{"lab": {"display_title": "Job Dekker, UMMS", "@id": "/labs/job-dekker-lab/", "status": "current", "correspondence": [{"contact_email": "am9iLmRla2tlckB1bWFzc21lZC5lZHU=", "@id": "/users/83b5073a-069b-4162-9b30-6f42d5551e34/", "display_title": "Job Dekker"}], "@type": ["Lab", "Item"], "title": "Job Dekker, UMMS", "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": {"center_title": "3U54HG007010-05S1", "@id": "/awards/3U54HG007010-05S1/", "name": "3U54HG007010-05S1", "uuid": "43fc2984-a074-49c4-a69f-c9d3f3eadeba", "status": "current", "display_title": "A COMPREHENSIVE CATALOG OF DNASE I HYPERSENSITIVE SITES", "project": "ENCODE", "@type": ["Award", "Item"], "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": {"title": "Biosample Metadata Incomplete", "badge_icon": "/static/img/badges/biosample-icon.svg", "display_title": "Biosample Metadata Incomplete", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "@type": ["Badge", "Item"], "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "warning": "Biosample Metadata Incomplete", "badge_classification": "Warning", "@id": "/badges/biosample-metadata-incomplete/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Biosample missing doubling_number", "Biosample missing morphology_image"]}], "status": "released", "aliases": ["dekker-lab:Biosample_A549_Homo-sapiens-A549-ENCBS009OIC"], "dbxrefs": ["ENCODE:ENCBS009OIC"], "accession": "4DNBSBB2NVAD", "biosource": [{"lab": {"status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "url": "https://www.encodeproject.org/biosamples/ENCBS009OIC/", "award": {"uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@type": ["Award", "Item"], "status": "current", "@id": "/awards/1U01CA200059-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"uuid": "111186bc-8535-4448-903e-854af460a233", "term_url": "http://purl.obolibrary.org/obo/UBERON_0002048", "preferred_name": "lung", "synonyms": ["pulmo"], "@id": "/ontology-terms/UBERON:0002048/", "term_id": "UBERON:0002048", "status": "released", "display_title": "lung", "term_name": "lung", "@type": ["OntologyTerm", "Item"], "slim_terms": [{"status": "released", "term_url": "http://purl.obolibrary.org/obo/UBERON_0001004", "synonyms": ["respiratory system", "apparatus respiratorius"], "term_name": "respiratory system", "term_id": "UBERON:0001004", "preferred_name": "respiratory system", "display_title": "respiratory system", "uuid": "111128bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0001004/", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "term_url": "http://purl.obolibrary.org/obo/UBERON_0002048", "synonyms": ["pulmo"], "term_name": "lung", "term_id": "UBERON:0002048", "preferred_name": "lung", "display_title": "lung", "uuid": "111186bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0002048/", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "term_url": "http://purl.obolibrary.org/obo/UBERON_0000925", "synonyms": ["entoderm", "Entire endoderm"], "term_name": "endoderm", "term_id": "UBERON:0000925", "preferred_name": "endoderm", "display_title": "endoderm", "uuid": "111121bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0000925/", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["dekker-lab:Biosource_A549"], "accession": "4DNSRFLY6T15", "cell_line": {"preferred_name": "A549", "display_title": "A549", "term_id": "EFO:0001086", "term_url": "http://www.ebi.ac.uk/efo/EFO_0001086", "@type": ["OntologyTerm", "Item"], "term_name": "A549", "status": "released", "synonyms": ["A-549", "A549 cell"], "@id": "/ontology-terms/EFO:0001086/", "uuid": "2fea36d1-69bd-4039-8c58-a5d9bf6bcdad", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"status": "released", "@id": "/individuals-human/4DNINRY29RK2/", "sex": "male", "uuid": "6db764c0-14fd-4ffb-966a-3f0e3412207f", "display_title": "4DNINRY29RK2", "@type": ["IndividualHuman", "Individual", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "references": [], "description": "Homo sapiens A549 immortalized cell