells", "display_title": "4DNBSUH1CEQ3", "biosource_summary": "IMR-90", "accession": "4DNBSUH1CEQ3", "treatments_summary": "None", "modifications_summary": "None", "@type": ["Biosample", "Item"], "status": "released", "uuid": "5561b359-76ca-4612-9b25-58f909eae368", "biosource": [{"lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "url": "https://www.atcc.org/Products/All/CCL-186.aspx", "award": {"@type": ["Award", "Item"], "@id": "/awards/1U01CA200059-01/", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"@id": "/ontology-terms/CL:0002553/", "@type": ["OntologyTerm", "Item"], "preferred_name": "fibroblast of lung", "term_id": "CL:0002553", "term_name": "fibroblast of lung", "uuid": "999f1c8c-f02b-4a2b-b269-53ec1234b26f", "slim_terms": [{"@id": "/ontology-terms/UBERON:0000925/", "display_title": "endoderm", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "111121bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/UBERON:0002048/", "display_title": "lung", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "111186bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/UBERON:0001004/", "display_title": "respiratory system", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "111128bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "status": "released", "synonyms": ["NHLF", "fibroblast of lung"], "display_title": "fibroblast of lung", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["4dn-dcic-lab:IMR90", "dcic:IMR90"], "accession": "4DNSRXXGU3CH", "cell_line": {"display_title": "IMR-90", "status": "released", "@type": ["OntologyTerm", "Item"], "synonyms": ["IMR90"], "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "status": "current", "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "status": "released", "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "term_name": "IMR-90", "@id": "/ontology-terms/EFO:0001196/", "uuid": "c45d70f2-980b-4a6c-b762-bb48fdd7913a", "term_id": "EFO:0001196", "preferred_name": "IMR-90", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"uuid": "2fc29bbe-5796-4c28-956e-8d0188f6664b", "protected_data": false, "status": "released", "display_title": "4DNINX7ADWH2", "@type": ["IndividualHuman", "Individual", "Item"], "@id": "/individuals-human/4DNINX7ADWH2/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "references": [], "description": "IMR-90 (CCL-186)", "date_created": "2017-04-09T17:24:20.718751+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-06-04T20:11:34.703877+00:00"}, "modifications": [], "biosource_type": "primary cell line", "cell_line_tier": "Unclassified", "public_release": "2017-04-09", "schema_version": "2", "project_release": "2017-04-09", "biosource_vendor": {"@id": "/vendors/american-type-culture-collection/", "uuid": "7a6f2efe-5be8-4db2-afa8-d82e9b4ad254", "display_title": "American Type Culture Collection", "status": "released", "@type": ["Vendor", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "alternate_accessions": [], "@id": "/biosources/4DNSRXXGU3CH/", "@type": ["Biosource", "Item"], "uuid": "26ebb2b1-2902-4446-a25f-9fc6523ed5cf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "IMR-90 - 4DNSRXXGU3CH", "external_references": [], "biosource_name": "IMR-90", "biosource_category": ["IMR-90"], "organism": {"name": "human", "@id": "/organisms/9606/", "@type": ["Organism", "Item"], "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "status": "released", "display_title": "H. sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "badges": [{"messages": ["Biosample missing Cell Culture Details"], "badge": {"title": "Biosample Metadata Incomplete", "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@type": ["Badge", "Item"], "@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.", "display_title": "Biosample Metadata Incomplete", "badge_classification": "Warning", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "DNA-MERFISH combined with RNA MERFISH to detect nascent RNA transcripts of 1137 genes overlapping with 1,041 genomic loci targeted by DNA-MERFISH, Biological replicate 1, Technical replicate 1", "sop_mapping": {"has_sop": "No"}, "date_created": "2024-10-17T14:36:35.704658+00:00", "submitted_by": {"error": "no view permissions"}, "imaging_paths": [{"path": {"@id": "/imaging-paths/7be4b194-b0bf-4583-a940-53d39fe96f94/", "uuid": "7be4b194-b0bf-4583-a940-53d39fe96f94", "labeled_probe": "DAPI", "status": "released", "@type": ["ImagingPath", "Item"], "display_title": "Chromosomes