{"lab": {"@type": ["Lab", "Item"], "uuid": "eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb", "correspondence": [{"contact_email": "emh1YW5nQGNoZW1pc3RyeS5oYXJ2YXJkLmVkdQ==", "@id": "/users/acfc5a08-19ff-47ef-9261-75e6134dc0fe/", "display_title": "Xiaowei Zhuang"}], "status": "current", "display_title": "Xiaowei Zhuang, HARVARD", "@id": "/labs/xiaowei-zhuang-lab/", "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": {"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.", "project": "4DN", "@id": "/awards/1UM1HG011585-01/", "center_title": "CDIMV - Ren", "display_title": "CENTER FOR INTEGRATED MULTI-MODAL AND MULTI-SCALE NUCLEOME RESEARCH", "name": "1UM1HG011585-01", "@type": ["Award", "Item"], "status": "current", "uuid": "ee89349a-1d43-4048-9142-bc750f0f3b32", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "badges": [{"badge": {"warning": "Replicate Numbers", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "display_title": "Replicate Numbers", "@id": "/badges/replicate-numbers/", "title": "Replicate Numbers", "description": "Issues with replicate numbers", "status": "released", "badge_classification": "Warning", "@type": ["Badge", "Item"], "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Replicate set contains only a single biological replicate"]}], "status": "released", "aliases": ["xiaowei-zhuang-lab:expset_dna-merfish_combined_rna-merfish"], "accession": "4DNES5C3XVFP", "condition": "DNA-MERFISH + RNA-MERFISH of 1137 genes", "description": "DNA-MERFISH combined with RNA-MERFISH to detect nascent RNA transcripts of 1137 genes overlapping with 1041 genomic loci targeted by DNA-MERFISH", "date_created": "2024-10-17T14:36:38.793241+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "Genome-scale imaging in IMR90 cells", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-06-26T16:57:11.688314+00:00"}, "public_release": "2024-10-18", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"display_title": "multiplexed FISH on IMR-90 - 4DNEXCWE7KU7", "status": "released", "@type": ["ExperimentMic", "Experiment", "Item"], "uuid": "cafbe517-c000-4af6-99e6-2682adc2baad", "@id": "/experiments-mic/4DNEXCWE7KU7/", "accession": "4DNEXCWE7KU7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_headers": [{"lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "status": "current", "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 [b489483d-e203-45e1-b52f-fe5e8c8538e0](https://data.4dnucleome.org/microscope-configurations/b489483d-e203-45e1-b52f-fe5e8c8538e0) or [849c69ce-a0b1-4fe7-8337-ebfc7b308622](https://data.4dnucleome.org/microscope-configurations/849c69ce-a0b1-4fe7-8337-ebfc7b308622) microscopes.", "name": "microscope_note_su_2020", "award": {"@id": "/awards/2U01CA200059-06/", "@type": ["Award", "Item"], "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Microscope configuration - Su JH et al. 2020", "status": "released", "aliases": ["4dn-dcic-lab:microscope_note_su_2020"], "options": {"filetype": "md", "collapsible": true, "default_open": true, "convert_ext_links": true}, "date_created": "2025-06-24T17:37:56.119173+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-06-24T17:37:56.121401+00:00"}, "schema_version": "2", "@id": "/static-sections/712b00f4-5423-4f4d-b4fe-e0623ffe5944/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "712b00f4-5423-4f4d-b4fe-e0623ffe5944", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.6f9809b1-b9b4-4f2f-8e6d-0762bce320ef"]}, "display_title": "Microscope configuration - Su JH et al. 2020", "external_references": [], "content": "The experiments associated with this study are derived from either [b489483d-e203-45e1-b52f-fe5e8c8538e0](https://data.4dnucleome.org/microscope-configurations/b489483d-e203-45e1-b52f-fe5e8c8538e0) or [849c69ce-a0b1-4fe7-8337-ebfc7b308622](https://data.4dnucleome.org/microscope-configurations/849c69ce-a0b1-4fe7-8337-ebfc7b308622) 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/b489483d-e203-45e1-b52f-fe5e8c8538e0\" rel=\"noopener noreferrer\" target=\"_blank\">b489483d-e203-45e1-b52f-fe5e8c8538e0</a> or <a href=\"https://data.4dnucleome.org/microscope-configurations/849c69ce-a0b1-4fe7-8337-ebfc7b308622\" rel=\"noopener noreferrer\" target=\"_blank\">849c69ce-a0b1-4fe7-8337-ebfc7b308622</a> microscopes.