{"lab": {"uuid": "795847de-20b6-4f8c-ba8d-185215469cbf", "@id": "/labs/bing-ren-lab/", "title": "Bing Ren, UCSD", "status": "current", "@type": ["Lab", "Item"], "display_title": "Bing Ren, UCSD", "correspondence": [{"contact_email": "YmlyZW5AdWNzZC5lZHU=", "@id": "/users/e3159ffc-a5a9-43a1-8cfa-90b776c39788/", "display_title": "Bing Ren"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.795847de-20b6-4f8c-ba8d-185215469cbf"]}}, "award": {"@type": ["Award", "Item"], "uuid": "4871e338-b07d-4665-a00a-357648e5bad6", "description": "NOFIC: The complete sequencing of the human genome has provided an unprecedented opportunity for the study of the structure and function of the human genome. While our genome has historically been viewed as a linear sequence of bases, it has progressively become clear that this is an inadequate way to represent our genetic information. Notably, research over the last 30 years has begun to shed light on the fact that the higher-order, 3-dimensional organization of our genome plays a critical role in the interpretation of the genetic information encoded in our genome. The structure of our genome in the nucleus has been clearly demonstrated to play influential roles in diverse nuclear processes including DNA replication and gene expression. Despite this, our understanding of the structure of our genome within the nucleus remains incomplete. The reasons for this include limitations in the resolution and throughput of existing tools in chromatin topology mapping, a scarcity of the analytical tools for studying genome structure datasets, and the difficulty to relate the nuclear structure to function. Due to recent advancements in molecular methods based on high-throughput DNA sequencing, single cell analytical approaches, and high-resolution microscopy, the time for breaking through these previous limitations has come. We will establish a highly collaborative, innovative team in order to develop the tools necessary to transform our understanding of chromatin architecture and function in mammalian cells. We will begin by developing datasets that establish gold standards for the study of nuclear structure and function using genetic, biochemical and imaging approaches. We will optimize current existing technologies for mapping genome wide chromatin interactions, while also developing novel, complementary approaches for studying chromatin structure. We will also develop innovative analytical methods to interpret the chromatin structural data, unraveling principles of structural- and temporal- chromatin organization. Our highly collaborative team will draw on the diverse experiences of its members to provide a synergistic environment to push the limits of our understanding of nuclear structure. We expect that the tools and datasets generated through the proposed research will dramatically advance our understanding of the chromatin structure and function in human cells.", "status": "current", "@id": "/awards/1U54DK107977-01/", "project": "4DN", "center_title": "NOFIC - Ren", "name": "1U54DK107977-01", "display_title": "SAN DIEGO CENTER FOR 4D NUCLEOME RESEARCH", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "badges": [{"badge": {"display_title": "Replicate Numbers", "badge_classification": "Warning", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "description": "Issues with replicate numbers", "@type": ["Badge", "Item"], "warning": "Replicate Numbers", "title": "Replicate Numbers", "@id": "/badges/replicate-numbers/", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Replicate set contains only a single biological replicate"]}], "status": "released", "aliases": ["bing-ren-lab:multi_DNA_fish_Sox2-4CBS-SE_expt"], "accession": "4DNESIGBIXQS", "condition": "4 CTCF sites inserted between Sox2 and SE", "description": "Chromosome tracing on 571 cells of a 210-kb genomic region containing Sox2 and super-enhancer (SE) loci in mouse F123 ESCs with an engineered replacement of 4 CTCF binding sites between Sox2 and SE on the CAST allele of the CAST X 129 hybrid background.", "date_created": "2021-10-14T15:32:57.141060+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "Chromatin