targeted by DAPI", "target": [{"organism_name": "unspecified", "status": "released", "display_title": "Chromosomes", "cellular_structure": "Chromosomes", "uuid": "655728f9-d4ab-4dd2-971c-1627ab2c8d33", "@type": ["BioFeature", "Item"], "@id": "/bio-features/655728f9-d4ab-4dd2-971c-1627ab2c8d33/", "feature_type": {"term_url": "http://purl.obolibrary.org/obo/GO_0005575", "uuid": "e47e2bea-bc1e-4989-881c-521fc0b33529", "term_id": "GO:0005575", "@id": "/ontology-terms/GO:0005575/", "display_title": "cellular_component", "@type": ["OntologyTerm", "Item"], "preferred_name": "cellular_component", "status": "released", "term_name": "cellular_component", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch00"}, {"path": {"@id": "/imaging-paths/3bb9a0aa-f440-4a12-997f-34d3d498fe3c/", "imaging_rounds": "1-18", "uuid": "3bb9a0aa-f440-4a12-997f-34d3d498fe3c", "labeled_probe": "imaging oligos", "other_probes": ["oligo probe library", "readout oligo library"], "status": "released", "@type": ["ImagingPath", "Item"], "display_title": "RNA-MERFISH to detect 1137 genes overlapping 1041 genomic loci (targeted by DNA MERFISH) by Alexa Flour 750-labeled imaging oligos", "override_display_title": "RNA-MERFISH to detect 1137 genes overlapping 1041 genomic loci (targeted by DNA MERFISH) by Alexa Flour 750-labeled imaging oligos", "target": [{"organism_name": "human", "status": "released", "display_title": "transcript", "uuid": "1a7f48ac-a39e-4570-88dd-d3c948774b53", "@type": ["BioFeature", "Item"], "@id": "/bio-features/1a7f48ac-a39e-4570-88dd-d3c948774b53/", "feature_type": {"term_url": "http://purl.obolibrary.org/obo/SO_0000673", "uuid": "e8f56a24-20ce-4e7c-9e8d-a4f409398574", "term_id": "SO:0000673", "@id": "/ontology-terms/SO:0000673/", "display_title": "transcript", "@type": ["OntologyTerm", "Item"], "preferred_name": "transcript", "status": "released", "term_name": "transcript", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch01"}, {"path": {"@id": "/imaging-paths/878fd648-7589-4942-8583-80e65e3036f1/", "imaging_rounds": "1-18", "uuid": "878fd648-7589-4942-8583-80e65e3036f1", "labeled_probe": "imaging oligos", "other_probes": ["oligo probe library", "readout oligo library"], "status": "released", "@type": ["ImagingPath", "Item"], "display_title": "RNA-MERFISH to detect 1137 genes overlapping 1041 genomic loci (targeted by DNA MERFISH) by Alexa Flour 647-labeled imaging oligos", "override_display_title": "RNA-MERFISH to detect 1137 genes overlapping 1041 genomic loci (targeted by DNA MERFISH) by Alexa Flour 647-labeled imaging oligos", "target": [{"organism_name": "human", "status": "released", "display_title": "transcript", "uuid": "1a7f48ac-a39e-4570-88dd-d3c948774b53", "@type": ["BioFeature", "Item"], "@id": "/bio-features/1a7f48ac-a39e-4570-88dd-d3c948774b53/", "feature_type": {"term_url": "http://purl.obolibrary.org/obo/SO_0000673", "uuid": "e8f56a24-20ce-4e7c-9e8d-a4f409398574", "term_id": "SO:0000673", "@id": "/ontology-terms/SO:0000673/", "display_title": "transcript", "@type": ["OntologyTerm", "Item"], "preferred_name": "transcript", "status": "released", "term_name": "transcript", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch02"}, {"path": {"@id": "/imaging-paths/fcd47739-3121-40ae-a77a-102e620c17d7/", "imaging_rounds": "1-18", "uuid": "fcd47739-3121-40ae-a77a-102e620c17d7", "labeled_probe": "imaging oligos", "other_probes": ["oligo probe library", "readout oligo library"], "status": "released", "@type": ["ImagingPath", "Item"], "display_title": "RNA-MERFISH to detect 1137 genes overlapping 1041 genomic loci (targeted by DNA MERFISH) by Cy3-labeled imaging oligos", "override_display_title": "RNA-MERFISH to detect 1137 genes overlapping 1041 genomic loci (targeted by DNA MERFISH) by Cy3-labeled imaging oligos", "target": [{"organism_name": "human", "status": "released", "display_title": "transcript", "uuid": "1a7f48ac-a39e-4570-88dd-d3c948774b53", "@type": ["BioFeature", "Item"], "@id": "/bio-features/1a7f48ac-a39e-4570-88dd-d3c948774b53/", "feature_type": {"term_url": "http://purl.obolibrary.org/obo/SO_0000673", "uuid": "e8f56a24-20ce-4e7c-9e8d-a4f409398574", "term_id": "SO:0000673", "@id": "/ontology-terms/SO:0000673/", "display_title": "transcript", "@type": ["OntologyTerm", "Item"], "preferred_name": "transcript", "status": "released", "term_name": "transcript", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch03"}, {"path": {"@id": "/imaging-paths/bd7dc770-1b7b-466d-bc5f-b3553468bc77/", "imaging_rounds": "1-50", "uuid": "bd7dc770-1b7b-466d-bc5f-b3553468bc77", "labeled_probe": "imaging