{"lab": {"correspondence": [{"contact_email": "c3pob25nQHVjc2QuZWR1", "@id": "/users/5549e16d-fa63-477c-a1ed-6189cecc1304/", "display_title": "Sheng Zhong"}], "display_title": "Sheng Zhong, UCSD", "@type": ["Lab", "Item"], "status": "current", "uuid": "3452dfa5-ee8b-4dbc-8068-00cadde268b9", "@id": "/labs/sheng-zhong-lab/", "title": "Sheng Zhong, UCSD", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.3452dfa5-ee8b-4dbc-8068-00cadde268b9"]}}, "award": {"center_title": "OH - Zhong", "uuid": "1a4da807-8221-47d2-96ab-7a31485974c3", "@id": "/awards/2U01CA200147-06/", "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.", "display_title": "THE SECOND PHASE OF NIH COMMON FUND 4D NUCLEOME NETWORK ORGANIZATIONAL HUB", "status": "current", "@type": ["Award", "Item"], "name": "2U01CA200147-06", "project": "4DN", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"accession": "4DNFI3D9EC2L", "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "file_type": "reads", "status": "released", "href": "/files-fastq/4DNFI3D9EC2L/@@download/4DNFI3D9EC2L.fastq.gz", "display_title": "4DNFI3D9EC2L.fastq.gz", "upload_key": "59cdddc6-6e20-46d1-be01-8d003abdcac7/4DNFI3D9EC2L.fastq.gz", "uuid": "59cdddc6-6e20-46d1-be01-8d003abdcac7", "@id": "/files-fastq/4DNFI3D9EC2L/", "paired_end": "1", "file_size": 45834210387, "@type": ["FileFastq", "File", "Item"], "file_format": {"file_format": "fastq", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"status": "released", "@id": "/files-fastq/4DNFINXFRNI5/", "file_type_detailed": "reads (fastq)", "paired_end": "2", "display_title": "4DNFINXFRNI5.fastq.gz", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "uuid": "aad9efd8-7c22-427b-b150-c3fe3c774689", "accession": "4DNFINXFRNI5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/88305dd2-f3af-431f-967f-a2d36671338d/", "status": "released", "Total Sequences": 1009524877, "display_title": "QualityMetricFastqc from 2021-07-01", "Sequence length": "101", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI3D9EC2L/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "uuid": "88305dd2-f3af-431f-967f-a2d36671338d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFINXFRNI5", "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "file_type": "reads", "status": "released", "href": "/files-fastq/4DNFINXFRNI5/@@download/4DNFINXFRNI5.fastq.gz", "display_title": "4DNFINXFRNI5.fastq.gz", "upload_key": "aad9efd8-7c22-427b-b150-c3fe3c774689/4DNFINXFRNI5.fastq.gz", "uuid": "aad9efd8-7c22-427b-b150-c3fe3c774689", "@id": "/files-fastq/4DNFINXFRNI5/", "paired_end": "2", "file_size": 48306058772, "@type": ["FileFastq", "File", "Item"], "file_format": {"file_format": "fastq", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"status": "released", "@id": "/files-fastq/4DNFI3D9EC2L/", "file_type_detailed": "reads (fastq)", "paired_end": "1", "display_title": "4DNFI3D9EC2L.fastq.gz", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "uuid": "59cdddc6-6e20-46d1-be01-8d003abdcac7", "accession": "4DNFI3D9EC2L", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/49c08947-0663-4366-b6a4-54df0f7ad2bb/", "status": "released", "Total Sequences": 1009524877, "display_title": "QualityMetricFastqc from 2021-07-01", "Sequence length": "101", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFINXFRNI5/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "uuid": "49c08947-0663-4366-b6a4-54df0f7ad2bb", "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-h1-control_B1_T1"], "protocol": {"status": "released", "@id": "/protocols/9cff4e20-40de-486e-9801-657bb59e5af1/", "display_title": "4DN Standard iMARGI Protocol", "@type": ["Protocol", "Item"], "uuid": "9cff4e20-40de-486e-9801-657bb59e5af1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEXD9E1MAB", "biosample": {"@type": ["Biosample", "Item"], "@id": "/biosamples/4DNBSKZY2OLH/", "status": "released", "treatments_summary": "None", "uuid": "4b1617da-1e3e-4600-b382-efbedb82d587", "modifications_summary": "None", "accession": "4DNBSKZY2OLH", "biosource_summary": "H1-hESC (Tier 1)", "display_title": "4DNBSKZY2OLH", "biosample_type": "stem cells", "badges": [{"messages": ["Biosample missing doubling_number", "Biosample missing morphology_image"], "badge": {"title": "Biosample Metadata Incomplete", "@type": ["Badge", "Item"], "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "status": "released", "warning": "Biosample Metadata