{"lab": {"uuid": "3452dfa5-ee8b-4dbc-8068-00cadde268b9", "@id": "/labs/sheng-zhong-lab/", "correspondence": [{"contact_email": "c3pob25nQHVjc2QuZWR1", "@id": "/users/5549e16d-fa63-477c-a1ed-6189cecc1304/", "display_title": "Sheng Zhong"}], "status": "current", "title": "Sheng Zhong, UCSD", "@type": ["Lab", "Item"], "display_title": "Sheng Zhong, UCSD", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3452dfa5-ee8b-4dbc-8068-00cadde268b9"]}}, "award": {"center_title": "OH - Zhong", "name": "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.", "project": "4DN", "display_title": "THE SECOND PHASE OF NIH COMMON FUND 4D NUCLEOME NETWORK ORGANIZATIONAL HUB", "status": "current", "@id": "/awards/2U01CA200147-06/", "uuid": "1a4da807-8221-47d2-96ab-7a31485974c3", "@type": ["Award", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"paired_end": "1", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFIVXUWMZO/@@download/4DNFIVXUWMZO.fastq.gz", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_size": 21709314106, "uuid": "e2942d68-3dc2-452c-b4bc-4a38a857a1ae", "upload_key": "e2942d68-3dc2-452c-b4bc-4a38a857a1ae/4DNFIVXUWMZO.fastq.gz", "status": "released", "accession": "4DNFIVXUWMZO", "display_title": "4DNFIVXUWMZO.fastq.gz", "@id": "/files-fastq/4DNFIVXUWMZO/", "file_classification": "raw file", "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIVXUWMZO/fastqc_report.html", "Sequence length": "101", "uuid": "2be3fdec-fa9f-47ba-afd4-bb8fb1c406fb", "Total Sequences": 328187383, "overall_quality_status": "PASS", "status": "released", "@id": "/quality-metrics-fastqc/2be3fdec-fa9f-47ba-afd4-bb8fb1c406fb/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2021-07-02", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"@id": "/files-fastq/4DNFINS3D2Y4/", "file_type_detailed": "reads (fastq)", "uuid": "ace2102b-7eb3-4429-9587-74f9bfc1fa19", "file_type": "reads", "accession": "4DNFINS3D2Y4", "display_title": "4DNFINS3D2Y4.fastq.gz", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"paired_end": "2", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFINS3D2Y4/@@download/4DNFINS3D2Y4.fastq.gz", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_size": 24677452910, "uuid": "ace2102b-7eb3-4429-9587-74f9bfc1fa19", "upload_key": "ace2102b-7eb3-4429-9587-74f9bfc1fa19/4DNFINS3D2Y4.fastq.gz", "status": "released", "accession": "4DNFINS3D2Y4", "display_title": "4DNFINS3D2Y4.fastq.gz", "@id": "/files-fastq/4DNFINS3D2Y4/", "file_classification": "raw file", "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFINS3D2Y4/fastqc_report.html", "Sequence length": "101", "uuid": "9518f229-6f94-4211-91e2-6c132d9819c9", "Total Sequences": 328187383, "overall_quality_status": "PASS", "status": "released", "@id": "/quality-metrics-fastqc/9518f229-6f94-4211-91e2-6c132d9819c9/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2021-07-02", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"@id": "/files-fastq/4DNFIVXUWMZO/", "file_type_detailed": "reads (fastq)", "uuid": "e2942d68-3dc2-452c-b4bc-4a38a857a1ae", "file_type": "reads", "accession": "4DNFIVXUWMZO", "display_title": "4DNFIVXUWMZO.fastq.gz", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}], "status": "released", "aliases": ["sheng-zhong-lab:experiment_hi-c-on-h1-RNase_B1_T1"], "protocol": {"display_title": "Zhong Lab Arima Protocol", "@type": ["Protocol", "Item"], "status": "released", "@id": "/protocols/60f31896-35b4-4539-8d79-8d25ce0f6944/", "uuid": "60f31896-35b4-4539-8d79-8d25ce0f6944", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEXW4D4EIM", "biosample": {"accession": "4DNBSJIETYUA", "display_title": "4DNBSJIETYUA", "biosource_summary": "H1-hESC (Tier 1)", "treatments_summary": "RNase A treatment (200.0 \u03bcg/mL, 10.0m at 20.0\u00b0C)", "status": "released", "@id": "/biosamples/4DNBSJIETYUA/", "biosample_type": "stem cells", "uuid": "868a24d4-ba1c-41da-867e-60f6280899ef", "@type": ["Biosample", "Item"], "modifications_summary": "None", "biosource": [{"lab": {"@id": "/labs/4dn-dcic-lab/", "status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "url": "https://www.wicell.org/home/stem-cell-lines/catalog-of-stem-cell-lines/wa01.cmsx", "award": {"uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@id": "/awards/1U01CA200059-01/", "status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"@id": "/ontology-terms/CL:0000034/", "preferred_name": "stem