{"lab": {"display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "correspondence": [{"contact_email": "am9iLmRla2tlckB1bWFzc21lZC5lZHU=", "@id": "/users/83b5073a-069b-4162-9b30-6f42d5551e34/", "display_title": "Job Dekker"}], "title": "Job Dekker, UMMS", "status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "award": {"name": "1U54DK107980-01", "project": "4DN", "@type": ["Award", "Item"], "center_title": "NOFIC - Dekker", "@id": "/awards/1U54DK107980-01/", "uuid": "ae6c618f-7a8c-441e-a886-e30bbbe591da", "description": "NOFIC: The spatial organization of the genome impinges on all genomic processes, including gene regulation, maintenance of genome stability and chromosome transmission to daughter cells. A detailed understanding of the spatial arrangement of the human genome, referred to as the 4D nucleome, and the biological and physical principles that drive chromosome folding requires combining approaches from the fields of molecular and cell biology, imaging, genetics and genomics with approaches from physics, computational biology, and computer simulation. We have assembled a highly interdisciplinary center with the goal of generating extensively validated maps of the 4D nucleome, its physical and dynamic properties and its role in regulating the activity of the genome. First, the center will further optimize and extensively validate a suite of genome-wide molecular methodologies, based on chromosome conformation capture (3C) that can probe the folding of chromosomes at the scale of single nucleosomes, chromatin fibers, chromosomes and the entire nucleus, across cell populations and in single cells. Given that chromosome and nuclear organization is tightly linked to biological state of the cell, the center will map the 4D nucleome for four key biological states representing different conformations during the cell cycle (interphase and mitosis), and during cell differentiation (pluripotent and differentiated states). We will obtain complementary data regarding the structure and dynamics of chromatin, at different length scales and in single cells using extensive high-throughput imaging, live cell imaging and super resolution microscopy. Data obtained with all approaches will be analyzed, integrated and modeled using a set of methods we will further develop to gain insights into the structure, physics and dynamics of chromosome folding over different length scales. Finally, a critical component of our proposal is the biological validation and further elaboration of the chromatin interaction maps that are generated from our conformational analyses. This validation will be achieved through site-specific editing of genomic sequence and epigenetic marks, the creation of new contact points within the genome, and the identification of factors (both protein and nucleic acid) that facilitat or restrict these interactions. Effects of such perturbations in the chromosome conformation on transcription will reveal relationships between specific chromosome structural features and gene expression.", "status": "current", "display_title": "CENTER FOR 3D STRUCTURE AND PHYSICS OF THE GENOME", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFIA461Y3W/@@download/4DNFIA461Y3W.fastq.gz", "accession": "4DNFIA461Y3W", "file_classification": "raw file", "status": "restricted", "file_type": "reads", "file_size": 73312824, "display_title": "4DNFIA461Y3W.fastq.gz", "uuid": "847387ea-2426-476c-9c8d-56b7d1fe3cc5", "upload_key": "847387ea-2426-476c-9c8d-56b7d1fe3cc5/4DNFIA461Y3W.fastq.gz", "dbxrefs": ["SRA:SRR11304457"], "@id": "/files-fastq/4DNFIA461Y3W/", "file_format": {"status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@type": ["FileFormat", "Item"], "display_title": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR11304457", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR11304457"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFIPKJQVNX/@@download/4DNFIPKJQVNX.fastq.gz", "accession": "4DNFIPKJQVNX", "file_classification": "raw file", "status": "restricted", "file_type": "reads", "file_size": 61896848, "display_title": "4DNFIPKJQVNX.fastq.gz", "uuid": "e5232af2-4066-482a-a594-0900c2754526", "upload_key": "e5232af2-4066-482a-a594-0900c2754526/4DNFIPKJQVNX.fastq.gz", "dbxrefs": ["SRA:SRR11304462"], "@id": "/files-fastq/4DNFIPKJQVNX/", "file_format": {"status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@type": ["FileFormat", "Item"], "display_title": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR11304462", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR11304462"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFIX3EAAM5/@@download/4DNFIX3EAAM5.fastq.gz", "accession": "4DNFIX3EAAM5", "file_classification": "raw