Tracing of Sox2 and SE with engineered CTCF insertions", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-04-06T10:07:51.883067+00:00"}, "public_release": "2022-04-06", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"uuid": "efc84aae-60b0-4bbd-a968-0475ab980992", "@id": "/experiments-mic/4DNEX63ENWXN/", "@type": ["ExperimentMic", "Experiment", "Item"], "display_title": "multiplexed FISH on F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE - 4DNEX63ENWXN", "accession": "4DNEX63ENWXN", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_headers": [{"lab": {"display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "Processed files in this dataset are provided in the 4DN standard FISH-Omics Format - Chromatin Tracing (FOF-CT).\n\nThis is a collection of tabular files, consisting of several tables.\nThe DNA-spot/trace core table is organized around individual DNA bright Spots that are spatially linked together in a three-dimensional (3D) polymeric Trace.\nAdditional optional tables can complement this information and vary according to the specific dataset. \n\nThe full documentation is available here: https://fish-omics-format.readthedocs.io/", "name": "fof-ct.note", "award": {"uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "@type": ["Award", "Item"], "@id": "/awards/2U01CA200059-06/", "status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "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": "
Processed files in this dataset are provided in the 4DN standard FISH-Omics Format - Chromatin Tracing (FOF-CT).
\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.
\nThe full documentation is available here: https://fish-omics-format.readthedocs.io/
"}], "project_release": "2022-04-06", "experiments_in_set": [{"accession": "4DNEX63ENWXN", "status": "released", "display_title": "multiplexed FISH on F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE - 4DNEX63ENWXN", "@type": ["ExperimentMic", "Experiment", "Item"], "@id": "/experiments-mic/4DNEX63ENWXN/", "uuid": "efc84aae-60b0-4bbd-a968-0475ab980992", "processed_files": [{"status": "released", "file_classification": "processed file", "file_format": {"@id": "/file-formats/csv/", "@type": ["FileFormat", "Item"], "display_title": "csv", "status": "released", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFI2RCYFJU/@@download/4DNFI2RCYFJU.csv", "genome_assembly": "GRCm38", "display_title": "4DNFI2RCYFJU.csv", "uuid": "ad8dff4b-cd51-45df-b7c7-cffaa147c2de", "upload_key": "ad8dff4b-cd51-45df-b7c7-cffaa147c2de/4DNFI2RCYFJU.csv", "file_type": "FOF-CT - DNA-spot/trace core", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "FOF-CT - DNA-spot/trace core (csv)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ad8dff4b-cd51-45df-b7c7-cffaa147c2de/4DNFI2RCYFJU.csv", "file_size": 3649133, "md5sum": "f4f42729347643116671e6759c33792c", "accession": "4DNFI2RCYFJU", "@id": "/files-processed/4DNFI2RCYFJU/", "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "multiplexed FISH", "experiment_bucket": "processed file", "assay_info": "42 consecutive 5-kb loci on chr3 (mouse), Chromosomes", "dataset": "Chromatin Tracing of Sox2 and SE with engineered CTCF insertions", "condition": "4 CTCF sites inserted between Sox2 and SE", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE", "lab_name": "Bing Ren, UCSD"}, "lab": {"name": "bing-ren-lab", "@type": ["Lab", "Item"], "uuid": "795847de-20b6-4f8c-ba8d-185215469cbf", "status": "current", "@id": "/labs/bing-ren-lab/", "display_title": "Bing Ren, UCSD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.795847de-20b6-4f8c-ba8d-185215469cbf"]}}, "external_references": [], "last_modified": {"date_modified": "2022-10-11T09:23:58.664191+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosample": {"uuid": "ae839174-d13d-455e-bba4-fe7eb7780e7a", "biosample_type": "stem cells", "@type": ["Biosample", "Item"], "@id": "/biosamples/4DNBSCHNIPZS/", "treatments_summary": "None", "biosample_category": ["Tier 2", "Mouse stem cell"], "accession": "4DNBSCHNIPZS", "biosource_summary": "F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE", "status": "released", "display_title": "4DNBSCHNIPZS", "modifications_summary": "RMCE