{"lab": {"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "display_title": "Job Dekker, UMMS", "title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "correspondence": [{"contact_email": "am9iLmRla2tlckB1bWFzc21lZC5lZHU=", "@id": "/users/83b5073a-069b-4162-9b30-6f42d5551e34/", "display_title": "Job Dekker"}], "status": "current", "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": "3U54HG007010-05S1", "@type": ["Award", "Item"], "@id": "/awards/3U54HG007010-05S1/", "uuid": "43fc2984-a074-49c4-a69f-c9d3f3eadeba", "status": "current", "display_title": "A COMPREHENSIVE CATALOG OF DNASE I HYPERSENSITIVE SITES", "project": "ENCODE", "center_title": "3U54HG007010-05S1", "description": "The overall aim of this proposal is to establish a comprehensive, high-quality, high-resolution catalogues of human and mouse DNasel hypersensitive sites (DHSs) spanning all major tissue lineages. Building on the prior success of the UW ENCODE center, we plan to localize DNasel hypersensitive sites, to define the locations of DNasel footprints therein, and to continue to provide relevant synergistic annotations including RNA-seq, histone modifications, and CTCF, as well as DNA methylation. The overriding focus of our production effort has been on data quality. Accordingly, samples will be rigorously screened in a pipeline fashion, with only a select set advancing to whole-genome data collection. To ensure the broadest possible coverage of both unique and non-unique genomic territories, we will employ a higher resolution, higher coverage sequencing strategy than the prior project period, significantly enhancing the information content of the data. This proposal integrates the UW-FHCRC Mouse ENCODE Center, which will be closely aligned with the human project to generate a comparative catalogue of regulatory DNA in carefully matched cells and tissues, providing an unparalleled resource. Since DNasel hypersensitive sites are generic markers of a broad spectrum of human cis-regulatory sequences, the utility of the catalogue will be greatly enhanced by the classification of DHSs into major functional categories including promoters, distal elements (enhancers, LCRs), and insulators. We plan to systematically connect distal DHSs with their cognate promoters and to perform in vivo validation of these connections using nuclease-mediated knockouts of distal DHSs in somatic cells.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "badges": [{"badge": {"warning": "Biosample Metadata Incomplete", "@type": ["Badge", "Item"], "badge_classification": "Warning", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "display_title": "Biosample Metadata Incomplete", "badge_icon": "/static/img/badges/biosample-icon.svg", "@id": "/badges/biosample-metadata-incomplete/", "title": "Biosample Metadata Incomplete", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Biosample missing doubling_number", "Biosample missing morphology_image"]}], "status": "released", "aliases": ["dekker-lab:Biosample_SK-N-MC_Homo-sapiens-SK-N-MC-ENCBS400ENC"], "dbxrefs": ["ENCODE:ENCBS400ENC"], "accession": "4DNBS1EJQPQT", "biosource": [{"lab": {"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "status": "current", "display_title": "Job Dekker, UMMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "url": "https://www.encodeproject.org/biosamples/ENCBS366AET/", "award": {"display_title": "A COMPREHENSIVE CATALOG OF DNASE I HYPERSENSITIVE SITES", "@id": "/awards/3U54HG007010-05S1/", "uuid": "43fc2984-a074-49c4-a69f-c9d3f3eadeba", "@type": ["Award", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"@type": ["OntologyTerm", "Item"], "term_url": "http://purl.obolibrary.org/obo/UBERON_0000955", "display_title": "brain", "uuid": "111170bc-8535-4448-903e-854af460a233", "preferred_name": "brain", "term_id": "UBERON:0000955", "status": "released", "synonyms": ["synganglion", "Entire brain", "encephalon"], "term_name": "brain", "@id": "/ontology-terms/UBERON:0000955/", "slim_terms": [{"preferred_name": "ectoderm", "term_id": "UBERON:0000924", "@type": ["OntologyTerm", "Item"], "term_name": "ectoderm", "uuid": "111119bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0000924/", "term_url": "http://purl.obolibrary.org/obo/UBERON_0000924", "status": "released", "display_title": "ectoderm", "synonyms": ["embryonic ectoderm"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"preferred_name": "central nervous system", "term_id": "UBERON:0001017", "@type": ["OntologyTerm", "Item"], "term_name": "central nervous system", "uuid": "111136bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0001017/", "term_url": "http://purl.obolibrary.org/obo/UBERON_0001017", "status": "released", "display_title": "central nervous system", "synonyms": ["systema nervosum centrale", "CNS", "cerebrospinal axis"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"preferred_name": "brain", "term_id": "UBERON:0000955", "@type": ["OntologyTerm", "Item"], "term_name": "brain", "uuid": "111170bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0000955/", "term_url": "http://purl.obolibrary.org/obo/UBERON_0000955", "status": "released", "display_title": "brain", "synonyms": ["synganglion", "Entire