file", "status": "restricted", "file_type": "reads", "file_size": 73804919, "display_title": "4DNFIX3EAAM5.fastq.gz", "uuid": "b60881ac-967a-49bd-b070-f7d4a0c1b726", "upload_key": "b60881ac-967a-49bd-b070-f7d4a0c1b726/4DNFIX3EAAM5.fastq.gz", "dbxrefs": ["SRA:SRR11304461"], "@id": "/files-fastq/4DNFIX3EAAM5/", "file_format": {"status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@type": ["FileFormat", "Item"], "display_title": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR11304461", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR11304461"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFIENL1TT3/@@download/4DNFIENL1TT3.fastq.gz", "accession": "4DNFIENL1TT3", "file_classification": "raw file", "status": "restricted", "file_type": "reads", "file_size": 74619723, "display_title": "4DNFIENL1TT3.fastq.gz", "uuid": "2ec7440f-fbd9-4fb2-b2bd-9d31f6a32fe0", "upload_key": "2ec7440f-fbd9-4fb2-b2bd-9d31f6a32fe0/4DNFIENL1TT3.fastq.gz", "dbxrefs": ["SRA:SRR11304460"], "@id": "/files-fastq/4DNFIENL1TT3/", "file_format": {"status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@type": ["FileFormat", "Item"], "display_title": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR11304460", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR11304460"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFIEMD37BR/@@download/4DNFIEMD37BR.fastq.gz", "accession": "4DNFIEMD37BR", "file_classification": "raw file", "status": "restricted", "file_type": "reads", "file_size": 68073851, "display_title": "4DNFIEMD37BR.fastq.gz", "uuid": "860db668-0bfe-439c-b348-1c7d8654f56b", "upload_key": "860db668-0bfe-439c-b348-1c7d8654f56b/4DNFIEMD37BR.fastq.gz", "dbxrefs": ["SRA:SRR11304459"], "@id": "/files-fastq/4DNFIEMD37BR/", "file_format": {"status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@type": ["FileFormat", "Item"], "display_title": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR11304459", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR11304459"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFI1H7FBSD/@@download/4DNFI1H7FBSD.fastq.gz", "accession": "4DNFI1H7FBSD", "file_classification": "raw file", "status": "restricted", "file_type": "reads", "file_size": 79753558, "display_title": "4DNFI1H7FBSD.fastq.gz", "uuid": "9d7e1c62-4761-456b-b2f9-c94e78ab3d29", "upload_key": "9d7e1c62-4761-456b-b2f9-c94e78ab3d29/4DNFI1H7FBSD.fastq.gz", "dbxrefs": ["SRA:SRR11304458"], "@id": "/files-fastq/4DNFI1H7FBSD/", "file_format": {"status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@type": ["FileFormat", "Item"], "display_title": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR11304458", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR11304458"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "status": "released", "aliases": ["dekker-lab:Experiment_C-Walks_21SEP-PacBio"], "dbxrefs": ["GEO:GSM4411227", "SRA:SRX7909613"], "protocol": {"status": "released", "uuid": "915ccfda-498d-477b-8f41-3798e8a0d180", "@type": ["Protocol", "Item"], "display_title": "in situ MC-3C protocol", "@id": "/protocols/915ccfda-498d-477b-8f41-3798e8a0d180/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEXHSB49UM", "biosample": {"biosource_summary": "HeLa-S3", "@type": ["Biosample", "Item"], "display_title": "4DNBSNN25XH5", "@id": "/biosamples/4DNBSNN25XH5/", "modifications_summary": "None", "accession": "4DNBSNN25XH5", "treatments_summary": "None", "biosample_type": "immortalized cells", "uuid": "d20e3ecf-7945-48ff-b3ef-13e8d6b2c021", "status": "released", "biosource": [{"lab": {"status": "current", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "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-2.2.aspx", "award": {"uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@type": ["Award", "Item"], "status": "current", "@id": "/awards/1U01CA200059-01/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"@type": ["OntologyTerm", "Item"], "term_id": "UBERON:0000002", "preferred_name": "uterine cervix", "uuid": "600fc714-c007-441b-b3a7-3d164ddc2689", "slim_terms": [{"@id": "/ontology-terms/UBERON:0000990/", "@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "reproductive system", "uuid": "111127bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/UBERON:0000926/", "@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "mesoderm", "uuid": "111120bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/ontology-terms/UBERON:0000002/", "term_name": "uterine cervix", "synonyms": ["uterine cervix", "caudal segment of uterus", "cervix uteri", "neck of uterus", "cervical canal