oligos", "other_probes": ["oligo probe library", "readout oligo library"], "status": "released", "@type": ["ImagingPath", "Item"], "display_title": "DNA-MERFISH to detect 100-kb 1041 genomic loci covering 22 automosome and X chromosome by Alexa Flour 750-labeled imaging oligos", "override_display_title": "DNA-MERFISH to detect 100-kb 1041 genomic loci covering 22 automosome and X chromosome by Alexa Flour 750-labeled imaging oligos", "target": [{"organism_name": "human", "status": "released", "display_title": "region", "uuid": "80d89b4d-616b-4903-b91d-0718568e5108", "@type": ["BioFeature", "Item"], "@id": "/bio-features/80d89b4d-616b-4903-b91d-0718568e5108/", "feature_type": {"term_url": "http://purl.obolibrary.org/obo/SO_0000001", "uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "term_id": "SO:0000001", "@id": "/ontology-terms/SO:0000001/", "display_title": "region", "@type": ["OntologyTerm", "Item"], "preferred_name": "region", "status": "released", "term_name": "region", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch01"}, {"path": {"@id": "/imaging-paths/ca8d476f-9c24-4fb6-aaf3-05343e8dc792/", "imaging_rounds": "1-50", "uuid": "ca8d476f-9c24-4fb6-aaf3-05343e8dc792", "labeled_probe": "imaging oligos", "other_probes": ["oligo probe library", "readout oligo library"], "status": "released", "@type": ["ImagingPath", "Item"], "display_title": "DNA-MERFISH to detect 100-kb 1041 genomic loci covering 22 automosome and X chromosome by Alexa Flour 647-labeled imaging oligos", "override_display_title": "DNA-MERFISH to detect 100-kb 1041 genomic loci covering 22 automosome and X chromosome by Alexa Flour 647-labeled imaging oligos", "target": [{"organism_name": "human", "status": "released", "display_title": "region", "uuid": "80d89b4d-616b-4903-b91d-0718568e5108", "@type": ["BioFeature", "Item"], "@id": "/bio-features/80d89b4d-616b-4903-b91d-0718568e5108/", "feature_type": {"term_url": "http://purl.obolibrary.org/obo/SO_0000001", "uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "term_id": "SO:0000001", "@id": "/ontology-terms/SO:0000001/", "display_title": "region", "@type": ["OntologyTerm", "Item"], "preferred_name": "region", "status": "released", "term_name": "region", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch02"}], "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-10-18T22:35:29.947467+00:00"}, "public_release": "2024-10-18", "schema_version": "3", "experiment_type": {"@id": "/experiment-types/multiplexed-fish/", "title": "multiplexed FISH", "uuid": "bcdda46a-489d-4d22-be80-c9c21552c915", "experiment_category": "Microscopy", "assay_subclass_short": "FISH", "display_title": "multiplexed FISH", "@type": ["ExperimentType", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"upload_key": "117fc3ae-25ef-49a8-b44a-d516c323d859/4DNFIXMERLJQ.csv", "accession": "4DNFIXMERLJQ", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "file_format": "csv", "@id": "/file-formats/csv/", "display_title": "csv", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/files-processed/4DNFIXMERLJQ/", "file_type": "FOF-CT - DNA-spot/trace core", "@type": ["FileProcessed", "File", "Item"], "href": "/files-processed/4DNFIXMERLJQ/@@download/4DNFIXMERLJQ.csv", "file_type_detailed": "FOF-CT - DNA-spot/trace core (csv)", "uuid": "117fc3ae-25ef-49a8-b44a-d516c323d859", "file_size": 516143068, "file_classification": "processed file", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/117fc3ae-25ef-49a8-b44a-d516c323d859/4DNFIXMERLJQ.csv", "display_title": "4DNFIXMERLJQ.csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Xiaowei Zhuang, HARVARD", "experiment_type": "multiplexed FISH", "experiment_bucket": "processed file", "assay_info": "Chromosomes, transcript, region", "dataset": "Genome-scale imaging in IMR90 cells", "condition": "DNA-MERFISH + RNA-MERFISH of 1137 genes", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "IMR-90", "lab_name": "Xiaowei