{"lab": {"uuid": "3452dfa5-ee8b-4dbc-8068-00cadde268b9", "@id": "/labs/sheng-zhong-lab/", "display_title": "Sheng Zhong, UCSD", "@type": ["Lab", "Item"], "title": "Sheng Zhong, UCSD", "correspondence": [{"contact_email": "c3pob25nQHVjc2QuZWR1", "@id": "/users/5549e16d-fa63-477c-a1ed-6189cecc1304/", "display_title": "Sheng Zhong"}], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3452dfa5-ee8b-4dbc-8068-00cadde268b9"]}, "pi": {"error": "no view permissions"}}, "award": {"status": "current", "@id": "/awards/2U01CA200147-06/", "project": "4DN", "description": "OH: The second phase of the 4DN program requires an efficient organizational center to synergize the activities of all the funded teams and integrate the research products. Accordingly, the 4DN Organizational Hub is proposed to: (1) coordinate and integrate the efforts of all the funded projects, (2) build an efficient consortium infrastructure to serve as a center for the collaborative efforts, and (3) provide the 4DN web portal as a central resource gateway to access all the 4DN-Network generated tools, policies, guidelines, protocols, reagents, cell lines, and as a central hub for the outreach activities. Our major deliverables are: (1) an organizational structure composed of a steering committee and problem-solving working groups with a clear report chain to enable effective communications and decision-making processes, establish co-organizers and schedule, clarify action items, and ensure execution of the action items; (2) 4DN Web Portal (https://www.4dnucleome.org/), which is the always up-to-date community-wide resource and point of access for all data, protocols, reagents, resources, and methods; (3) 4DN internal wiki, the central organized resource for all teams, centers, and working groups to document internal progresses. (4) 4DN annual meetings, including the \"\"kick-off\"\" meeting in winter 2020 and the subsequent annual meetings and 4DN-ASCB (American Society of Cell Biology) satellite meetings; (5) 4DN outreach workshops at Keystone symposia and American Society of Human Genetics (ASHG) meetings, and on 4DN YouTube channel.", "uuid": "1a4da807-8221-47d2-96ab-7a31485974c3", "@type": ["Award", "Item"], "display_title": "THE SECOND PHASE OF NIH COMMON FUND 4D NUCLEOME NETWORK ORGANIZATIONAL HUB", "center_title": "OH - Zhong", "name": "2U01CA200147-06", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"file_type_detailed": "reads (fastq)", "upload_key": "3d93b950-9f06-42fd-9fa0-38002aa9f52c/4DNFITT6FUSA.fastq.gz", "@type": ["FileFastq", "File", "Item"], "file_classification": "raw file", "file_size": 19225064927, "display_title": "4DNFITT6FUSA.fastq.gz", "uuid": "3d93b950-9f06-42fd-9fa0-38002aa9f52c", "href": "/files-fastq/4DNFITT6FUSA/@@download/4DNFITT6FUSA.fastq.gz", "file_type": "reads", "status": "released", "paired_end": "1", "@id": "/files-fastq/4DNFITT6FUSA/", "accession": "4DNFITT6FUSA", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "d7924d84-5fc4-44ed-bd00-2c925fd9fa8b", "@id": "/files-fastq/4DNFIAO2STTB/", "display_title": "4DNFIAO2STTB.fastq.gz", "paired_end": "2", "file_type_detailed": "reads (fastq)", "accession": "4DNFIAO2STTB", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"Total Sequences": 355231477, "uuid": "8740d1fb-1c73-4a01-b721-61f625fde30e", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-11-28", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFITT6FUSA/fastqc_report.html", "@id": "/quality-metrics-fastqc/8740d1fb-1c73-4a01-b721-61f625fde30e/", "Sequence length": "100", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "reads (fastq)", "upload_key": "d7924d84-5fc4-44ed-bd00-2c925fd9fa8b/4DNFIAO2STTB.fastq.gz", "@type": ["FileFastq", "File", "Item"], "file_classification": "raw file", "file_size": 20307222720, "display_title": "4DNFIAO2STTB.fastq.gz", "uuid": "d7924d84-5fc4-44ed-bd00-2c925fd9fa8b", "href": "/files-fastq/4DNFIAO2STTB/@@download/4DNFIAO2STTB.fastq.gz", "file_type": "reads", "status": "released", "paired_end": "2", "@id": "/files-fastq/4DNFIAO2STTB/", "accession": "4DNFIAO2STTB", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "3d93b950-9f06-42fd-9fa0-38002aa9f52c", "@id": "/files-fastq/4DNFITT6FUSA/", "display_title": "4DNFITT6FUSA.fastq.gz", "paired_end": "1", "file_type_detailed": "reads (fastq)", "accession": "4DNFITT6FUSA", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"Total Sequences": 355231477, "uuid": "fbc9cc0f-0fa0-4656-9ce7-446828aff2f3", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-11-28", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIAO2STTB/fastqc_report.html", "@id": "/quality-metrics-fastqc/fbc9cc0f-0fa0-4656-9ce7-446828aff2f3/", "Sequence