line", "date_created": "2017-05-05T18:42:43.274917+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-10-20T07:55:53.805735+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": {"name": "american-type-culture-collection", "@id": "/vendors/american-type-culture-collection/", "display_title": "American Type Culture Collection", "status": "released", "@type": ["Vendor", "Item"], "uuid": "7a6f2efe-5be8-4db2-afa8-d82e9b4ad254", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "alternate_accessions": [], "@id": "/biosources/4DNSRFLY6T15/", "@type": ["Biosource", "Item"], "uuid": "044733e7-db6c-412c-b1c3-eb77c811dd3e", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "A549 - 4DNSRFLY6T15", "external_references": [], "biosource_name": "A549", "biosource_category": ["Other"], "organism": {"uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "name": "human", "status": "released", "@id": "/organisms/9606/", "display_title": "H. sapiens", "@type": ["Organism", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "references": [], "treatments": [], "description": "Homo sapiens A549 immortalized cell line", "date_created": "2017-05-05T18:43:00.125244+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-05-08T15:44:31.719579+00:00"}, "modifications": [], "public_release": "2017-07-26", "schema_version": "2", "project_release": "2017-07-26", "alternate_accessions": [], "cell_culture_details": [{"lab": {"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "status": "current", "@id": "/labs/job-dekker-lab/", "@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", "status": "current", "@id": "/awards/3U54HG007010-05S1/", "display_title": "A COMPREHENSIVE CATALOG OF DNASE I HYPERSENSITIVE SITES", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["dekker-lab:BiosampleCellCulture_A549_Homo-sapiens-A549-ENCBS009OIC"], "dbxrefs": ["ENCODE:ENCBS009OIC"], "karyotype": "This is a hypotriploid human cell line with the modal chromosome number of 66, occurring in 24% of cells. Cells with 64 (22%), 65, and 67 chromosome counts also occurred at relatively high frequencies; the rate with higher ploidies was low at 0.4%. There were 6 markers present in single copies in all cells. They include der(6)t(1;6) (q11;q27); ?del(6) (p23); del(11) (q21), del(2) (q11), M4 and M5. Most cells had two X and two Y chromosomes. However, one or both Y chromosomes were lost in 40% of 50 cells analyzed. Chromosomes N2 and N6 had single copies per cell; and N12 and N17 usually had 4 copies. Note: Cytogenetic information is based on initial seed stock at ATCC. Cytogenetic instability has been reported in the literature for some cell lines.", "description": "Homo sapiens A549 immortalized cell line", "date_created": "2017-05-05T18:42:51.656628+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-05-20T20:16:57.120263+00:00"}, "passage_number": 5, "public_release": "2017-07-26", "schema_version": "2", "project_release": "2017-07-26", "culture_duration": 14, "culture_start_date": "2010-03-11", "culture_harvest_date": "2010-03-25", "in_vitro_differentiated": "No", "@id": "/biosample-cell-cultures/129b3b49-8b48-45a9-b141-4c9b7dda6eac/", "@type": ["BiosampleCellCulture", "Item"], "uuid": "129b3b49-8b48-45a9-b141-4c9b7dda6eac", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "BiosampleCellCulture from 2017-05-05", "external_references": [{"ref": "ENCODE:ENCBS009OIC", "uri": "https://www.encodeproject.org/ENCBS009OIC"}]}], "@id": "/biosamples/4DNBSBB2NVAD/", "@type": ["Biosample", "Item"], "uuid": "2d909442-e142-4acf-a3ee-de92b598c7e2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNBSBB2NVAD", "external_references": [{"ref": "ENCODE:ENCBS009OIC", "uri": "https://www.encodeproject.org/ENCBS009OIC"}], "modifications_summary": "None", "modifications_summary_short": "None", "treatments_summary": "None", "tissue_organ_info": {"tissue_source": "lung", "organ_system": ["respiratory system", "lung", "endoderm"]}, "biosource_summary": "A549", "biosample_type": "immortalized cells", "biosample_category": ["Other"], "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSBB2NVAD/", "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": []}