Zhuang, HARVARD"}, "external_references": []}, {"upload_key": "a607c36b-8c1e-4acd-a1a6-f55b9708761a/4DNFI7UYX9PP.csv", "accession": "4DNFI7UYX9PP", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "file_format": "csv", "@id": "/file-formats/csv/", "display_title": "csv", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/files-processed/4DNFI7UYX9PP/", "file_type": "FOF-CT - spot biological data", "@type": ["FileProcessed", "File", "Item"], "href": "/files-processed/4DNFI7UYX9PP/@@download/4DNFI7UYX9PP.csv", "file_type_detailed": "FOF-CT - spot biological data (csv)", "uuid": "a607c36b-8c1e-4acd-a1a6-f55b9708761a", "file_size": 184291863, "file_classification": "processed file", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a607c36b-8c1e-4acd-a1a6-f55b9708761a/4DNFI7UYX9PP.csv", "display_title": "4DNFI7UYX9PP.csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Xiaowei Zhuang, HARVARD", "experiment_type": "multiplexed FISH", "experiment_bucket": "processed file", "assay_info": "Chromosomes, transcript, region", "dataset": "Genome-scale imaging in IMR90 cells", "condition": "DNA-MERFISH + RNA-MERFISH of 1137 genes", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "IMR-90", "lab_name": "Xiaowei Zhuang, HARVARD"}, "external_references": []}, {"upload_key": "cd9cc04e-09e8-4ebd-92ac-c08ddfa5c6d7/4DNFI6HBZKKH.csv", "accession": "4DNFI6HBZKKH", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "file_format": "csv", "@id": "/file-formats/csv/", "display_title": "csv", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/files-processed/4DNFI6HBZKKH/", "file_type": "FOF-CT - RNA-spot", "@type": ["FileProcessed", "File", "Item"], "href": "/files-processed/4DNFI6HBZKKH/@@download/4DNFI6HBZKKH.csv", "file_type_detailed": "FOF-CT - RNA-spot (csv)", "uuid": "cd9cc04e-09e8-4ebd-92ac-c08ddfa5c6d7", "file_size": 300600794, "file_classification": "processed file", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/cd9cc04e-09e8-4ebd-92ac-c08ddfa5c6d7/4DNFI6HBZKKH.csv", "display_title": "4DNFI6HBZKKH.csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Xiaowei Zhuang, HARVARD", "experiment_type": "multiplexed FISH", "experiment_bucket": "processed file", "assay_info": "Chromosomes, transcript, region", "dataset": "Genome-scale imaging in IMR90 cells", "condition": "DNA-MERFISH + RNA-MERFISH of 1137 genes", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "IMR-90", "lab_name": "Xiaowei Zhuang, HARVARD"}, "external_references": []}], "project_release": "2024-10-18", "reference_files": [{"display_title": "4DNFIQZONHBV.zip", "file_type": "oligo sequences", "status": "released", "@id": "/files-reference/4DNFIQZONHBV/", "file_classification": "ancillary file", "@type": ["FileReference", "File", "Item"], "file_type_detailed": "oligo sequences (zip)", "file_size": 11642533, "uuid": "073451b2-7bc7-460c-af5a-f3c040862eee", "accession": "4DNFIQZONHBV", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "uuid": "d13d06cf-218e-4f61-44f0-91f226248b2c", "@id": "/file-formats/zip/", "display_title": "zip", "file_format": "zip", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "4DNFI845HUSN.bed.gz", "file_type": "target regions", "status": "released", "@id": "/files-reference/4DNFI845HUSN/", "file_classification": "ancillary file", "@type": ["FileReference", "File", "Item"], "file_type_detailed": "target regions (bed)", "file_size": 6461, "uuid": "a98bae85-0c76-47c3-8b4e-f1e11fa939b8", "accession": "4DNFI845HUSN", "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/8343ae6b-87f6-48dd-bf2f-72b1ada99609/", "display_title": "4DNFI845HUSN", "status": "released", "uuid": "8343ae6b-87f6-48dd-bf2f-72b1ada99609", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "@id": "/file-formats/bed/", "display_title": "bed", "file_format": "bed", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "4DNFIM7F5AX2.txt", "file_type": "target genes", "status": "released", "@id": "/files-reference/4DNFIM7F5AX2/", "file_classification": "ancillary file", "@type": ["FileReference", "File", "Item"], "file_type_detailed": "target genes (txt)", "file_size": 60567, "uuid": "bd6574ee-e4d6-47ea-a5d0-35ff26695414", "accession": "4DNFIM7F5AX2", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "@id": "/file-formats/txt/", "display_title": "txt", "file_format": "txt", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "extinguishing_method": "fluorophore