replacement", "biosource": [{"override_biosource_name": "F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE", "biosource_type": "stem cell derived cell line", "display_title": "F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE - 4DNSR9TIV5EV", "status": "released", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "uuid": "c1f610d2-a25d-400a-b807-5306c34fe3fc", "@id": "/biosources/4DNSR9TIV5EV/", "accession": "4DNSR9TIV5EV", "tissue": {"@type": ["OntologyTerm", "Item"], "status": "released", "term_name": "stem cell", "term_id": "CL:0000034", "@id": "/ontology-terms/CL:0000034/", "display_title": "stem cell", "preferred_name": "stem cell", "synonyms": ["animal stem cell"], "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "cell_line": {"preferred_name": "F123-CASTx129", "status": "released", "@id": "/ontology-terms/EFO:0009319/", "display_title": "F123-CASTx129", "uuid": "b75930ee-182a-4f7a-8360-ecd6b7ac532f", "term_name": "F123-CASTx129", "synonyms": ["F123"], "term_id": "EFO:0009319", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"status": "current", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"@type": ["Organism", "Item"], "name": "mouse", "status": "released", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "display_title": "M. musculus", "@id": "/organisms/10090/", "scientific_name": "Mus musculus", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [{"@id": "/modifications/f6a26102-664a-4788-b1c8-2d0aaf332267/", "genomic_change": "replacement", "display_title": "RMCE replacement", "@type": ["Modification", "Item"], "uuid": "f6a26102-664a-4788-b1c8-2d0aaf332267", "modification_name": "RMCE replacement", "modification_type": "RMCE", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing Cell Culture Details"], "badge": {"badge_classification": "Warning", "warning": "Biosample Metadata Incomplete", "display_title": "Biosample Metadata Incomplete", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "@id": "/badges/biosample-metadata-incomplete/", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-icon.svg", "title": "Biosample Metadata Incomplete", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "reference_files": [{"status": "released", "file_size": 1212274, "uuid": "11415598-89ec-489d-9cf9-fb3765e03c0d", "@type": ["FileReference", "File", "Item"], "@id": "/files-reference/4DNFIGEXQNTH/", "md5sum": "3b2333f404b87c6fa997912166629b73", "accession": "4DNFIGEXQNTH", "file_type_detailed": "oligo sequences (tsv)", "file_type": "oligo sequences", "file_classification": "ancillary file", "href": "/files-reference/4DNFIGEXQNTH/@@download/4DNFIGEXQNTH.tsv", "display_title": "4DNFIGEXQNTH.tsv", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "file_format": "tsv", "@id": "/file-formats/tsv/", "uuid": "5e8f64b8-6323-410a-8af2-05aba0472f8e", "display_title": "tsv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/bing-ren-lab/", "display_title": "Bing Ren, UCSD", "name": "bing-ren-lab", "uuid": "795847de-20b6-4f8c-ba8d-185215469cbf", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.795847de-20b6-4f8c-ba8d-185215469cbf"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "file_size": 3501, "uuid": "12f22ef8-8794-480b-8551-dc12f56fade6", "@type": ["FileReference", "File", "Item"], "@id": "/files-reference/4DNFI75D9K15/", "md5sum": "4c2a29324472ebc4d80e76f75a0832d7", "accession": "4DNFI75D9K15", "file_type_detailed": "oligo sequences (tsv)", "file_type": "oligo sequences", "file_classification": "ancillary file", "href": "/files-reference/4DNFI75D9K15/@@download/4DNFI75D9K15.tsv", "display_title": "4DNFI75D9K15.tsv", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "file_format": "tsv", "@id": "/file-formats/tsv/", "uuid": "5e8f64b8-6323-410a-8af2-05aba0472f8e", "display_title": "tsv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/bing-ren-lab/", "display_title": "Bing Ren, UCSD", "name": "bing-ren-lab", "uuid": "795847de-20b6-4f8c-ba8d-185215469cbf", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.795847de-20b6-4f8c-ba8d-185215469cbf"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "external_references": [], "last_modified": {"date_modified": "2022-04-06T10:07:54.092194+00:00"}, "experiment_type": {"display_title": "multiplexed