of uterus", "canalis cervicis uteri"], "display_title": "uterine cervix", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["dcic:HeLaS3", "4dn-dcic-lab:HeLaS3"], "accession": "4DNSRGTEEYSL", "cell_line": {"uuid": "840525af-614c-4559-9997-23a30e288858", "term_name": "HeLa-S3", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "status": "current", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "status": "released", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "display_title": "HeLa-S3", "term_id": "EFO:0002791", "@id": "/ontology-terms/EFO:0002791/", "preferred_name": "HeLa-S3", "status": "released", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"status": "released", "@id": "/individuals-human/4DNINEL8T2GK/", "protected_data": true, "display_title": "4DNINEL8T2GK", "@type": ["IndividualHuman", "Individual", "Item"], "uuid": "8b2bd1cc-3d14-441c-bd82-8bc004ac326a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "references": [], "description": "HeLa-S3 (CCL-2.2)", "date_created": "2017-04-09T17:24:23.689668+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-06-04T19:55:25.199930+00:00"}, "modifications": [], "biosource_type": "immortalized cell line", "cell_line_tier": "Unclassified", "public_release": "2017-04-09T17:24:23.689668+00:00", "schema_version": "2", "project_release": "2017-04-09T17:24:23.689668+00:00", "biosource_vendor": {"uuid": "7a6f2efe-5be8-4db2-afa8-d82e9b4ad254", "@type": ["Vendor", "Item"], "status": "released", "display_title": "American Type Culture Collection", "@id": "/vendors/american-type-culture-collection/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "alternate_accessions": [], "@id": "/biosources/4DNSRGTEEYSL/", "@type": ["Biosource", "Item"], "uuid": "a7aa4e34-de17-4336-9e0c-2844fd326a96", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "HeLa-S3 - 4DNSRGTEEYSL", "external_references": [], "biosource_name": "HeLa-S3", "biosource_category": ["Other"], "organism": {"status": "released", "display_title": "H. sapiens", "@type": ["Organism", "Item"], "@id": "/organisms/9606/", "name": "human", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "modifications": [], "badges": [{"messages": ["Biosample missing morphology_image"], "badge": {"badge_classification": "Warning", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "status": "released", "title": "Biosample Metadata Incomplete", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "badge_icon": "/static/img/badges/biosample-icon.svg", "display_title": "Biosample Metadata Incomplete", "warning": "Biosample Metadata Incomplete", "@type": ["Badge", "Item"], "@id": "/badges/biosample-metadata-incomplete/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "treatments": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "3C-PacBio-Interphase-R2T1: cWalks (3C experiment for PacBio sequencing) on interphase non synchronous Cells", "sop_mapping": {"has_sop": "No"}, "date_created": "2018-05-25T19:45:03.654279+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-09-17T17:52:10.628857+00:00"}, "ligation_time": 240, "digestion_time": 960.0, "public_release": "2020-09-17", "schema_version": "2", "experiment_type": {"@type": ["ExperimentType", "Item"], "title": "MC-3C", "status": "released", "@id": "/experiment-types/mc-3c/", "experiment_category": "Sequencing", "uuid": "e88b436f-aa52-432b-b6fd-5e15e22ff17a", "assay_subclass_short": "Hi-C (multi-contact)", "display_title": "MC-3C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "ligation_volume": 1.2, "project_release": "2020-09-17", "digestion_enzyme": {"display_title": "DpnII", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "@id": "/enzymes/DpnII/", "name": "DpnII", "@type": ["Enzyme", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "crosslinking_time": 10, "biosample_quantity": 5000000, "authentication_docs": [{"@type": ["Protocol", "Item"], "@id": "/protocols/38ba905e-9c2c-4915-aa69-cf982204ca2f/", "status": "released", "uuid": "38ba905e-9c2c-4915-aa69-cf982204ca2f", "display_title": "15SEPT17-1.1_Large_Fragment_Bastiaan_Dekker_samples_Dekker.pdf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["Protocol", "Item"], "@id": "/protocols/58684a0f-4b85-4a7b-b7ad-55f2de594acc/", "status": "released", "uuid": "58684a0f-4b85-4a7b-b7ad-55f2de594acc", "display_title": "Interphase_replicate_cwalk.pdf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "crosslinking_method": "1% Formaldehyde", "ligation_temperature": 16, "digestion_temperature": 37, "biosample_quantity_units": "cells", "crosslinking_temperature": 