cell", "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "status": "released", "@type": ["OntologyTerm", "Item"], "synonyms": ["animal stem cell"], "term_name": "stem cell", "display_title": "stem cell", "term_id": "CL:0000034", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["dcic:h1wa01T1", "4dn-dcic-lab:h1wa01T1"], "accession": "4DNSRV3SKQ8M", "cell_line": {"@type": ["OntologyTerm", "Item"], "term_id": "EFO:0003042", "preferred_name": "H1-hESC", "@id": "/ontology-terms/EFO:0003042/", "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "status": "released", "display_title": "H1-hESC", "synonyms": ["H1"], "term_name": "H1-hESC", "slim_terms": [{"status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"protected_data": false, "display_title": "4DNIN3RG3ZKE", "status": "released", "@id": "/individuals-human/4DNIN3RG3ZKE/", "uuid": "c97775b7-3d00-4132-9598-863797b8ef14", "@type": ["IndividualHuman", "Individual", "Item"], "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-220126_2.pdf", "@type": ["Protocol", "Item"], "status": "released", "uuid": "c0319394-33f9-4f4e-8e20-b3d413c4eed6", "@id": "/protocols/c0319394-33f9-4f4e-8e20-b3d413c4eed6/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-08-29T13:33:38.896302+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": {"display_title": "WiCell.org", "@id": "/vendors/wicellorg/", "uuid": "41784f69-697d-42c2-82b1-b52bc5ea3519", "@type": ["Vendor", "Item"], "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"], "@id": "/organisms/9606/", "name": "human", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "status": "released", "display_title": "H. sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "treatments": [{"temperature": 20.0, "chemical": "RNase A", "duration": 10.0, "description": "200 \u03bcg/mL RNase A", "@type": ["TreatmentAgent", "Treatment", "Item"], "treatment_type": "Chemical", "@id": "/treatments-agent/f5c4fd17-bdb9-4c15-aa0c-26dc7cc4b467/", "concentration_units": "\u03bcg/mL", "duration_units": "minute", "uuid": "f5c4fd17-bdb9-4c15-aa0c-26dc7cc4b467", "concentration": 200.0, "status": "released", "display_title": "RNase A treatment (200.0 \u03bcg/mL, 10.0m at 20.0\u00b0C)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing doubling_number", "Biosample missing morphology_image"], "badge": {"badge_classification": "Warning", "status": "released", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "warning": "Biosample Metadata Incomplete", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "display_title": "Biosample Metadata Incomplete", "@type": ["Badge", "Item"], "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "title": "Biosample Metadata Incomplete", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pcr_cycles": 10, "sop_mapping": {"has_sop": "No"}, "date_created": "2021-07-01T17:47:44.996435+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-07-15T14:02:27.171639+00:00"}, "ligation_time": 15.0, "biotin_removed": "No", "public_release": "2021-07-27", "schema_version": "2", "tagging_method": "Arima-Buffer B, Enzyme B", "experiment_type": {"status": "released", "experiment_category": "Sequencing", "@type": ["ExperimentType", "Item"], "display_title": "in situ Hi-C", "assay_subclass_short": "Hi-C", "title": "in situ Hi-C", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "@id": "/experiment-types/in-situ-hi-c/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "ligation_volume": 0.082, "processed_files": [{"file_size": 67893013765, "uuid": "503c281b-e430-4a7e-afe5-9fef72742c68", "file_type_detailed": "alignments (bam)", "@id": "/files-processed/4DNFIKMOG63A/", "href": "/files-processed/4DNFIKMOG63A/@@download/4DNFIKMOG63A.bam", "status": "released", "accession": "4DNFIKMOG63A", "file_type": "alignments", "file_classification": "processed file", "display_title": "4DNFIKMOG63A.bam", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/503c281b-e430-4a7e-afe5-9fef72742c68/4DNFIKMOG63A.bam", "@type": ["FileProcessed", "File", "Item"], "file_format": {"display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "file_format": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "upload_key": "503c281b-e430-4a7e-afe5-9fef72742c68/4DNFIKMOG63A.bam", "quality_metric": {"uuid": "fa0cae7e-72dd-4a6a-97f0-6f46df3d86a3", "overall_quality_status": "PASS", "status": "released", "display_title": "QualityMetricBamqc from 