length": "100", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "reads (fastq)", "upload_key": "17538155-d37e-45be-bcf7-6d1f94846c46/4DNFIEBWU2IP.fastq.gz", "@type": ["FileFastq", "File", "Item"], "file_classification": "raw file", "file_size": 19020828826, "display_title": "4DNFIEBWU2IP.fastq.gz", "uuid": "17538155-d37e-45be-bcf7-6d1f94846c46", "href": "/files-fastq/4DNFIEBWU2IP/@@download/4DNFIEBWU2IP.fastq.gz", "file_type": "reads", "status": "released", "paired_end": "1", "@id": "/files-fastq/4DNFIEBWU2IP/", "accession": "4DNFIEBWU2IP", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "f0df3807-7c84-473d-a764-c407780767ea", "@id": "/files-fastq/4DNFI76P8SDA/", "display_title": "4DNFI76P8SDA.fastq.gz", "paired_end": "2", "file_type_detailed": "reads (fastq)", "accession": "4DNFI76P8SDA", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"Total Sequences": 346251192, "uuid": "8fe2fb53-9e77-4919-949f-1dfb89f9c4ca", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2021-07-02", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIEBWU2IP/fastqc_report.html", "@id": "/quality-metrics-fastqc/8fe2fb53-9e77-4919-949f-1dfb89f9c4ca/", "Sequence length": "100", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "reads (fastq)", "upload_key": "f0df3807-7c84-473d-a764-c407780767ea/4DNFI76P8SDA.fastq.gz", "@type": ["FileFastq", "File", "Item"], "file_classification": "raw file", "file_size": 20647685695, "display_title": "4DNFI76P8SDA.fastq.gz", "uuid": "f0df3807-7c84-473d-a764-c407780767ea", "href": "/files-fastq/4DNFI76P8SDA/@@download/4DNFI76P8SDA.fastq.gz", "file_type": "reads", "status": "released", "paired_end": "2", "@id": "/files-fastq/4DNFI76P8SDA/", "accession": "4DNFI76P8SDA", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "17538155-d37e-45be-bcf7-6d1f94846c46", "@id": "/files-fastq/4DNFIEBWU2IP/", "display_title": "4DNFIEBWU2IP.fastq.gz", "paired_end": "1", "file_type_detailed": "reads (fastq)", "accession": "4DNFIEBWU2IP", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"Total Sequences": 346251192, "uuid": "5b59ddc1-3def-434d-aefd-16c6bb0dd2bb", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2021-07-02", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI76P8SDA/fastqc_report.html", "@id": "/quality-metrics-fastqc/5b59ddc1-3def-434d-aefd-16c6bb0dd2bb/", "Sequence length": "100", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "reads (fastq)", "upload_key": "3ab3512f-a421-4888-81f9-cfe5a495ccb7/4DNFIJ1CGQ9D.fastq.gz", "@type": ["FileFastq", "File", "Item"], "file_classification": "raw file", "file_size": 20021050062, "display_title": "4DNFIJ1CGQ9D.fastq.gz", "uuid": "3ab3512f-a421-4888-81f9-cfe5a495ccb7", "href": "/files-fastq/4DNFIJ1CGQ9D/@@download/4DNFIJ1CGQ9D.fastq.gz", "file_type": "reads", "status": "released", "paired_end": "1", "@id": "/files-fastq/4DNFIJ1CGQ9D/", "accession": "4DNFIJ1CGQ9D", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "ee8fd843-ff0b-42b7-9e30-3d1f784424b6", "@id": "/files-fastq/4DNFIZBJ24LP/", "display_title": "4DNFIZBJ24LP.fastq.gz", "paired_end": "2", "file_type_detailed": "reads (fastq)", "accession": "4DNFIZBJ24LP", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"Total Sequences": 345685077, "uuid": "bcfe2bde-a3a1-42af-a311-3cfc460ea578", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2021-07-02", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJ1CGQ9D/fastqc_report.html", "@id": "/quality-metrics-fastqc/bcfe2bde-a3a1-42af-a311-3cfc460ea578/", "Sequence length": "100", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "reads (fastq)", "upload_key": "ee8fd843-ff0b-42b7-9e30-3d1f784424b6/4DNFIZBJ24LP.fastq.gz", "@type": ["FileFastq", "File", "Item"], "file_classification": "raw file", "file_size": 21122895363, "display_title": "4DNFIZBJ24LP.fastq.gz", "uuid": "ee8fd843-ff0b-42b7-9e30-3d1f784424b6", "href": "/files-fastq/4DNFIZBJ24LP/@@download/4DNFIZBJ24LP.fastq.gz", "file_type": "reads", "status": "released", "paired_end": "2", "@id": "/files-fastq/4DNFIZBJ24LP/", "accession": "4DNFIZBJ24LP", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "3ab3512f-a421-4888-81f9-cfe5a495ccb7", "@id": "/files-fastq/4DNFIJ1CGQ9D/", "display_title": "4DNFIJ1CGQ9D.fastq.gz", "paired_end": "1", "file_type_detailed": "reads (fastq)", "accession": "4DNFIJ1CGQ9D", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"Total Sequences": 