</p></div>"}, {"lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "status": "current", "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"], "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "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": "2024-10-18", "experiments_in_set": [{"accession": "4DNEXCWE7KU7", "status": "released", "@id": "/experiments-mic/4DNEXCWE7KU7/", "display_title": "multiplexed FISH on IMR-90 - 4DNEXCWE7KU7", "@type": ["ExperimentMic", "Experiment", "Item"], "uuid": "cafbe517-c000-4af6-99e6-2682adc2baad", "processed_files": [{"uuid": "117fc3ae-25ef-49a8-b44a-d516c323d859", "@id": "/files-processed/4DNFIXMERLJQ/", "file_type": "FOF-CT - DNA-spot/trace core", "upload_key": "117fc3ae-25ef-49a8-b44a-d516c323d859/4DNFIXMERLJQ.csv", "md5sum": "8d87aef771fa2999df96146964e713d3", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/117fc3ae-25ef-49a8-b44a-d516c323d859/4DNFIXMERLJQ.csv", "file_format": {"status": "released", "@id": "/file-formats/csv/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "display_title": "csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_classification": "processed file", "display_title": "4DNFIXMERLJQ.csv", "file_type_detailed": "FOF-CT - DNA-spot/trace core (csv)", "status": "released", "href": "/files-processed/4DNFIXMERLJQ/@@download/4DNFIXMERLJQ.csv", "file_size": 516143068, "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIXMERLJQ", "genome_assembly": "GRCh38", "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"}, "lab": {"uuid": "eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb", "@id": "/labs/xiaowei-zhuang-lab/", "status": "current", "name": "xiaowei-zhuang-lab", "@type": ["Lab", "Item"], "display_title": "Xiaowei Zhuang, HARVARD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "last_modified": {"date_modified": "2024-12-03T17:55:32.222800+00:00"}}, {"uuid": "a607c36b-8c1e-4acd-a1a6-f55b9708761a", "@id": "/files-processed/4DNFI7UYX9PP/", "file_type": "FOF-CT - spot biological data", "upload_key": "a607c36b-8c1e-4acd-a1a6-f55b9708761a/4DNFI7UYX9PP.csv", "md5sum": "85b9def244c5e673eb6788246ab561de", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a607c36b-8c1e-4acd-a1a6-f55b9708761a/4DNFI7UYX9PP.csv", "file_format": {"status": "released", "@id": "/file-formats/csv/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "display_title": "csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_classification": "processed file", "display_title": "4DNFI7UYX9PP.csv", "file_type_detailed": "FOF-CT - spot biological data (csv)", "status": "released", "href": "/files-processed/4DNFI7UYX9PP/@@download/4DNFI7UYX9PP.csv", "file_size": 184291863, "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFI7UYX9PP", "genome_assembly": "GRCh38", "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"}, "lab": {"uuid": "eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb", "@id": "/labs/xiaowei-zhuang-lab/", "status": "current", "name": "xiaowei-zhuang-lab", "@type": ["Lab", "Item"], "display_title": "Xiaowei Zhuang, HARVARD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "last_modified": {"date_modified": "2024-12-03T17:55:27.394641+00:00"}}, {"uuid": "cd9cc04e-09e8-4ebd-92ac-c08ddfa5c6d7", "@id": "/files-processed/4DNFI6HBZKKH/", "file_type": "FOF-CT - RNA-spot", "upload_key": "cd9cc04e-09e8-4ebd-92ac-c08ddfa5c6d7/4DNFI6HBZKKH.csv", "md5sum": "f3c4bf03161f900877d9188367412146", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/cd9cc04e-09e8-4ebd-92ac-c08ddfa5c6d7/4DNFI6HBZKKH.csv", "file_format": {"status": "released", "@id": "/file-formats/csv/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "display_title": "csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_classification": "processed