2021-07-15", "@id": "/quality-metrics-bamqc/fa0cae7e-72dd-4a6a-97f0-6f46df3d86a3/", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "quality_metric_summary": [{"title": "Total Reads", "value": "328187383", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "7.059", "tooltip": "Percent of total reads (=23.17m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "11.08", "tooltip": "Percent of total reads (=36.36m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "2.424", "tooltip": "Percent of total reads (=7.96m)", "numberType": "percent"}, {"title": "Walks", "value": "6.536", "tooltip": "Percent of total reads (=21.45m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.253", "tooltip": "Percent of total reads (=0.83m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Sheng Zhong, UCSD", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on H1 cells", "condition": "RNaseA", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_size": 4683826933, "uuid": "03e43fce-e1b5-4cfa-8b68-4a83c92dbeb5", "file_type_detailed": "contact list-replicate (pairs)", "@id": "/files-processed/4DNFI7RFIOHO/", "href": "/files-processed/4DNFI7RFIOHO/@@download/4DNFI7RFIOHO.pairs.gz", "status": "released", "accession": "4DNFI7RFIOHO", "file_type": "contact list-replicate", "file_classification": "processed file", "display_title": "4DNFI7RFIOHO.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/03e43fce-e1b5-4cfa-8b68-4a83c92dbeb5/4DNFI7RFIOHO.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "file_format": {"display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "upload_key": "03e43fce-e1b5-4cfa-8b68-4a83c92dbeb5/4DNFI7RFIOHO.pairs.gz", "quality_metric": {"uuid": "a6ce1f62-c3ce-4875-964d-4c378501e209", "overall_quality_status": "PASS", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI7RFIOHO/pairsqc_report.html", "display_title": "QualityMetricPairsqc from 2021-07-15", "Total reads": 239250488, "@id": "/quality-metrics-pairsqc/a6ce1f62-c3ce-4875-964d-4c378501e209/", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "quality_metric_summary": [{"title": "Filtered Reads", "value": "239250488", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "42.365", "tooltip": "Percent of filtered reads (=101.36m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "22.503", "tooltip": "Percent of filtered reads (=53.84m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "35.132", "tooltip": "Percent of filtered reads (=84.05m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Sheng Zhong, UCSD", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on H1 cells", "condition": "RNaseA", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}], "project_release": "2021-07-27", "digestion_enzyme": {"@type": ["Enzyme", "Item"], "name": "Arima - A1, A2", "uuid": "1b967af3-f275-4480-93d7-c6ce62a908c6", "status": "released", "@id": "/enzymes/Arima%20-%20A1,%20A2/", "display_title": "Arima - A1, A2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "library_prep_kit": "KAPA HyperPrep kit", "crosslinking_time": 10.0, "enzyme_lot_number": "A1:180601001, A2: 180525012", "biosample_quantity": 3.0, "crosslinking_method": "1% Formaldehyde", "fragment_size_range": "200-600", "fragmentation_method": "sonication", "ligation_temperature": 23.0, "average_fragment_size": 473, "other_processed_files": [{"type": "preliminary", "files": [{"file_size": 67573927814, "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIS5Z3ZV6.bam", "@id": "/files-processed/4DNFIS5Z3ZV6/", "file_type": "alignments", "file_type_detailed": "alignments (bam)", "href": "/files-processed/4DNFIS5Z3ZV6/@@download/4DNFIS5Z3ZV6.bam", "status": "released", "uuid": "ef540050-7e68-4138-89c4-3369699061ab", "accession": "4DNFIS5Z3ZV6", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ef540050-7e68-4138-89c4-3369699061ab/4DNFIS5Z3ZV6.bam", "track_and_facet_info": {"experimental_lab": "Sheng Zhong, UCSD", "experiment_type": "in situ Hi-C", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on H1 cells", "condition": "RNaseA", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}, "file_format": {"@id": "/file-formats/bam/", "file_format": "bam", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2024-08-08T01:03:42.567192+00:00"}}, {"file_size": 4660260145, "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI6XO8FSU.pairs.gz", "@id": "/files-processed/4DNFI6XO8FSU/", "file_type": "contact