345685077, "uuid": "bd8136b0-ca78-4ff9-a4b3-53d1681deb16", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2021-07-02", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIZBJ24LP/fastqc_report.html", "@id": "/quality-metrics-fastqc/bd8136b0-ca78-4ff9-a4b3-53d1681deb16/", "Sequence length": "100", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "reads (fastq)", "upload_key": "55756007-bc06-46c7-bc28-bdf63a52c308/4DNFIGNS31NB.fastq.gz", "@type": ["FileFastq", "File", "Item"], "file_classification": "raw file", "file_size": 20399275513, "display_title": "4DNFIGNS31NB.fastq.gz", "uuid": "55756007-bc06-46c7-bc28-bdf63a52c308", "href": "/files-fastq/4DNFIGNS31NB/@@download/4DNFIGNS31NB.fastq.gz", "file_type": "reads", "status": "released", "paired_end": "1", "@id": "/files-fastq/4DNFIGNS31NB/", "accession": "4DNFIGNS31NB", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "aff10413-107b-4d08-904a-7e3f1195acbc", "@id": "/files-fastq/4DNFI3Q4FQ44/", "display_title": "4DNFI3Q4FQ44.fastq.gz", "paired_end": "2", "file_type_detailed": "reads (fastq)", "accession": "4DNFI3Q4FQ44", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"Total Sequences": 354287691, "uuid": "1102a44b-5340-4080-b208-e1e2f6170eba", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2021-07-02", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIGNS31NB/fastqc_report.html", "@id": "/quality-metrics-fastqc/1102a44b-5340-4080-b208-e1e2f6170eba/", "Sequence length": "100", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "reads (fastq)", "upload_key": "aff10413-107b-4d08-904a-7e3f1195acbc/4DNFI3Q4FQ44.fastq.gz", "@type": ["FileFastq", "File", "Item"], "file_classification": "raw file", "file_size": 22259130818, "display_title": "4DNFI3Q4FQ44.fastq.gz", "uuid": "aff10413-107b-4d08-904a-7e3f1195acbc", "href": "/files-fastq/4DNFI3Q4FQ44/@@download/4DNFI3Q4FQ44.fastq.gz", "file_type": "reads", "status": "released", "paired_end": "2", "@id": "/files-fastq/4DNFI3Q4FQ44/", "accession": "4DNFI3Q4FQ44", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "55756007-bc06-46c7-bc28-bdf63a52c308", "@id": "/files-fastq/4DNFIGNS31NB/", "display_title": "4DNFIGNS31NB.fastq.gz", "paired_end": "1", "file_type_detailed": "reads (fastq)", "accession": "4DNFIGNS31NB", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"Total Sequences": 354287691, "uuid": "e7e303b3-0e2a-45c7-bfa4-41e44685b17b", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2021-07-02", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI3Q4FQ44/fastqc_report.html", "@id": "/quality-metrics-fastqc/e7e303b3-0e2a-45c7-bfa4-41e44685b17b/", "Sequence length": "100", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "status": "released", "aliases": ["sheng-zhong-lab:experiment_iMARGI-on-hff_B2_T1"], "protocol": {"uuid": "9cff4e20-40de-486e-9801-657bb59e5af1", "@id": "/protocols/9cff4e20-40de-486e-9801-657bb59e5af1/", "@type": ["Protocol", "Item"], "status": "released", "display_title": "4DN Standard iMARGI Protocol", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEXHKOYO1A", "biosample": {"treatments_summary": "None", "modifications_summary": "None", "@type": ["Biosample", "Item"], "biosample_type": "immortalized cells", "@id": "/biosamples/4DNBSV478OCC/", "display_title": "4DNBSV478OCC", "uuid": "a275efcf-a35f-4160-bc6f-61abef1cc791", "accession": "4DNBSV478OCC", "status": "released", "biosource_summary": "HFFc6 (Tier 1)", "biosource": [{"lab": {"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "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"]}}, "award": {"@id": "/awards/1U54DK107980-01/", "display_title": "CENTER FOR 3D STRUCTURE AND PHYSICS OF THE GENOME", "status": "current", "uuid": "ae6c618f-7a8c-441e-a886-e30bbbe591da", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"@type": ["OntologyTerm", "Item"], "preferred_name": "skin fibroblast", "display_title": "skin fibroblast", "uuid": "1a658f38-8dee-4ed2-92ca-c694b5cef902", "@id": "/ontology-terms/CL:0002620/", "term_name": "skin fibroblast", "term_id": "CL:0002620", "status": "released", "slim_terms": [{"display_title": "integumental system", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "111134bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0002416/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "ectoderm", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "111119bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0000924/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "skin", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "111188bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0002097/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "@type": ["OntologyTerm", "Item"], "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["dcic:hffc6", "dekker-lab:Biosource_HFFc6"], "accession": "4DNSRC6ZVYVP", "cell_line": {"term_id": "EFO:0009318", "uuid": "426ef4ff-c1f7-486e-bfcf-612ebb52c8b0", "preferred_name": "HFFc6", "display_title": "HFFc6", "synonyms": ["HFF-hTERT