file", "display_title": "4DNFI6HBZKKH.csv", "file_type_detailed": "FOF-CT - RNA-spot (csv)", "status": "released", "href": "/files-processed/4DNFI6HBZKKH/@@download/4DNFI6HBZKKH.csv", "file_size": 300600794, "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFI6HBZKKH", "genome_assembly": "GRCh38", "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"}, "lab": {"uuid": "eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb", "@id": "/labs/xiaowei-zhuang-lab/", "status": "current", "name": "xiaowei-zhuang-lab", "@type": ["Lab", "Item"], "display_title": "Xiaowei Zhuang, HARVARD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "last_modified": {"date_modified": "2024-12-03T17:55:17.252347+00:00"}}], "biosample": {"biosource_summary": "IMR-90", "biosample_category": ["IMR-90"], "uuid": "5561b359-76ca-4612-9b25-58f909eae368", "accession": "4DNBSUH1CEQ3", "modifications_summary": "None", "treatments_summary": "None", "@type": ["Biosample", "Item"], "biosample_type": "primary cells", "@id": "/biosamples/4DNBSUH1CEQ3/", "status": "released", "display_title": "4DNBSUH1CEQ3", "biosource": [{"@id": "/biosources/4DNSRXXGU3CH/", "biosource_type": "primary cell line", "cell_line_tier": "Unclassified", "status": "released", "display_title": "IMR-90 - 4DNSRXXGU3CH", "accession": "4DNSRXXGU3CH", "uuid": "26ebb2b1-2902-4446-a25f-9fc6523ed5cf", "@type": ["Biosource", "Item"], "cell_line": {"display_title": "IMR-90", "preferred_name": "IMR-90", "@type": ["OntologyTerm", "Item"], "synonyms": ["IMR90"], "@id": "/ontology-terms/EFO:0001196/", "uuid": "c45d70f2-980b-4a6c-b762-bb48fdd7913a", "term_name": "IMR-90", "term_id": "EFO:0001196", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"status": "current", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"status": "released", "@type": ["Organism", "Item"], "@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "scientific_name": "Homo sapiens", "name": "human", "display_title": "H. sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"uuid": "999f1c8c-f02b-4a2b-b269-53ec1234b26f", "@type": ["OntologyTerm", "Item"], "term_name": "fibroblast of lung", "display_title": "fibroblast of lung", "@id": "/ontology-terms/CL:0002553/", "preferred_name": "fibroblast of lung", "synonyms": ["NHLF", "fibroblast of lung"], "term_id": "CL:0002553", "status": "released", "slim_terms": [{"display_title": "endoderm", "uuid": "111121bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0000925/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "lung", "uuid": "111186bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0002048/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "respiratory system", "uuid": "111128bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0001004/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"organ_system": ["endoderm", "lung", "respiratory system"], "tissue_source": "fibroblast of lung"}, "badges": [{"messages": ["Biosample missing Cell Culture Details"], "badge": {"description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "badge_classification": "Warning", "badge_icon": "/static/img/badges/biosample-icon.svg", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "warning": "Biosample Metadata Incomplete", "display_title": "Biosample Metadata Incomplete", "@type": ["Badge", "Item"], "@id": "/badges/biosample-metadata-incomplete/", "title": "Biosample Metadata Incomplete", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "reference_files": [{"file_size": 11642533, "uuid": "073451b2-7bc7-460c-af5a-f3c040862eee", "file_type_detailed": "oligo sequences (zip)", "status": "released", "@type": ["FileReference", "File", "Item"], "file_type": "oligo sequences", "@id": "/files-reference/4DNFIQZONHBV/", "accession": "4DNFIQZONHBV", "display_title": "4DNFIQZONHBV.zip", "file_classification": "ancillary