Incomplete", "display_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", "badge_classification": "Warning", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "biosource": [{"lab": {"status": "current", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "url": "https://www.wicell.org/home/stem-cell-lines/catalog-of-stem-cell-lines/wa01.cmsx", "award": {"@id": "/awards/1U01CA200059-01/", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@type": ["Award", "Item"], "status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"slim_terms": [{"display_title": "cell", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "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"]}}], "term_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "synonyms": ["animal stem cell"], "@type": ["OntologyTerm", "Item"], "status": "released", "term_id": "CL:0000034", "preferred_name": "stem cell", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["dcic:h1wa01T1", "4dn-dcic-lab:h1wa01T1"], "accession": "4DNSRV3SKQ8M", "cell_line": {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/EFO:0003042/", "status": "released", "slim_terms": [{"display_title": "cell", "status": "released", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "status": "released", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "display_title": "H1-hESC", "synonyms": ["H1"], "term_name": "H1-hESC", "preferred_name": "H1-hESC", "term_id": "EFO:0003042", "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@type": ["IndividualHuman", "Individual", "Item"], "@id": "/individuals-human/4DNIN3RG3ZKE/", "uuid": "c97775b7-3d00-4132-9598-863797b8ef14", "protected_data": false, "status": "released", "display_title": "4DNIN3RG3ZKE", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "references": [], "description": "Homo sapiens male H1 embryonic stem cell (WA01)", "date_created": "2017-04-10T01:14:03.094143+00:00", "submitted_by": {"error": "no view permissions"}, "SOP_cell_line": {"display_title": "4DN_H1_SOP_210728.pdf", "status": "released", "uuid": "f0803d31-35b4-4bea-99c9-cddeb60e6c07", "@id": "/protocols/f0803d31-35b4-4bea-99c9-cddeb60e6c07/", "@type": ["Protocol", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-07-29T21:18:38.685494+00:00"}, "modifications": [], "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "public_release": "2017-07-26", "schema_version": "2", "project_release": "2017-07-26", "biosource_vendor": {"uuid": "41784f69-697d-42c2-82b1-b52bc5ea3519", "display_title": "WiCell.org", "@type": ["Vendor", "Item"], "@id": "/vendors/wicellorg/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "alternate_accessions": [], "@id": "/biosources/4DNSRV3SKQ8M/", "@type": ["Biosource", "Item"], "uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "external_references": [], "biosource_name": "H1-hESC (Tier 1)", "biosource_category": ["H1-hESC", "Human stem cell"], "organism": {"@type": ["Organism", "Item"], "status": "released", "display_title": "H. sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@id": "/organisms/9606/", "name": "human", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "sop_mapping": {"has_sop": "No"}, "date_created": "2021-07-01T17:47:51.465079+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-12-15T16:58:42.227166+00:00"}, "digestion_time": 600.0, "public_release": "2021-07-27", "schema_version": "5", "experiment_type": {"status": "released", "@type": ["ExperimentType", "Item"], "uuid": "fd5f574f-69f0-4038-864d-c8a8a5c8d144", "experiment_category": "Sequencing", "@id": "/experiment-types/margi/", "display_title": "MARGI", "title": "MARGI", "assay_subclass_short": "RNA-DNA HiC", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_size": 171306188134, "href": "/files-processed/4DNFIPDRQ419/@@download/4DNFIPDRQ419.bam", "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "display_title": "bam", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/649b8462-0dc3-46a2-8dbe-215e1a9ed0ee/4DNFIPDRQ419.bam", "file_type_detailed": "alignments (bam)", "file_classification": "processed file", "status": "released", "uuid": "649b8462-0dc3-46a2-8dbe-215e1a9ed0ee", "upload_key": "649b8462-0dc3-46a2-8dbe-215e1a9ed0ee/4DNFIPDRQ419.bam", "display_title": "4DNFIPDRQ419.bam", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIPDRQ419", "@id": "/files-processed/4DNFIPDRQ419/", "file_type": "alignments", "track_and_facet_info": {"experimental_lab": "Sheng Zhong, UCSD", "experiment_type": "MARGI", "experiment_bucket": "processed file", "assay_info": "AluI", "dataset": "iMARGI on H1 cells", "condition": "No treatment control", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 5250003988, "href": "/files-processed/4DNFI4XXEOJ4/@@download/4DNFI4XXEOJ4.pairs.gz", "file_format": {"file_format": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "display_title": "pairs", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a281fa64-bc12-4e4d-912e-9d9b67b98eda/4DNFI4XXEOJ4.pairs.gz", "file_type_detailed": "contact list-replicate (pairs)", "file_classification": "processed file", "status": "released", "uuid": "a281fa64-bc12-4e4d-912e-9d9b67b98eda", "upload_key": "a281fa64-bc12-4e4d-912e-9d9b67b98eda/4DNFI4XXEOJ4.pairs.gz", "display_title": "4DNFI4XXEOJ4.