brain", "encephalon"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["dekker-lab:Biosource_SK-N-MC"], "accession": "4DNSRW6BI5JA", "cell_line": {"display_title": "SK-N-MC", "@id": "/ontology-terms/EFO:0002860/", "term_name": "SK-N-MC", "term_id": "EFO:0002860", "term_url": "http://www.ebi.ac.uk/efo/EFO_0002860", "status": "released", "synonyms": ["SKNMc"], "uuid": "5b45eb03-5c97-431e-bca7-71263a0d6f43", "@type": ["OntologyTerm", "Item"], "preferred_name": "SK-N-MC", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@type": ["IndividualHuman", "Individual", "Item"], "uuid": "e1ec0377-391f-4fb9-8629-eae455beb202", "status": "released", "display_title": "4DNINPA6QKHP", "sex": "female", "@id": "/individuals-human/4DNINPA6QKHP/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "references": [], "description": "This cell line was previously described as a neuroepithelioma (ATCC HTB-10). However recent evidence reveals it is Ewing's Sarcoma - http://www.ncbi.nlm.nih.gov/biosample/3151999, http://www.ncbi.nlm.nih.gov/pubmed/25453903", "date_created": "2017-05-05T18:42:43.600747+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-06-05T14:22:44.845012+00:00"}, "modifications": [], "biosource_type": "immortalized cell line", "cell_line_tier": "Unclassified", "public_release": "2017-07-26", "schema_version": "2", "project_release": "2017-07-26", "biosource_vendor": {"uuid": "7a6f2efe-5be8-4db2-afa8-d82e9b4ad254", "display_title": "American Type Culture Collection", "status": "released", "@id": "/vendors/american-type-culture-collection/", "@type": ["Vendor", "Item"], "name": "american-type-culture-collection", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "alternate_accessions": [], "@id": "/biosources/4DNSRW6BI5JA/", "@type": ["Biosource", "Item"], "uuid": "2a9cf0be-0ed3-4e2e-bd06-db1098c2b6f2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "SK-N-MC - 4DNSRW6BI5JA", "external_references": [], "biosource_name": "SK-N-MC", "biosource_category": ["Other"], "organism": {"display_title": "H. sapiens", "status": "released", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@id": "/organisms/9606/", "name": "human", "@type": ["Organism", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "references": [], "treatments": [], "description": "Homo sapiens SK-N-MC immortalized cell line", "date_created": "2017-05-05T18:43:01.139458+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-05-20T20:06:42.051895+00:00"}, "modifications": [], "public_release": "2017-07-26", "schema_version": "2", "project_release": "2017-07-26", "biosample_protocols": [{"@id": "/protocols/4b2f1d6a-35e6-49d4-8535-ed4e250a6135/", "uuid": "4b2f1d6a-35e6-49d4-8535-ed4e250a6135", "status": "released", "date_created": "2017-05-05T18:42:33.758107+00:00", "display_title": "SK-N-MC_Stam_protocol.pdf", "attachment": {"href": "@@download/attachment/SK-N-MC_Stam_protocol.pdf", "type": "application/pdf", "md5sum": "5b27ae07051025d4d601d1a8eeb35d36", "blob_id": "895e5ea5-dafc-49d3-9328-32846cc0d2ee", "download": "SK-N-MC_Stam_protocol.pdf"}, "protocol_type": "Cell culture protocol", "@type": ["Protocol", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "alternate_accessions": [], "cell_culture_details": [{"lab": {"@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "award": {"uuid": "43fc2984-a074-49c4-a69f-c9d3f3eadeba", "display_title": "A COMPREHENSIVE CATALOG OF DNASE I HYPERSENSITIVE SITES", "@id": "/awards/3U54HG007010-05S1/", "status": "current", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["dekker-lab:BiosampleCellCulture_SK-N-MC_Homo-sapiens-SK-N-MC-ENCBS400ENC"], "dbxrefs": ["ENCODE:ENCBS400ENC"], "karyotype": "The cell line is a pseudodiploid human female (XX), with chromosome counts in the diploid range and a modal chromosome number of 46. Normal chromosomes N3 and N10 are absent, and many (N1, N2, N4, N15, N16, N17, N21, and N22) are monosomic. Normal chromosome N8 is most often tetrasomic. The remainder of normal chromosomes were usually paired. Numerous marker chromosomes are present including: 1p+, der(3)t(2;3)(q24;q27), del(4)(p12), 11q+, del(2)(q23), ampl.(17)(p12), ampl.(16)(q13), del(15)(q13q22), 21p+, iso(3q), del(22)(q11q13). Marker chromosomes M2 and M3 appear to us to be identical to two markers (M4 and M3, respectively) described by R.C. Seeger, et al.for this cell line.", "description": "Homo sapiens SK-N-MC immortalized cell line", "date_created": "2017-05-05T18:42:52.577713+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-05-14T18:24:08.339171+00:00"}, "passage_number": 4, "public_release": "2017-07-26", "schema_version": "2", "project_release": "2017-07-26", "culture_duration": 16, "culture_start_date": "2010-03-07", "culture_harvest_date": "2010-04-02", "in_vitro_differentiated": "No", "@id": "/biosample-cell-cultures/000588aa-e86d-433a-b9c4-3435d72e2eeb/", "@type": ["BiosampleCellCulture", "Item"], "uuid": "000588aa-e86d-433a-b9c4-3435d72e2eeb", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "BiosampleCellCulture from 2017-05-05", "external_references": [{"ref": "ENCODE:ENCBS400ENC", "uri": "https://www.encodeproject.org/ENCBS400ENC"}]}], "@id": "/biosamples/4DNBS1EJQPQT/", "@type": ["Biosample", "Item"], "uuid": "44de7904-c9f0-4af1-8e3e-edbc59ea8082", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNBS1EJQPQT", "external_references": [{"ref": "ENCODE:ENCBS400ENC", "uri": "https://www.encodeproject.org/ENCBS400ENC"}], "modifications_summary": "None", "modifications_summary_short": "None", "treatments_summary": "None", "tissue_organ_info": {"tissue_source": "brain", "organ_system": ["ectoderm", "central nervous system", "brain"]}, "biosource_summary": "SK-N-MC", "biosample_type": "immortalized cells", "biosample_category": ["Other"], "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBS1EJQPQT/", "embedded_path": "badges", "item": {"messages": ["Biosample missing doubling_number", "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": []}