list-replicate", "file_type_detailed": "contact list-replicate (pairs)", "href": "/files-processed/4DNFI6XO8FSU/@@download/4DNFI6XO8FSU.pairs.gz", "status": "released", "uuid": "c02c928e-5780-4eba-b96e-caa51f32c7bf", "accession": "4DNFI6XO8FSU", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c02c928e-5780-4eba-b96e-caa51f32c7bf/4DNFI6XO8FSU.pairs.gz", "quality_metric": {"@id": "/quality-metrics-pairsqc/239062f4-8a4a-4b9b-9e81-2370d37d3273/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI6XO8FSU/pairsqc_report.html", "uuid": "239062f4-8a4a-4b9b-9e81-2370d37d3273", "overall_quality_status": "PASS", "status": "released", "display_title": "QualityMetricPairsqc from 2024-07-09", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "252655282", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "42.286", "tooltip": "Percent of filtered reads (=106.84m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "22.219", "tooltip": "Percent of filtered reads (=56.14m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "35.495", "tooltip": "Percent of filtered reads (=89.68m)", "numberType": "percent"}]}, "track_and_facet_info": {"experimental_lab": "Sheng Zhong, UCSD", "experiment_type": "in situ Hi-C", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on H1 cells", "condition": "RNaseA", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}, "file_format": {"@id": "/file-formats/pairs/", "file_format": "pairs", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2024-08-08T00:55:38.656083+00:00"}}], "title": "HiC Processing Pipeline - v0.3.0", "description": "These are files generated using the updated Hi-C processing pipeline. They should be largely similar to those available in the Processed Files tab, which were generated with the previous version of the standard pipeline.  One potential difference of note is that the version of cooler used to generate the mcool file has a bug fix to prevent a pixel duplication issue which is observed in some files generated by the previous version of the pipeline.  Another notable difference is that a filter is applied to remove reads with MAPQ scores below 30 prior to mcool file generation."}], "biosample_quantity_units": "\u03bcg", "crosslinking_temperature": 23.0, "library_preparation_date": "2019-04-12", "fragment_size_selection_method": "SPRI beads", "@id": "/experiments-hi-c/4DNEXW4D4EIM/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "9e511090-5b69-42a5-a8cc-ebe105086ec2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "in situ Hi-C on H1-hESC (Tier 1) with Arima - A1, A2 - 4DNEXW4D4EIM", "external_references": [], "experiment_sets": [{"accession": "4DNES4AABNEZ", "experimentset_type": "replicate", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "70556039-648a-46b1-9245-d50be853b7a9", "@id": "/experiment-set-replicates/4DNES4AABNEZ/", "display_title": "4DNES4AABNEZ", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"title": "Genome-wide analysis of the interplay between chromatin-associated RNA and 3D  genome organization in human cells.", "display_title": "Calandrelli R et al. (2023) PMID:37845234", "status": "current", "@type": ["Publication", "Item"], "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.", "@id": "/publications/8334e5bc-68fd-490e-8a63-44fa66066cf5/", "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": "PMID:37845234", "uuid": "8334e5bc-68fd-490e-8a63-44fa66066cf5", "journal": "Nature communications", "date_published": "2023-10-16", "short_attribution": "Calandrelli R et al. (2023)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"date_published": "2023-10-16", "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", "status": "current", "short_attribution": "Calandrelli R et al. (2023)", "display_title": "Calandrelli R et al. (2023) PMID:37845234", "title": "Genome-wide analysis of the interplay between chromatin-associated RNA and 3D  genome organization in human cells.", "uuid": "8334e5bc-68fd-490e-8a63-44fa66066cf5", "ID": "PMID:37845234", "@type": ["Publication", "Item"], "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/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Enzyme", "value": "Arima - A1, A2", "combined": "Enzyme: Arima - A1, A2"}, "experiment_summary": "in situ Hi-C on H1-hESC (Tier 1) with Arima - A1, A2", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSJIETYUA/", "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": []}