file", "href": "/files-reference/4DNFIQZONHBV/@@download/4DNFIQZONHBV.zip", "md5sum": "ae951e8f51bfcf770eb4929d01946c66", "lab": {"uuid": "eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb", "name": "xiaowei-zhuang-lab", "@type": ["Lab", "Item"], "status": "current", "display_title": "Xiaowei Zhuang, HARVARD", "@id": "/labs/xiaowei-zhuang-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb"]}}, "file_format": {"status": "released", "@id": "/file-formats/zip/", "file_format": "zip", "uuid": "d13d06cf-218e-4f61-44f0-91f226248b2c", "display_title": "zip", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 6461, "uuid": "a98bae85-0c76-47c3-8b4e-f1e11fa939b8", "file_type_detailed": "target regions (bed)", "status": "released", "@type": ["FileReference", "File", "Item"], "file_type": "target regions", "@id": "/files-reference/4DNFI845HUSN/", "accession": "4DNFI845HUSN", "display_title": "4DNFI845HUSN.bed.gz", "file_classification": "ancillary file", "href": "/files-reference/4DNFI845HUSN/@@download/4DNFI845HUSN.bed.gz", "md5sum": "9a40cd074e69630b7e2429e422602253", "lab": {"uuid": "eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb", "name": "xiaowei-zhuang-lab", "@type": ["Lab", "Item"], "status": "current", "display_title": "Xiaowei Zhuang, HARVARD", "@id": "/labs/xiaowei-zhuang-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb"]}}, "file_format": {"status": "released", "@id": "/file-formats/bed/", "file_format": "bed", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "display_title": "bed", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@id": "/higlass-view-configs/8343ae6b-87f6-48dd-bf2f-72b1ada99609/", "uuid": "8343ae6b-87f6-48dd-bf2f-72b1ada99609", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "display_title": "4DNFI845HUSN", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 60567, "uuid": "bd6574ee-e4d6-47ea-a5d0-35ff26695414", "file_type_detailed": "target genes (txt)", "status": "released", "@type": ["FileReference", "File", "Item"], "file_type": "target genes", "@id": "/files-reference/4DNFIM7F5AX2/", "accession": "4DNFIM7F5AX2", "display_title": "4DNFIM7F5AX2.txt", "file_classification": "ancillary file", "href": "/files-reference/4DNFIM7F5AX2/@@download/4DNFIM7F5AX2.txt", "md5sum": "3cf30c393e9a11980ede53bf32cbb148", "lab": {"uuid": "eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb", "name": "xiaowei-zhuang-lab", "@type": ["Lab", "Item"], "status": "current", "display_title": "Xiaowei Zhuang, HARVARD", "@id": "/labs/xiaowei-zhuang-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.eb9725d9-44bb-4e4b-a5ad-e152fb3a06eb"]}}, "file_format": {"status": "released", "@id": "/file-formats/txt/", "file_format": "txt", "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "display_title": "txt", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "combined": "Target: Chromosomes, transcript, region", "value": "Chromosomes, transcript, region"}, "experiment_type": {"@type": ["ExperimentType", "Item"], "uuid": "bcdda46a-489d-4d22-be80-c9c21552c915", "experiment_category": "Microscopy", "other_tags": ["Single Cell"], "assay_classification": "Fluorescence Localization", "status": "released", "title": "multiplexed FISH", "@id": "/experiment-types/multiplexed-fish/", "assay_subclass_short": "FISH", "assay_subclassification": "Chromatin Tracing", "display_title": "multiplexed FISH", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "last_modified": {"date_modified": "2024-10-18T22:35:29.947467+00:00"}}], "experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNES5C3XVFP/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "e69ae529-ccc8-4303-b7d9-9b7b0641abe8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNES5C3XVFP", "external_references": [], "produced_in_pub": {"authors": ["Su JH", "Zheng P", "Kinrot SS", "Bintu B", "Zhuang X"], "display_title": "Su JH et