clone 6"], "slim_terms": [{"status": "current", "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/EFO:0009318/", "term_name": "HFFc6", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@id": "/individuals-human/4DNINE5V67ON/", "protected_data": false, "display_title": "4DNINE5V67ON", "status": "released", "uuid": "0cce9739-e53b-4155-912e-74ddbaedd695", "@type": ["IndividualHuman", "Individual", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "references": [], "description": "Subclone c6 of HFF-hTERT (distributed at passage 7)", "date_created": "2017-11-14T20:11:47.541627+00:00", "submitted_by": {"error": "no view permissions"}, "SOP_cell_line": {"@id": "/protocols/84ee9070-e0c0-478f-9bec-7df22f3e89c2/", "display_title": "4DN_HFFc6_SOP_170829.pdf", "uuid": "84ee9070-e0c0-478f-9bec-7df22f3e89c2", "status": "released", "@type": ["Protocol", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-10-03T20:30:45.856687+00:00"}, "modifications": [], "biosource_type": "immortalized cell line", "cell_line_tier": "Tier 1", "public_release": "2017-09-14", "schema_version": "2", "project_release": "2017-09-14", "biosource_vendor": {"display_title": "Dekker Lab", "@type": ["Vendor", "Item"], "uuid": "12f2ec60-5611-4cba-9e78-584e115d8845", "status": "released", "@id": "/vendors/dekker-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "alternate_accessions": [], "@id": "/biosources/4DNSRC6ZVYVP/", "@type": ["Biosource", "Item"], "uuid": "10aa2d32-9fd4-46ce-a585-827d8c7810c3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "HFFc6 (Tier 1) - 4DNSRC6ZVYVP", "external_references": [], "biosource_name": "HFFc6 (Tier 1)", "biosource_category": ["HFF (c6 or hTERT)"], "organism": {"@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "name": "human", "display_title": "H. sapiens", "@type": ["Organism", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "badges": [{"messages": ["Biosample missing doubling_number", "Biosample missing morphology_image"], "badge": {"@type": ["Badge", "Item"], "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "title": "Biosample Metadata Incomplete", "badge_classification": "Warning", "warning": "Biosample Metadata Incomplete", "status": "released", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "sop_mapping": {"has_sop": "No"}, "date_created": "2021-07-01T17:48:30.479817+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-12-15T16:58:52.093334+00:00"}, "digestion_time": 600.0, "public_release": "2021-07-27", "schema_version": "5", "experiment_type": {"uuid": "fd5f574f-69f0-4038-864d-c8a8a5c8d144", "assay_subclass_short": "RNA-DNA HiC", "status": "released", "experiment_category": "Sequencing", "@id": "/experiment-types/margi/", "display_title": "MARGI", "@type": ["ExperimentType", "Item"], "title": "MARGI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"@type": ["FileProcessed", "File", "Item"], "status": "released", "file_size": 57231923123, "file_type_detailed": "alignments (bam)", "@id": "/files-processed/4DNFI6QMNKB9/", "file_type": "alignments", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "file_format": "bam", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFI6QMNKB9/@@download/4DNFI6QMNKB9.bam", "uuid": "6496503a-58ae-4d03-8861-0f7be0bfae9d", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/6496503a-58ae-4d03-8861-0f7be0bfae9d/4DNFI6QMNKB9.bam", "file_classification": "processed file", "upload_key": "6496503a-58ae-4d03-8861-0f7be0bfae9d/4DNFI6QMNKB9.bam", "accession": "4DNFI6QMNKB9", "display_title": "4DNFI6QMNKB9.bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"lab_name": "4DN DCIC, HMS"}}, {"@type": ["FileProcessed", "File", "Item"], "status": "released", "file_size": 977080792, "file_type_detailed": "contact list-replicate (pairs)", "@id": "/files-processed/4DNFIYN8SZ4V/", "file_type": "contact list-replicate", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFIYN8SZ4V/@@download/4DNFIYN8SZ4V.pairs.gz", "uuid": "289ef947-2351-4a9c-9370-c472607b88d0", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/289ef947-2351-4a9c-9370-c472607b88d0/4DNFIYN8SZ4V.pairs.gz", "file_classification": "processed file", "upload_key": "289ef947-2351-4a9c-9370-c472607b88d0/4DNFIYN8SZ4V.pairs.gz", "accession": "4DNFIYN8SZ4V", "display_title": "4DNFIYN8SZ4V.pairs.