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFI4XXEOJ4", "@id": "/files-processed/4DNFI4XXEOJ4/", "file_type": "contact list-replicate", "quality_metric": {"@id": "/quality-metrics-margi/df4c8cd8-1adf-429e-965a-c984d8e6ebca/", "@type": ["QualityMetricMargi", "QualityMetric", "Item"], "uuid": "df4c8cd8-1adf-429e-965a-c984d8e6ebca", "overall_quality_status": "PASS", "display_title": "QualityMetricMargi from 2021-07-20", "status": "released", "quality_metric_summary": [{"title": "Filtered Reads", "value": "144257913", "numberType": "integer"}, {"title": "Cis reads (>200000)", "value": "10.865", "tooltip": "Percent of total interactions (=15.67m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "26.169", "tooltip": "Percent of total interactions (=37.75m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "62.966", "tooltip": "Percent of total interactions (=90.83m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Sheng Zhong, UCSD", "experiment_type": "MARGI", "experiment_bucket": "processed file", "assay_info": "AluI", "dataset": "iMARGI on H1 cells", "condition": "No treatment control", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "project_release": "2021-07-27", "digestion_enzyme": {"display_title": "AluI", "uuid": "1db70ad9-5209-4596-85a5-71ac489c7ee7", "status": "released", "@type": ["Enzyme", "Item"], "@id": "/enzymes/AluI/", "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": [{"file_type_detailed": "intensity values (bw)", "href": "/files-processed/4DNFI2LXIREI/@@download/4DNFI2LXIREI.bw", "file_size": 421195008, "uuid": "6e9ef48a-04f0-4f8a-a079-483ad657424c", "status": "released", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFI2LXIREI", "genome_assembly": "GRCh38", "file_type": "intensity values", "@id": "/files-processed/4DNFI2LXIREI/", "display_title": "4DNFI2LXIREI.bw", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/6e9ef48a-04f0-4f8a-a079-483ad657424c/4DNFI2LXIREI.bw", "higlass_uid": "37ba52a0-ff62-47d1-804e-cf285df555b2", "file_format": {"status": "released", "display_title": "bw", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "file_format": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "@id": "/higlass-view-configs/aae17431-4803-4e1a-a883-e38a64c1f665/", "display_title": "4DNFI2LXIREI - intensity values for H1-hESC (Tier 1) MARGI AluI", "uuid": "aae17431-4803-4e1a-a883-e38a64c1f665", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 H1 cells", "condition": "No treatment control", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "Sheng Zhong, UCSD", "track_title": "intensity values for H1-hESC (Tier 1) MARGI AluI"}, "last_modified": {"date_modified": "2022-03-09T21:47:18.172239+00:00"}}, {"file_type_detailed": "intensity values (bw)", "href": "/files-processed/4DNFIOYVWEYZ/@@download/4DNFIOYVWEYZ.bw", "file_size": 447174302, "uuid": "45bfbf45-9b4c-433b-a649-0551af82a9d8", "status": "released", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIOYVWEYZ", "genome_assembly": "GRCh38", "file_type": "intensity values", "@id": "/files-processed/4DNFIOYVWEYZ/", "display_title": "4DNFIOYVWEYZ.bw", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/45bfbf45-9b4c-433b-a649-0551af82a9d8/4DNFIOYVWEYZ.bw", "higlass_uid": "343e86f6-d015-4a8a-9cb0-3dc205a0e2c6", "file_format": {"status": "released", "display_title": "bw", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "file_format": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "@id": "/higlass-view-configs/15b05e32-8eb5-4603-ae97-db8055bcaa75/", "display_title": "4DNFIOYVWEYZ - intensity values for H1-hESC (Tier 1) MARGI AluI", "uuid": "15b05e32-8eb5-4603-ae97-db8055bcaa75", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 H1 cells", "condition": "No treatment control", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "Sheng Zhong, UCSD", "track_title": "intensity values for H1-hESC (Tier 1) MARGI AluI"}, "last_modified": {"date_modified": "2022-03-09T21:47:16.043669+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": "2019-03-20", "fragment_size_selection_method": "gel", "@id": "/experiments-seq/4DNEXD9E1MAB/", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "81c90bb4-be64-4340-abca-324823a2a1a8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "MARGI on H1-hESC (Tier 1) - 