al. (2020) PMID:32822575", "ID": "PMID:32822575", "@id": "/publications/bd20862a-7c4c-4a95-9721-e880181da2d4/", "uuid": "bd20862a-7c4c-4a95-9721-e880181da2d4", "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.", "journal": "Cell", "url": "https://www.ncbi.nlm.nih.gov/pubmed/32822575", "short_attribution": "Su JH et al. (2020)", "date_published": "2020-09-17", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"uuid": "bd20862a-7c4c-4a95-9721-e880181da2d4", "ID": "PMID:32822575", "display_title": "Su JH et al. (2020) PMID:32822575", "date_published": "2020-09-17", "authors": ["Su JH", "Zheng P", "Kinrot SS", "Bintu B", "Zhuang X"], "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.", "@type": ["Publication", "Item"], "journal": "Cell", "status": "current", "title": "Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of  Chromatin.", "@id": "/publications/bd20862a-7c4c-4a95-9721-e880181da2d4/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 1, "imaging_paths": [{"path": {"@type": ["ImagingPath", "Item"], "status": "released", "uuid": "7be4b194-b0bf-4583-a940-53d39fe96f94", "display_title": "Chromosomes targeted by DAPI", "labeled_probe": "DAPI", "@id": "/imaging-paths/7be4b194-b0bf-4583-a940-53d39fe96f94/", "target": [{"cellular_structure": "Chromosomes", "display_title": "Chromosomes", "@id": "/bio-features/655728f9-d4ab-4dd2-971c-1627ab2c8d33/", "@type": ["BioFeature", "Item"], "uuid": "655728f9-d4ab-4dd2-971c-1627ab2c8d33", "status": "released", "organism_name": "unspecified", "feature_type": {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005575/", "status": "released", "uuid": "e47e2bea-bc1e-4989-881c-521fc0b33529", "display_title": "cellular_component", "term_url": "http://purl.obolibrary.org/obo/GO_0005575", "preferred_name": "cellular_component", "term_name": "cellular_component", "term_id": "GO:0005575", "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": {"override_display_title": "RNA-MERFISH to detect 1137 genes overlapping 1041 genomic loci (targeted by DNA MERFISH) by Alexa Flour 750-labeled imaging oligos", "@type": ["ImagingPath", "Item"], "status": "released", "uuid": "3bb9a0aa-f440-4a12-997f-34d3d498fe3c", "imaging_rounds": "1-18", "display_title": "RNA-MERFISH to detect 1137 genes overlapping 1041 genomic loci (targeted by DNA MERFISH) by Alexa Flour 750-labeled imaging oligos", "other_probes": ["oligo probe library", "readout oligo library"], "labeled_probe": "imaging oligos", "@id": "/imaging-paths/3bb9a0aa-f440-4a12-997f-34d3d498fe3c/", "target": [{"display_title": "transcript", "@id": "/bio-features/1a7f48ac-a39e-4570-88dd-d3c948774b53/", "@type": ["BioFeature", "Item"], "uuid": "1a7f48ac-a39e-4570-88dd-d3c948774b53", "status": "released", "organism_name": "human", "feature_type": {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/SO:0000673/", "status": "released", "uuid": "e8f56a24-20ce-4e7c-9e8d-a4f409398574", "display_title": "transcript", "term_url": "http://purl.obolibrary.org/obo/SO_0000673", "preferred_name": "transcript", "term_name": "transcript", "term_id": "SO:0000673", "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": {"override_display_title": "RNA-MERFISH to detect 1137 genes overlapping 1041 genomic loci (targeted by DNA MERFISH) by Alexa Flour 647-labeled imaging oligos", "@type": ["ImagingPath", "Item"], "status": "released", "uuid": "878fd648-7589-4942-8583-80e65e3036f1", "imaging_rounds": "1-18", "display_title": "RNA-MERFISH to detect 1137 genes overlapping 1041 genomic loci (targeted by DNA MERFISH) by Alexa Flour 647-labeled imaging oligos", "other_probes": ["oligo probe library", "readout oligo library"], "labeled_probe": "imaging