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"@type": ["QualityMetricMargi", "QualityMetric", "Item"], "overall_quality_status": "PASS", "@id": "/quality-metrics-margi/45315d46-81ea-4d9b-abdf-6cfff7911e4b/", "status": "released", "display_title": "QualityMetricMargi from 2019-09-19", "uuid": "45315d46-81ea-4d9b-abdf-6cfff7911e4b", "quality_metric_summary": [{"title": "Filtered Reads", "value": "27354113", "numberType": "integer"}, {"title": "Cis reads (>200000)", "value": "7.726", "tooltip": "Percent of total interactions (=2.11m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "56.855", "tooltip": "Percent of total interactions (=15.55m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "35.419", "tooltip": "Percent of total interactions (=9.69m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "track_and_facet_info": {"lab_name": "4DN DCIC, HMS"}}, {"@type": ["FileProcessed", "File", "Item"], "status": "released", "file_size": 58098718801, "file_type_detailed": "alignments (bam)", "@id": "/files-processed/4DNFI7UOV3O2/", "file_type": "alignments", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "file_format": "bam", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFI7UOV3O2/@@download/4DNFI7UOV3O2.bam", "uuid": "42e3c7b3-3d26-47fb-9e95-92aa993d1a55", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/42e3c7b3-3d26-47fb-9e95-92aa993d1a55/4DNFI7UOV3O2.bam", "file_classification": "processed file", "upload_key": "42e3c7b3-3d26-47fb-9e95-92aa993d1a55/4DNFI7UOV3O2.bam", "accession": "4DNFI7UOV3O2", "display_title": "4DNFI7UOV3O2.bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Sheng Zhong, UCSD", "experiment_type": "MARGI", "experiment_bucket": "processed file", "assay_info": "AluI", "dataset": "iMARGI on HFFc6 cells", "condition": "No treatment control", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HFFc6 (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"@type": ["FileProcessed", "File", "Item"], "status": "released", "file_size": 1035888042, "file_type_detailed": "contact list-replicate (pairs)", "@id": "/files-processed/4DNFIF33L9BN/", "file_type": "contact list-replicate", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFIF33L9BN/@@download/4DNFIF33L9BN.pairs.gz", "uuid": "4eaaf7c1-dbbe-4958-9a07-736c40ced008", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/4eaaf7c1-dbbe-4958-9a07-736c40ced008/4DNFIF33L9BN.pairs.gz", "file_classification": "processed file", "upload_key": "4eaaf7c1-dbbe-4958-9a07-736c40ced008/4DNFIF33L9BN.pairs.gz", "accession": "4DNFIF33L9BN", "display_title": "4DNFIF33L9BN.pairs.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"@type": ["QualityMetricMargi", "QualityMetric", "Item"], "overall_quality_status": "PASS", "@id": "/quality-metrics-margi/d5db7845-8cd1-427d-a86c-a3fcf3f9ebae/", "status": "released", "display_title": "QualityMetricMargi from 2021-07-16", "uuid": "d5db7845-8cd1-427d-a86c-a3fcf3f9ebae", "quality_metric_summary": [{"title": "Filtered Reads", "value": "29082026", "numberType": "integer"}, {"title": "Cis reads (>200000)", "value": "7.969", "tooltip": "Percent of total interactions (=2.32m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "54.994", "tooltip": "Percent of total interactions (=15.99m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "37.038", "tooltip": "Percent of total interactions (=10.77m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Sheng Zhong, UCSD", "experiment_type": "MARGI", "experiment_bucket": "processed file", "assay_info": "AluI", "dataset": "iMARGI on HFFc6 cells", "condition": "No treatment control", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HFFc6 (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"@type": ["FileProcessed", "File", "Item"], "status": "released", "file_size": 59547466084, "file_type_detailed": "alignments (bam)", "@id": "/files-processed/4DNFI393MNU2/", "file_type": "alignments", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "file_format": "bam", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFI393MNU2/@@download/4DNFI393MNU2.bam", "uuid": "c8a4d75f-8ffb-4dd3-b8a1-e8111f253625", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c8a4d75f-8ffb-4dd3-b8a1-e8111f253625/4DNFI393MNU2.bam", "file_classification": "processed file", "upload_key": "c8a4d75f-8ffb-4dd3-b8a1-e8111f253625/4DNFI393MNU2.bam", "accession": "4DNFI393MNU2", "display_title": "4DNFI393MNU2.bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Sheng