{"lab": {"@type": ["Lab", "Item"], "status": "current", "title": "Job Dekker, UMMS", "correspondence": [{"contact_email": "am9iLmRla2tlckB1bWFzc21lZC5lZHU=", "@id": "/users/83b5073a-069b-4162-9b30-6f42d5551e34/", "display_title": "Job Dekker"}], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@id": "/labs/job-dekker-lab/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "award": {"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.", "project": "ENCODE", "status": "current", "@type": ["Award", "Item"], "name": "3U54HG007010-05S1", "center_title": "3U54HG007010-05S1", "display_title": "A COMPREHENSIVE CATALOG OF DNASE I HYPERSENSITIVE SITES", "uuid": "43fc2984-a074-49c4-a69f-c9d3f3eadeba", "@id": "/awards/3U54HG007010-05S1/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "badges": [{"badge": {"badge_icon": "/static/img/badges/biosample-icon.svg", "status": "released", "@type": ["Badge", "Item"], "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "display_title": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "warning": "Biosample Metadata Incomplete", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "badge_classification": "Warning", "@id": "/badges/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_RPMI-7951_Homo-sapiens-RPMI-7951-ENCBS262AAA"], "dbxrefs": ["ENCODE:ENCBS262AAA"], "accession": "4DNBST5DKF6B", "biosource": [{"lab": {"display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "url": "https://www.encodeproject.org/biosamples/ENCBS262AAA/", "award": {"status": "current", "display_title": "A COMPREHENSIVE CATALOG OF DNASE I HYPERSENSITIVE SITES", "uuid": "43fc2984-a074-49c4-a69f-c9d3f3eadeba", "@type": ["Award", "Item"], "@id": "/awards/3U54HG007010-05S1/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"display_title": "skin", "term_name": "skin of body", "term_id": "UBERON:0002097", "synonyms": ["skin organ", "entire skin"], "@id": "/ontology-terms/UBERON:0002097/", "status": "released", "term_url": "http://purl.obolibrary.org/obo/UBERON_0002097", "preferred_name": "skin", "@type": ["OntologyTerm", "Item"], "uuid": "111188bc-8535-4448-903e-854af460a233", "slim_terms": [{"uuid": "111134bc-8535-4448-903e-854af460a233", "preferred_name": "integumental system", "status": "released", "@type": ["OntologyTerm", "Item"], "term_url": "http://purl.obolibrary.org/obo/UBERON_0002416", "term_id": "UBERON:0002416", "@id": "/ontology-terms/UBERON:0002416/", "term_name": "integumental system", "synonyms": ["integumentary system"], "display_title": "integumental system", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111119bc-8535-4448-903e-854af460a233", "preferred_name": "ectoderm", "status": "released", "@type": ["OntologyTerm", "Item"], "term_url": "http://purl.obolibrary.org/obo/UBERON_0000924", "term_id": "UBERON:0000924", "@id": "/ontology-terms/UBERON:0000924/", "term_name": "ectoderm", "synonyms": ["embryonic ectoderm"], "display_title": "ectoderm", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111188bc-8535-4448-903e-854af460a233", "preferred_name": "skin", "status": "released", "@type": ["OntologyTerm", "Item"], "term_url": "http://purl.obolibrary.org/obo/UBERON_0002097", "term_id": "UBERON:0002097", "@id": "/ontology-terms/UBERON:0002097/", "term_name": "skin of body", "synonyms": ["skin organ", "entire skin"], "display_title": "skin", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["dekker-lab:Biosource_RPMI-7951"], "accession": "4DNSRQW8GWCI", "cell_line": {"synonyms": ["RPMI 7951", "RPMI_7951", "RPMI7951"], "preferred_name": "RPMI-7951", "term_name": "RPMI-7951", "status": "released", "@id": "/ontology-terms/EFO:0005712/", "term_id": "EFO:0005712", "uuid": "ef123dc5-2ee1-48fd-93e4-ed06eb5f645a", "term_url": "http://www.ebi.ac.uk/efo/EFO_0005712", "@type": ["OntologyTerm", "Item"], "display_title": "RPMI-7951", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"sex": "female", "@id": "/individuals-human/4DNIN5JK2UEV/", "@type": ["IndividualHuman", "Individual", "Item"], "uuid": "ae1c7b93-6ac1-49c8-9747-6bab2480be6a", "status": "released", "display_title": "4DNIN5JK2UEV", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "references": [], "description": "Human Skin Malignant Melanoma Cells, This is a hyperdiploid human cell line with the modal chromosome number of 49, occurring in 24% of cells. Polyploid cells occurred at 22%, which is high.", "date_created": "2017-05-05T18:42:42.534012+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-06-05T14:40:21.147155+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", "@id": "/vendors/american-type-culture-collection/", "name": "american-type-culture-collection", "status": "released", "@type": ["Vendor", "Item"], "display_title": "American