FISH", "uuid": "bcdda46a-489d-4d22-be80-c9c21552c915", "other_tags": ["Single Cell"], "assay_subclass_short": "FISH", "status": "released", "assay_classification": "Fluorescence Localization", "experiment_category": "Microscopy", "@type": ["ExperimentType", "Item"], "assay_subclassification": "Chromatin Tracing", "title": "multiplexed FISH", "@id": "/experiment-types/multiplexed-fish/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"value": "42 consecutive 5-kb loci on chr3 (mouse), Chromosomes", "combined": "Target: 42 consecutive 5-kb loci on chr3 (mouse), Chromosomes", "field": "Target"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESIGBIXQS/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "68cf5b9e-bae0-4646-96b8-c1872331c86b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESIGBIXQS", "external_references": [], "produced_in_pub": {"@type": ["Publication", "Item"], "abstract": "Insulators play a critical role in spatiotemporal gene regulation in animals. The evolutionarily conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but not all of its binding sites act as insulators. Here we explore the sequence requirements of CTCF-mediated transcriptional insulation using a sensitive insulator reporter in mouse embryonic stem cells. We find that insulation potency depends on the number of CTCF-binding sites in tandem. Furthermore, CTCF-mediated insulation is dependent on upstream flanking sequences at its binding sites. CTCF-binding sites at topologically associating domain boundaries are more likely to function as insulators than those outside topologically associating domain boundaries, independently of binding strength. We demonstrate that insulators form local chromatin domain boundaries and weaken enhancer-promoter contacts. Taken together, our results provide genetic, molecular and structural evidence connecting chromatin topology to the action of insulators in the mammalian genome.", "display_title": "Huang H et al. (2021) PMID:34002095", "ID": "PMID:34002095", "title": "CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains.", "url": "https://www.ncbi.nlm.nih.gov/pubmed/34002095", "uuid": "4f766397-5ead-416e-b891-1c95391dcd77", "journal": "Nature genetics", "authors": ["Huang H", "Zhu Q", "Jussila A", "Han Y", "Bintu B", "Kern C", "Conte M", "Zhang Y", "Bianco S", "Chiariello AM", "Yu M", "Hu R", "Tastemel M", "Juric I", "Hu M", "Nicodemi M", "Zhuang X", "Ren B"], "@id": "/publications/4f766397-5ead-416e-b891-1c95391dcd77/", "status": "current", "short_attribution": "Huang H et al. (2021)", "date_published": "2021-07", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"date_published": "2021-07", "authors": ["Huang H", "Zhu Q", "Jussila A", "Han Y", "Bintu B", "Kern C", "Conte M", "Zhang Y", "Bianco S", "Chiariello AM", "Yu M", "Hu R", "Tastemel M", "Juric I", "Hu M", "Nicodemi M", "Zhuang X", "Ren B"], "@type": ["Publication", "Item"], "@id": "/publications/4f766397-5ead-416e-b891-1c95391dcd77/", "display_title": "Huang H et al. (2021) PMID:34002095", "title": "CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains.", "ID": "PMID:34002095", "journal": "Nature genetics", "uuid": "4f766397-5ead-416e-b891-1c95391dcd77", "abstract": "Insulators play a critical role in spatiotemporal gene regulation in animals. The evolutionarily conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but not all of its binding sites act as insulators. Here we explore the sequence requirements of CTCF-mediated transcriptional insulation using a sensitive insulator reporter in mouse embryonic stem cells. We find that insulation potency depends on the number of CTCF-binding sites in tandem. Furthermore, CTCF-mediated insulation is dependent on upstream flanking sequences at its binding sites. CTCF-binding sites at topologically associating domain boundaries are more likely to function as insulators than those outside topologically associating domain boundaries, independently of binding