Zhong, UCSD", "experiment_type": "MARGI", "experiment_bucket": "processed file", "assay_info": "AluI", "dataset": "iMARGI on HFFc6 cells", "condition": "No treatment control", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HFFc6 (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"@type": ["FileProcessed", "File", "Item"], "status": "released", "file_size": 1039999986, "file_type_detailed": "contact list-replicate (pairs)", "@id": "/files-processed/4DNFIRTVQEG5/", "file_type": "contact list-replicate", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFIRTVQEG5/@@download/4DNFIRTVQEG5.pairs.gz", "uuid": "b4abd222-bebc-4db4-ad35-72e23bd346b5", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/b4abd222-bebc-4db4-ad35-72e23bd346b5/4DNFIRTVQEG5.pairs.gz", "file_classification": "processed file", "upload_key": "b4abd222-bebc-4db4-ad35-72e23bd346b5/4DNFIRTVQEG5.pairs.gz", "accession": "4DNFIRTVQEG5", "display_title": "4DNFIRTVQEG5.pairs.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"@type": ["QualityMetricMargi", "QualityMetric", "Item"], "overall_quality_status": "PASS", "@id": "/quality-metrics-margi/2788cf46-e461-4247-b3ae-7fe1f5987f92/", "status": "released", "display_title": "QualityMetricMargi from 2021-07-16", "uuid": "2788cf46-e461-4247-b3ae-7fe1f5987f92", "quality_metric_summary": [{"title": "Filtered Reads", "value": "29167167", "numberType": "integer"}, {"title": "Cis reads (>200000)", "value": "7.979", "tooltip": "Percent of total interactions (=2.33m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "54.916", "tooltip": "Percent of total interactions (=16.02m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "37.105", "tooltip": "Percent of total interactions (=10.82m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Sheng Zhong, UCSD", "experiment_type": "MARGI", "experiment_bucket": "processed file", "assay_info": "AluI", "dataset": "iMARGI on HFFc6 cells", "condition": "No treatment control", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HFFc6 (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"@type": ["FileProcessed", "File", "Item"], "status": "released", "file_size": 61449804145, "file_type_detailed": "alignments (bam)", "@id": "/files-processed/4DNFI2NILLQB/", "file_type": "alignments", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "file_format": "bam", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFI2NILLQB/@@download/4DNFI2NILLQB.bam", "uuid": "55d4f250-db72-4050-b60d-712b97a19d26", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/55d4f250-db72-4050-b60d-712b97a19d26/4DNFI2NILLQB.bam", "file_classification": "processed file", "upload_key": "55d4f250-db72-4050-b60d-712b97a19d26/4DNFI2NILLQB.bam", "accession": "4DNFI2NILLQB", "display_title": "4DNFI2NILLQB.bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Sheng Zhong, UCSD", "experiment_type": "MARGI", "experiment_bucket": "processed file", "assay_info": "AluI", "dataset": "iMARGI on HFFc6 cells", "condition": "No treatment control", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HFFc6 (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"@type": ["FileProcessed", "File", "Item"], "status": "released", "file_size": 1044224352, "file_type_detailed": "contact list-replicate (pairs)", "@id": "/files-processed/4DNFIFHM9CMR/", "file_type": "contact list-replicate", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFIFHM9CMR/@@download/4DNFIFHM9CMR.pairs.gz", "uuid": "e084522c-5a21-46c1-9d26-6c9ed00c2fcf", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e084522c-5a21-46c1-9d26-6c9ed00c2fcf/4DNFIFHM9CMR.pairs.gz", "file_classification": "processed file", "upload_key": "e084522c-5a21-46c1-9d26-6c9ed00c2fcf/4DNFIFHM9CMR.pairs.gz", "accession": "4DNFIFHM9CMR", "display_title": "4DNFIFHM9CMR.pairs.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"@type": ["QualityMetricMargi", "QualityMetric", "Item"], "overall_quality_status": "PASS", "@id": "/quality-metrics-margi/191fc52d-9478-442f-9767-e95bdf18f54e/", "status": "released", "display_title": "QualityMetricMargi from 2021-07-16", "uuid": "191fc52d-9478-442f-9767-e95bdf18f54e", "quality_metric_summary": [{"title": "Filtered Reads", "value": "29281673", "numberType": "integer"}, {"title": "Cis reads (>200000)", "value": "7.919", "tooltip": "Percent of total interactions (=2.32m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "55.304", "tooltip": "Percent of total interactions (=16.19m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "36.777", "tooltip": "Percent of total interactions (=10.77m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Sheng