oligos", "@id": "/imaging-paths/878fd648-7589-4942-8583-80e65e3036f1/", "target": [{"display_title": "transcript", "@id": "/bio-features/1a7f48ac-a39e-4570-88dd-d3c948774b53/", "@type": ["BioFeature", "Item"], "uuid": "1a7f48ac-a39e-4570-88dd-d3c948774b53", "status": "released", "organism_name": "human", "feature_type": {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/SO:0000673/", "status": "released", "uuid": "e8f56a24-20ce-4e7c-9e8d-a4f409398574", "display_title": "transcript", "term_url": "http://purl.obolibrary.org/obo/SO_0000673", "preferred_name": "transcript", "term_name": "transcript", "term_id": "SO:0000673", "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": {"override_display_title": "RNA-MERFISH to detect 1137 genes overlapping 1041 genomic loci (targeted by DNA MERFISH) by Cy3-labeled imaging oligos", "@type": ["ImagingPath", "Item"], "status": "released", "uuid": "fcd47739-3121-40ae-a77a-102e620c17d7", "imaging_rounds": "1-18", "display_title": "RNA-MERFISH to detect 1137 genes overlapping 1041 genomic loci (targeted by DNA MERFISH) by Cy3-labeled imaging oligos", "other_probes": ["oligo probe library", "readout oligo library"], "labeled_probe": "imaging oligos", "@id": "/imaging-paths/fcd47739-3121-40ae-a77a-102e620c17d7/", "target": [{"display_title": "transcript", "@id": "/bio-features/1a7f48ac-a39e-4570-88dd-d3c948774b53/", "@type": ["BioFeature", "Item"], "uuid": "1a7f48ac-a39e-4570-88dd-d3c948774b53", "status": "released", "organism_name": "human", "feature_type": {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/SO:0000673/", "status": "released", "uuid": "e8f56a24-20ce-4e7c-9e8d-a4f409398574", "display_title": "transcript", "term_url": "http://purl.obolibrary.org/obo/SO_0000673", "preferred_name": "transcript", "term_name": "transcript", "term_id": "SO:0000673", "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": {"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", "@type": ["ImagingPath", "Item"], "status": "released", "uuid": "bd7dc770-1b7b-466d-bc5f-b3553468bc77", "imaging_rounds": "1-50", "display_title": "DNA-MERFISH to detect 100-kb 1041 genomic loci covering 22 automosome and X chromosome by Alexa Flour 750-labeled imaging oligos", "other_probes": ["oligo probe library", "readout oligo library"], "labeled_probe": "imaging oligos", "@id": "/imaging-paths/bd7dc770-1b7b-466d-bc5f-b3553468bc77/", "target": [{"display_title": "region", "@id": "/bio-features/80d89b4d-616b-4903-b91d-0718568e5108/", "@type": ["BioFeature", "Item"], "uuid": "80d89b4d-616b-4903-b91d-0718568e5108", "status": "released", "organism_name": "human", "feature_type": {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/SO:0000001/", "status": "released", "uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "display_title": "region", "term_url": "http://purl.obolibrary.org/obo/SO_0000001", "preferred_name": "region", "term_name": "region", "term_id": "SO:0000001", "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": {"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", "@type": ["ImagingPath", "Item"], "status": "released", "uuid": "ca8d476f-9c24-4fb6-aaf3-05343e8dc792", "imaging_rounds": "1-50", "display_title": "DNA-MERFISH to detect 100-kb 1041 genomic loci covering 22 automosome and X chromosome by Alexa Flour 647-labeled imaging oligos", "other_probes": ["oligo probe library", "readout oligo library"], "labeled_probe": "imaging oligos", "@id": "/imaging-paths/ca8d476f-9c24-4fb6-aaf3-05343e8dc792/", "target": [{"display_title": "region", "@id": "/bio-features/80d89b4d-616b-4903-b91d-0718568e5108/", "@type": ["BioFeature", "Item"], "uuid": "80d89b4d-616b-4903-b91d-0718568e5108", "status": "released", "organism_name": "human", "feature_type": {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/SO:0000001/", "status": "released", "uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "display_title": "region", "term_url": "http://purl.obolibrary.org/obo/SO_0000001", "preferred_name": "region", "term_name": "region", "term_id": "SO:0000001", "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"}], "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSUH1CEQ3/", "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/4DNES5C3XVFP/", "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": []}