strength. We demonstrate that insulators form local chromatin domain boundaries and weaken enhancer-promoter contacts. Taken together, our results provide genetic, molecular and structural evidence connecting chromatin topology to the action of insulators in the mammalian genome.", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 1, "imaging_paths": [{"path": {"display_title": "Chromosomes targeted by DAPI", "@id": "/imaging-paths/9cb9e4fa-d6e6-4d5c-81a1-7a9c0e636bff/", "labeled_probe": "DAPI", "@type": ["ImagingPath", "Item"], "uuid": "9cb9e4fa-d6e6-4d5c-81a1-7a9c0e636bff", "imaging_rounds": "0", "status": "released", "target": [{"@type": ["BioFeature", "Item"], "@id": "/bio-features/655728f9-d4ab-4dd2-971c-1627ab2c8d33/", "status": "released", "cellular_structure": "Chromosomes", "display_title": "Chromosomes", "organism_name": "unspecified", "uuid": "655728f9-d4ab-4dd2-971c-1627ab2c8d33", "feature_type": {"term_id": "GO:0005575", "@id": "/ontology-terms/GO:0005575/", "term_url": "http://purl.obolibrary.org/obo/GO_0005575", "status": "released", "@type": ["OntologyTerm", "Item"], "term_name": "cellular_component", "display_title": "cellular_component", "uuid": "e47e2bea-bc1e-4989-881c-521fc0b33529", "preferred_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": "ch04"}, {"path": {"display_title": "505/515nm fiducial beads", "@id": "/imaging-paths/c44aed0c-bf78-4cbe-af8b-b5d1941c183c/", "labeled_probe": "505/515nm fiducial beads", "@type": ["ImagingPath", "Item"], "uuid": "c44aed0c-bf78-4cbe-af8b-b5d1941c183c", "imaging_rounds": "0-14", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch03"}, {"path": {"display_title": "14 5-kb loci on chr3 (mouse) targeted by oligo probe library, readout probes (with Cy3-labeled imaging oligos).", "other_probes": ["oligo probe library", "readout probes"], "@id": "/imaging-paths/39447bb0-aadf-4073-bd44-c4e3b7b62c72/", "labeled_probe": "imaging oligos", "@type": ["ImagingPath", "Item"], "uuid": "39447bb0-aadf-4073-bd44-c4e3b7b62c72", "imaging_rounds": "1-14", "status": "released", "override_display_title": "14 5-kb loci on chr3 (mouse) targeted by oligo probe library, readout probes (with Cy3-labeled imaging oligos).", "target": [{"@type": ["BioFeature", "Item"], "@id": "/bio-features/e802b345-eac1-458b-90e5-7e65e031317d/", "status": "released", "preferred_label": "42 consecutive 5-kb loci on chr3", "display_title": "42 consecutive 5-kb loci on chr3 (mouse)", "organism_name": "mouse", "uuid": "e802b345-eac1-458b-90e5-7e65e031317d", "genome_location": [{"uuid": "78393c8b-829e-49b7-b6b6-6b092cf3d45f", "status": "released", "chromosome": "3", "@id": "/genomic-regions/78393c8b-829e-49b7-b6b6-6b092cf3d45f/", "genome_assembly": "GRCm38", "@type": ["GenomicRegion", "Item"], "end_coordinate": 34811078, "start_coordinate": 34601078, "display_title": "GRCm38:3:34601078-34811078", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "relevant_genes": [{"@id": "/genes/20674/", "display_title": "Sox2", "preferred_symbol": "Sox2", "geneid": "20674", "status": "released", "uuid": "db4fa807-b3aa-4cf5-84da-3c0bb4d4c857", "@type": ["Gene", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "feature_type": {"term_id": "SO:0000001", "@id": "/ontology-terms/SO:0000001/", "term_url": "http://purl.obolibrary.org/obo/SO_0000001", "status": "released", "@type": ["OntologyTerm", "Item"], "term_name": "region", "display_title": "region", "uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "preferred_name": "region", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_type": {"title": "DNA FISH", "display_title": "DNA FISH", "@id": "/experiment-types/dna-fish/", "status": "released", "uuid": "5761d0ec-35b0-4aa8-8b81-aac94def59b8", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch02"}, {"path": {"display_title": "14 5-kb loci on chr3 (mouse) targeted by oligo probe library, readout probes (with Cy5-labeled imaging oligos).", "other_probes": ["oligo probe library", "readout probes"], "@id": "/imaging-paths/605bcfe7-b49b-4d4c-bd1c-1ed5f51249d9/", "labeled_probe": "imaging oligos", "@type": ["ImagingPath", "Item"], "uuid": "605bcfe7-b49b-4d4c-bd1c-1ed5f51249d9", "imaging_rounds": "1-14", "status": "released", "override_display_title": "14 