Zhong, UCSD", "experiment_type": "MARGI", "experiment_bucket": "processed file", "assay_info": "AluI", "dataset": "iMARGI on HFFc6 cells", "condition": "No treatment control", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HFFc6 (Tier 1)", "lab_name": "4DN DCIC, HMS"}}], "project_release": "2021-07-27", "digestion_enzyme": {"display_title": "AluI", "@id": "/enzymes/AluI/", "status": "released", "uuid": "1db70ad9-5209-4596-85a5-71ac489c7ee7", "@type": ["Enzyme", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "library_prep_kit": "custom (see protocol document)", "enzyme_lot_number": "10051117", "biosample_quantity": 20000000.0, "fragment_size_range": "100-600", "fragmentation_method": "see protocol document", "average_fragment_size": 200, "digestion_temperature": 37.0, "other_processed_files": [{"type": "supplementary", "files": [{"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/eb3b4fbc-3807-4a7e-8473-a9fbf0274f1f/4DNFIKHQNWL6.bw", "display_title": "4DNFIKHQNWL6.bw", "accession": "4DNFIKHQNWL6", "href": "/files-processed/4DNFIKHQNWL6/@@download/4DNFIKHQNWL6.bw", "status": "released", "higlass_uid": "d6c14e01-ee20-4682-966a-6bce215dc43a", "genome_assembly": "GRCh38", "file_type_detailed": "intensity values (bw)", "file_size": 235533489, "file_type": "intensity values", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIKHQNWL6/", "uuid": "eb3b4fbc-3807-4a7e-8473-a9fbf0274f1f", "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@id": "/higlass-view-configs/611fafe7-208d-4289-8342-194e06499d47/", "status": "released", "uuid": "611fafe7-208d-4289-8342-194e06499d47", "display_title": "4DNFIKHQNWL6 - intensity values for HFFc6 (Tier 1) MARGI AluI", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bw", "file_format": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Sheng Zhong, UCSD", "experiment_type": "MARGI", "experiment_bucket": "Chromatin-associated nascent RNA measured by iMARGI RNA ends - Zhong lab", "assay_info": "AluI", "dataset": "iMARGI on HFFc6 cells", "condition": "No treatment control", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HFFc6 (Tier 1)", "lab_name": "Sheng Zhong, UCSD", "track_title": "intensity values for HFFc6 (Tier 1) MARGI AluI"}, "last_modified": {"date_modified": "2022-03-09T21:46:29.054550+00:00"}}, {"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/26339015-87b9-4b2c-83f0-dbafb29a5e34/4DNFIX9GWMET.bw", "display_title": "4DNFIX9GWMET.bw", "accession": "4DNFIX9GWMET", "href": "/files-processed/4DNFIX9GWMET/@@download/4DNFIX9GWMET.bw", "status": "released", "higlass_uid": "0b4f6318-ac01-46f8-8866-4499d425390a", "genome_assembly": "GRCh38", "file_type_detailed": "intensity values (bw)", "file_size": 240329802, "file_type": "intensity values", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIX9GWMET/", "uuid": "26339015-87b9-4b2c-83f0-dbafb29a5e34", "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@id": "/higlass-view-configs/8c520d27-581d-485d-8ede-2e1c13899031/", "status": "released", "uuid": "8c520d27-581d-485d-8ede-2e1c13899031", "display_title": "4DNFIX9GWMET - intensity values for HFFc6 (Tier 1) MARGI AluI", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bw", "file_format": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Sheng Zhong, UCSD", "experiment_type": "MARGI", "experiment_bucket": "Chromatin-associated nascent RNA measured by iMARGI RNA ends - Zhong lab", "assay_info": "AluI", "dataset": "iMARGI on HFFc6 cells", "condition": "No treatment control", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HFFc6 (Tier 1)", "lab_name": "Sheng Zhong, UCSD", "track_title": "intensity values for HFFc6 (Tier 1) MARGI AluI"}, "last_modified": {"date_modified": "2022-03-09T21:46:26.968479+00:00"}}], "title": "Chromatin-associated nascent RNA measured by iMARGI RNA ends - Zhong lab", "description": "The results are derived from RNA, DNA interactions represented in bedpe files generated by iMARGI docker (Wu et,. 2019). The RNA end abundance bigwig file is generated by calculating the pileup reads coverage (R, coverage function) on the genome using RNA ends only in a strand specific manner."