23, "library_preparation_date": "2017-09-11", "fragment_size_selection_method": "gel", "@id": "/experiments-hi-c/4DNEXHSB49UM/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "97e4a229-6075-41df-ac8f-36605874ca69", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "MC-3C on HeLa-S3 with DpnII - 4DNEXHSB49UM", "external_references": [{"ref": "GEO:GSM4411227", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4411227"}, {"ref": "SRA:SRX7909613", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX7909613"}], "experiment_sets": [{"uuid": "f7d26a40-6e66-465e-8070-32ff0c596333", "status": "released", "accession": "4DNESKHB7GPW", "display_title": "4DNESKHB7GPW", "@id": "/experiment-set-replicates/4DNESKHB7GPW/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "experimentset_type": "replicate", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"abstract": "During interphase, the eukaryotic genome is organized into chromosome territories that are spatially segregated into compartment domains. The extent to which interacting domains or chromosomes are entangled is not known. We analyze series  of co-occurring chromatin interactions using multi-contact 3C (MC-3C) in human cells to provide insights into the topological entanglement of chromatin. Multi-contact interactions represent percolation paths (C-walks) through three-dimensional (3D) chromatin space. We find that the order of interactions within C-walks that occur across interfaces where chromosomes or compartment domains interact is not random. Polymer simulations show that such C-walks are consistent with distal domains being topologically insulated, that is, not catenated. Simulations show that even low levels of random strand passage, for example by topoisomerase II, would result in entanglements, increased mixing at domain interfaces and an order of interactions within C-walks not consistent with experimental MC-3C data. Our results indicate that, during interphase, entanglements between chromosomes and chromosomal domains are rare.", "uuid": "186038e2-7055-4d38-be81-4686bc90ee0b", "short_attribution": "Tavares-Cadete F et al. (2020)", "journal": "Nature structural & molecular biology", "authors": ["Tavares-Cadete F", "Norouzi D", "Dekker B", "Liu Y", "Dekker J"], "ID": "PMID:32929283", "@id": "/publications/186038e2-7055-4d38-be81-4686bc90ee0b/", "date_published": "2020-09-14", "display_title": "Tavares-Cadete F et al. (2020) PMID:32929283", "title": "Multi-contact 3C reveals that the human genome during interphase is largely not entangled.", "status": "current", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"display_title": "Tavares-Cadete F et al. (2020) PMID:32929283", "authors": ["Tavares-Cadete F", "Norouzi D", "Dekker B", "Liu Y", "Dekker J"], "@type": ["Publication", "Item"], "date_published": "2020-09-14", "journal": "Nature structural & molecular biology", "short_attribution": "Tavares-Cadete F et al. (2020)", "ID": "PMID:32929283", "uuid": "186038e2-7055-4d38-be81-4686bc90ee0b", "abstract": "During interphase, the eukaryotic genome is organized into chromosome territories that are spatially segregated into compartment domains. The extent to which interacting domains or chromosomes are entangled is not known. We analyze series  of co-occurring chromatin interactions using multi-contact 3C (MC-3C) in human cells to provide insights into the topological entanglement of chromatin. Multi-contact interactions represent percolation paths (C-walks) through three-dimensional (3D) chromatin space. We find that the order of interactions within C-walks that occur across interfaces where chromosomes or compartment domains interact is not random. Polymer simulations show that such C-walks are consistent with distal domains being topologically insulated, that is, not catenated. Simulations show that even low levels of random strand passage, for example by topoisomerase II, would result in entanglements, increased mixing at domain interfaces and an order of interactions within C-walks not consistent with experimental MC-3C data. Our results indicate that, during interphase, entanglements between chromosomes and chromosomal domains are rare.", "status": "current", "@id": "/publications/186038e2-7055-4d38-be81-4686bc90ee0b/", "title": "Multi-contact 3C reveals that the human genome during interphase is largely not entangled.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Enzyme", "value": "DpnII", "combined": "Enzyme: DpnII"}, "experiment_summary": "MC-3C on HeLa-S3 with DpnII", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSNN25XH5/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample missing morphology_image"], "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": []}