Type Culture Collection", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "alternate_accessions": [], "@id": "/biosources/4DNSRQW8GWCI/", "@type": ["Biosource", "Item"], "uuid": "4e23a36b-3a27-461d-a6ab-8b4f4231fb8d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "RPMI-7951 - 4DNSRQW8GWCI", "external_references": [], "biosource_name": "RPMI-7951", "biosource_category": ["Other"], "organism": {"@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "status": "released", "@type": ["Organism", "Item"], "name": "human", "display_title": "H. sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "references": [], "treatments": [], "description": "Human Skin Malignant Melanoma Cells, This is a hyperdiploid human cell line with the modal chromosome number of 49, occurring in 24% of cells. Polyploid cells occurred at 22%, which is high.", "date_created": "2017-05-05T18:42:58.664592+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-05-08T15:44:35.841464+00:00"}, "modifications": [], "public_release": "2017-07-26", "schema_version": "2", "project_release": "2017-07-26", "biosample_protocols": [{"uuid": "10f1ad74-81c3-479e-9765-7db7038f060c", "@type": ["Protocol", "Item"], "date_created": "2017-05-05T18:42:32.704836+00:00", "display_title": "RPMI7951_Stam_protocol.pdf", "@id": "/protocols/10f1ad74-81c3-479e-9765-7db7038f060c/", "status": "released", "protocol_type": "Cell culture protocol", "attachment": {"href": "@@download/attachment/RPMI7951_Stam_protocol.pdf", "type": "application/pdf", "md5sum": "6d9bbd042f5b9b76832a9ba976dd6012", "blob_id": "0e2a2095-83cd-4462-b880-536b0f54a149", "download": "RPMI7951_Stam_protocol.pdf"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "alternate_accessions": [], "cell_culture_details": [{"lab": {"status": "current", "@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "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", "@type": ["Award", "Item"], "display_title": "A COMPREHENSIVE CATALOG OF DNASE I HYPERSENSITIVE SITES", "status": "current", "@id": "/awards/3U54HG007010-05S1/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["dekker-lab:BiosampleCellCulture_RPMI-7951_Homo-sapiens-RPMI-7951-ENCBS262AAA"], "dbxrefs": ["ENCODE:ENCBS262AAA"], "karyotype": "modal number= 49; range = 47 to 66.This is a hyperdiploid human cell line with the modal chromosome number of 49, occurring in 24% of cells. Polyploid cells occurred at 22%, which is high. Seven marker chromosomes were common to most cells, including t(10p14q); t(15q17p), t(Xp8p), del(17) (p13.1) and three others. Five others occurred only in some cells. Normal X chromosomes were absent. N14, N17 and N22 were mostly single-copied and N2 had three copies. Fluorescence examination did not show the presence of any Y-like chromosome.", "description": "Human Skin Malignant Melanoma Cells, This is a hyperdiploid human cell line with the modal chromosome number of 49, occurring in 24% of cells. Polyploid cells occurred at 22%, which is high.", "date_created": "2017-05-05T18:42:50.392165+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-05-14T18:24:29.938515+00:00"}, "passage_number": 7, "public_release": "2017-07-26", "schema_version": "2", "project_release": "2017-07-26", "culture_duration": 20, "culture_start_date": "2011-10-19", "culture_harvest_date": "2011-11-08", "in_vitro_differentiated": "No", "@id": "/biosample-cell-cultures/d3ecda2d-32ba-4296-b9d9-6f6cdb91fee4/", "@type": ["BiosampleCellCulture", "Item"], "uuid": "d3ecda2d-32ba-4296-b9d9-6f6cdb91fee4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "BiosampleCellCulture from 2017-05-05", "external_references": [{"ref": "ENCODE:ENCBS262AAA", "uri": "https://www.encodeproject.org/ENCBS262AAA"}]}], "@id": "/biosamples/4DNBST5DKF6B/", "@type": ["Biosample", "Item"], "uuid": "423863d2-f338-4adf-a09a-833bd5325c81", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNBST5DKF6B", "external_references": [{"ref": "ENCODE:ENCBS262AAA", "uri": "https://www.encodeproject.org/ENCBS262AAA"}], "modifications_summary": "None", "modifications_summary_short": "None", "treatments_summary": "None", "tissue_organ_info": {"tissue_source": "skin", "organ_system": ["integumental system", "ectoderm", "skin"]}, "biosource_summary": "RPMI-7951", "biosample_type": "immortalized cells", "biosample_category": ["Other"], "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBST5DKF6B/", "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": []}