cleavage", "microscopy_technique": "Widefield", "@id": "/experiments-mic/4DNEXCWE7KU7/", "@type": ["ExperimentMic", "Experiment", "Item"], "uuid": "cafbe517-c000-4af6-99e6-2682adc2baad", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "multiplexed FISH on IMR-90 - 4DNEXCWE7KU7", "external_references": [], "experiment_sets": [{"@id": "/experiment-set-replicates/4DNES5C3XVFP/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNES5C3XVFP", "accession": "4DNES5C3XVFP", "uuid": "e69ae529-ccc8-4303-b7d9-9b7b0641abe8", "experimentset_type": "replicate", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"@type": ["Publication", "Item"], "status": "current", "title": "Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of  Chromatin.", "abstract": "The 3D organization of chromatin regulates many genome functions. Our  understanding of 3D genome organization requires tools to directly visualize  chromatin conformation in its native context. Here we report an imaging  technology for visualizing chromatin organization across multiple scales in  single cells with high genomic throughput. First we demonstrate multiplexed  imaging of hundreds of genomic loci by sequential hybridization, which allows  high-resolution conformation tracing of whole chromosomes. Next we report a  multiplexed error-robust fluorescence in situ hybridization (MERFISH)-based  method for genome-scale chromatin tracing and demonstrate simultaneous imaging of  more than 1,000 genomic loci and nascent transcripts of more than 1,000 genes  together with landmark nuclear structures. Using this technology, we characterize  chromatin domains, compartments, and trans-chromosomal interactions and their  relationship to transcription in single cells. We envision broad application of  this high-throughput, multi-scale, and multi-modal imaging technology, which  provides an integrated view of chromatin organization in its native structural  and functional context.", "@id": "/publications/bd20862a-7c4c-4a95-9721-e880181da2d4/", "ID": "PMID:32822575", "display_title": "Su JH et al. (2020) PMID:32822575", "journal": "Cell", "uuid": "bd20862a-7c4c-4a95-9721-e880181da2d4", "authors": ["Su JH", "Zheng P", "Kinrot SS", "Bintu B", "Zhuang X"], "date_published": "2020-09-17", "short_attribution": "Su JH et al. (2020)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"short_attribution": "Su JH et al. (2020)", "display_title": "Su JH et al. (2020) PMID:32822575", "journal": "Cell", "authors": ["Su JH", "Zheng P", "Kinrot SS", "Bintu B", "Zhuang X"], "uuid": "bd20862a-7c4c-4a95-9721-e880181da2d4", "abstract": "The 3D organization of chromatin regulates many genome functions. Our  understanding of 3D genome organization requires tools to directly visualize  chromatin conformation in its native context. Here we report an imaging  technology for visualizing chromatin organization across multiple scales in  single cells with high genomic throughput. First we demonstrate multiplexed  imaging of hundreds of genomic loci by sequential hybridization, which allows  high-resolution conformation tracing of whole chromosomes. Next we report a  multiplexed error-robust fluorescence in situ hybridization (MERFISH)-based  method for genome-scale chromatin tracing and demonstrate simultaneous imaging of  more than 1,000 genomic loci and nascent transcripts of more than 1,000 genes  together with landmark nuclear structures. Using this technology, we characterize  chromatin domains, compartments, and trans-chromosomal interactions and their  relationship to transcription in single cells. We envision broad application of  this high-throughput, multi-scale, and multi-modal imaging technology, which  provides an integrated view of chromatin organization in its native structural  and functional context.", "title": "Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of  Chromatin.", "status": "current", "ID": "PMID:32822575", "date_published": "2020-09-17", "@id": "/publications/bd20862a-7c4c-4a95-9721-e880181da2d4/", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "value": "Chromosomes, transcript, region", "combined": "Target: Chromosomes, transcript, region"}, "experiment_summary": "multiplexed FISH on IMR-90", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSUH1CEQ3/", "embedded_path": "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."}}}]}, "validation-errors": []}