}], "biosample_quantity_units": "cells", "library_preparation_date": "2018-08-14", "fragment_size_selection_method": "gel", "@id": "/experiments-seq/4DNEXHKOYO1A/", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "057c0b90-a878-483a-b5a0-5c28341bb63f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "MARGI on HFFc6 (Tier 1) - 4DNEXHKOYO1A", "external_references": [], "experiment_sets": [{"@id": "/experiment-set-replicates/4DNES9Y1GHK4/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "status": "released", "accession": "4DNES9Y1GHK4", "experimentset_type": "replicate", "display_title": "4DNES9Y1GHK4", "uuid": "1e6cd038-f88a-45c0-b0df-b3168d367244", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"display_title": "Calandrelli R et al. (2023) PMID:37845234", "authors": ["Calandrelli R", "Wen X", "Charles Richard JL", "Luo Z", "Nguyen TC", "Chen CJ", "Qi Z", "Xue S", "Chen W", "Yan Z", "Wu W", "Zaleta-Rivera K", "Hu R", "Yu M", "Wang Y", "Li W", "Ma J", "Ren B", "Zhong S"], "short_attribution": "Calandrelli R et al. (2023)", "date_published": "2023-10-16", "uuid": "8334e5bc-68fd-490e-8a63-44fa66066cf5", "ID": "PMID:37845234", "@type": ["Publication", "Item"], "status": "current", "@id": "/publications/8334e5bc-68fd-490e-8a63-44fa66066cf5/", "title": "Genome-wide analysis of the interplay between chromatin-associated RNA and 3D  genome organization in human cells.", "abstract": "The interphase genome is dynamically organized in the nucleus and decorated with  chromatin-associated RNA (caRNA). It remains unclear whether the genome  architecture modulates the spatial distribution of caRNA and vice versa. Here, we  generate a resource of genome-wide RNA-DNA and DNA-DNA contact maps in human  cells. These maps reveal the chromosomal domains demarcated by locally  transcribed RNA, hereafter termed RNA-defined chromosomal domains. Further, the  spreading of caRNA is constrained by the boundaries of topologically associating  domains (TADs), demonstrating the role of the 3D genome structure in modulating  the spatial distribution of RNA. Conversely, stopping transcription or acute  depletion of RNA induces thousands of chromatin loops genome-wide. Activation or  suppression of the transcription of specific genes suppresses or creates  chromatin loops straddling these genes. Deletion of a specific caRNA-producing  genomic sequence promotes chromatin loops that straddle the interchromosomal  target sequences of this caRNA. These data suggest a feedback loop where the 3D  genome modulates the spatial distribution of RNA, which in turn affects the  dynamic 3D genome organization.", "journal": "Nature communications", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"@type": ["Publication", "Item"], "uuid": "8334e5bc-68fd-490e-8a63-44fa66066cf5", "title": "Genome-wide analysis of the interplay between chromatin-associated RNA and 3D  genome organization in human cells.", "date_published": "2023-10-16", "display_title": "Calandrelli R et al. (2023) PMID:37845234", "ID": "PMID:37845234", "abstract": "The interphase genome is dynamically organized in the nucleus and decorated with  chromatin-associated RNA (caRNA). It remains unclear whether the genome  architecture modulates the spatial distribution of caRNA and vice versa. Here, we  generate a resource of genome-wide RNA-DNA and DNA-DNA contact maps in human  cells. These maps reveal the chromosomal domains demarcated by locally  transcribed RNA, hereafter termed RNA-defined chromosomal domains. Further, the  spreading of caRNA is constrained by the boundaries of topologically associating  domains (TADs), demonstrating the role of the 3D genome structure in modulating  the spatial distribution of RNA. Conversely, stopping transcription or acute  depletion of RNA induces thousands of chromatin loops genome-wide. Activation or  suppression of the transcription of specific genes suppresses or creates  chromatin loops straddling these genes. Deletion of a specific caRNA-producing  genomic sequence promotes chromatin loops that straddle the interchromosomal  target sequences of this caRNA. These data suggest a feedback loop where the 3D  genome modulates the spatial distribution of RNA, which in turn affects the  dynamic 3D genome organization.", "status": "current", "short_attribution": "Calandrelli R et al. (2023)", "authors": ["Calandrelli R", "Wen X", "Charles Richard JL", "Luo Z", "Nguyen TC", "Chen CJ", "Qi Z", "Xue S", "Chen W", "Yan Z", "Wu W", "Zaleta-Rivera K", "Hu R", "Yu M", "Wang Y", "Li W", "Ma J", "Ren B", "Zhong S"], "@id": "/publications/8334e5bc-68fd-490e-8a63-44fa66066cf5/", "journal": "Nature communications", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Enzyme", "value": "AluI", "combined": "Enzyme: AluI"}, "experiment_summary": "MARGI on HFFc6 (Tier 1)", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSV478OCC/", "embedded_path": "biosample.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": []}