4DNEXD9E1MAB", "external_references": [], "experiment_sets": [{"@id": "/experiment-set-replicates/4DNESNOJ7HY7/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "33219c87-723d-45e7-888e-6368fdaf1880", "accession": "4DNESNOJ7HY7", "experimentset_type": "replicate", "status": "released", "display_title": "4DNESNOJ7HY7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"authors": ["Calandrelli R", "Wen X", "Nguyen TC", "Chen C-J", "Qi Z", "Chen W", "Yan Z", "Wu W", "Zaleta-Rivera K", "Hu R", "Yu M", "Wang Y", "Ma J", "Ren B", "Zhong S"], "uuid": "d313c2a4-aab7-417a-b9b4-bcf5ec5cdbac", "@id": "/publications/d313c2a4-aab7-417a-b9b4-bcf5ec5cdbac/", "display_title": "Calandrelli R et al. (2021) doi:10.1101/2021.06.10.447969", "short_attribution": "Calandrelli R et al. (2021)", "status": "current", "abstract": "Chromatin-associated RNA (caRNA) is a vital component of the interphase nucleus; yet its distribution and role in the three-dimensional (3D) genome organization and function remain poorly understood. Here, we map caRNAs spatial distribution on the 3D genome in human embryonic stem cells, fibroblasts, and myelogenous leukemia cells. We find that the relative abundance of trans-acting caRNA reflects the functional nuclear compartmentalization of the 3D genome, and the caRNAs sequence features are predictive of its spatial localization. We observe extensive caRNA-genome interactions that span several hundred kilobases to several megabases. These caRNA domains correlate with chromatin loops and enhancer-promoter interactions. We report a tradeoff of caRNAs promotive and suppressive roles to chromatin interactions. As a result, caRNA promotes chromatin interactions outside the anchors of chromatin loops, whereas caRNA exhibits an overall suppressive impact to chromatin interactions between loop anchors. Furthermore, caRNA suppresses chromatin loops number and strengths genome-wide, and this suppression depends on electric charge-mediated RNA interactions. These results reveal caRNAs multifaced role in regulating 3D chromatin organization and highlight caRNAs ability to modulate chromatin looping.", "date_published": "2021-07-14", "title": "Three-dimensional organization of chromatin associated RNAs and their role in chromatin architecture in human cells", "ID": "doi:10.1101/2021.06.10.447969", "@type": ["Publication", "Item"], "journal": "bioRxiv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"uuid": "d313c2a4-aab7-417a-b9b4-bcf5ec5cdbac", "@id": "/publications/d313c2a4-aab7-417a-b9b4-bcf5ec5cdbac/", "authors": ["Calandrelli R", "Wen X", "Nguyen TC", "Chen C-J", "Qi Z", "Chen W", "Yan Z", "Wu W", "Zaleta-Rivera K", "Hu R", "Yu M", "Wang Y", "Ma J", "Ren B", "Zhong S"], "title": "Three-dimensional organization of chromatin associated RNAs and their role in chromatin architecture in human cells", "ID": "doi:10.1101/2021.06.10.447969", "@type": ["Publication", "Item"], "display_title": "Calandrelli R et al. (2021) doi:10.1101/2021.06.10.447969", "short_attribution": "Calandrelli R et al. (2021)", "date_published": "2021-07-14", "abstract": "Chromatin-associated RNA (caRNA) is a vital component of the interphase nucleus; yet its distribution and role in the three-dimensional (3D) genome organization and function remain poorly understood. Here, we map caRNAs spatial distribution on the 3D genome in human embryonic stem cells, fibroblasts, and myelogenous leukemia cells. We find that the relative abundance of trans-acting caRNA reflects the functional nuclear compartmentalization of the 3D genome, and the caRNAs sequence features are predictive of its spatial localization. We observe extensive caRNA-genome interactions that span several hundred kilobases to several megabases. These caRNA domains correlate with chromatin loops and enhancer-promoter interactions. We report a tradeoff of caRNAs promotive and suppressive roles to chromatin interactions. As a result, caRNA promotes chromatin interactions outside the anchors of chromatin loops, whereas caRNA exhibits an overall suppressive impact to chromatin interactions between loop anchors. Furthermore, caRNA suppresses chromatin loops number and strengths genome-wide, and this suppression depends on electric charge-mediated RNA interactions. These results reveal caRNAs multifaced role in regulating 3D chromatin organization and highlight caRNAs ability to modulate chromatin looping.", "status": "current", "journal": "bioRxiv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Enzyme", "value": "AluI", "combined": "Enzyme: AluI"}, "experiment_summary": "MARGI on H1-hESC (Tier 1)", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSKZY2OLH/", "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": []}