5-kb loci on chr3 (mouse) targeted by oligo probe library, readout probes (with Cy5-labeled imaging oligos).", "target": [{"@type": ["BioFeature", "Item"], "@id": "/bio-features/e802b345-eac1-458b-90e5-7e65e031317d/", "status": "released", "preferred_label": "42 consecutive 5-kb loci on chr3", "display_title": "42 consecutive 5-kb loci on chr3 (mouse)", "organism_name": "mouse", "uuid": "e802b345-eac1-458b-90e5-7e65e031317d", "genome_location": [{"uuid": "78393c8b-829e-49b7-b6b6-6b092cf3d45f", "status": "released", "chromosome": "3", "@id": "/genomic-regions/78393c8b-829e-49b7-b6b6-6b092cf3d45f/", "genome_assembly": "GRCm38", "@type": ["GenomicRegion", "Item"], "end_coordinate": 34811078, "start_coordinate": 34601078, "display_title": "GRCm38:3:34601078-34811078", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "relevant_genes": [{"@id": "/genes/20674/", "display_title": "Sox2", "preferred_symbol": "Sox2", "geneid": "20674", "status": "released", "uuid": "db4fa807-b3aa-4cf5-84da-3c0bb4d4c857", "@type": ["Gene", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "feature_type": {"term_id": "SO:0000001", "@id": "/ontology-terms/SO:0000001/", "term_url": "http://purl.obolibrary.org/obo/SO_0000001", "status": "released", "@type": ["OntologyTerm", "Item"], "term_name": "region", "display_title": "region", "uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "preferred_name": "region", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_type": {"title": "DNA FISH", "display_title": "DNA FISH", "@id": "/experiment-types/dna-fish/", "status": "released", "uuid": "5761d0ec-35b0-4aa8-8b81-aac94def59b8", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch01"}, {"path": {"display_title": "14 5-kb loci on chr3 (mouse) targeted by oligo probe library, readout probes (with Alexa Fluor 750-labeled imaging oligos).", "other_probes": ["oligo probe library", "readout probes"], "@id": "/imaging-paths/d7470a10-796d-43e9-bbed-ef102b305be9/", "labeled_probe": "imaging oligos", "@type": ["ImagingPath", "Item"], "uuid": "d7470a10-796d-43e9-bbed-ef102b305be9", "imaging_rounds": "1-14", "status": "released", "override_display_title": "14 5-kb loci on chr3 (mouse) targeted by oligo probe library, readout probes (with Alexa Fluor 750-labeled imaging oligos).", "target": [{"@type": ["BioFeature", "Item"], "@id": "/bio-features/e802b345-eac1-458b-90e5-7e65e031317d/", "status": "released", "preferred_label": "42 consecutive 5-kb loci on chr3", "display_title": "42 consecutive 5-kb loci on chr3 (mouse)", "organism_name": "mouse", "uuid": "e802b345-eac1-458b-90e5-7e65e031317d", "genome_location": [{"uuid": "78393c8b-829e-49b7-b6b6-6b092cf3d45f", "status": "released", "chromosome": "3", "@id": "/genomic-regions/78393c8b-829e-49b7-b6b6-6b092cf3d45f/", "genome_assembly": "GRCm38", "@type": ["GenomicRegion", "Item"], "end_coordinate": 34811078, "start_coordinate": 34601078, "display_title": "GRCm38:3:34601078-34811078", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "relevant_genes": [{"@id": "/genes/20674/", "display_title": "Sox2", "preferred_symbol": "Sox2", "geneid": "20674", "status": "released", "uuid": "db4fa807-b3aa-4cf5-84da-3c0bb4d4c857", "@type": ["Gene", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "feature_type": {"term_id": "SO:0000001", "@id": "/ontology-terms/SO:0000001/", "term_url": "http://purl.obolibrary.org/obo/SO_0000001", "status": "released", "@type": ["OntologyTerm", "Item"], "term_name": "region", "display_title": "region", "uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "preferred_name": "region", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_type": {"title": "DNA FISH", "display_title": "DNA FISH", "@id": "/experiment-types/dna-fish/", "status": "released", "uuid": "5761d0ec-35b0-4aa8-8b81-aac94def59b8", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "channel": "ch00"}], "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSCHNIPZS/", "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/4DNESIGBIXQS/", "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": []}