{"lab": {"correspondence": [{"contact_email": "d3lzb2NrYUBzdGFuZm9yZC5lZHU=", "@id": "/users/1cc9469d-ff0c-4ef0-b0c7-5ed4d0966a13/", "display_title": "Joanna Wysocka"}], "uuid": "88ba2aa9-321a-43a5-af1e-75fca4236907", "status": "current", "display_title": "Joanna Wysocka, STANFORD", "@type": ["Lab", "Item"], "title": "Joanna Wysocka, STANFORD", "@id": "/labs/joanna-wysocka-lab/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.88ba2aa9-321a-43a5-af1e-75fca4236907"]}}, "award": {"display_title": "ELUCIDATING THE ROLE OF NASCENT RNA IN ENHANCER-PROMOTER COMMUNICATION AND THREE-DIMENSIONAL GENOME ORGANIZATION", "status": "current", "name": "TCPA-2017-01", "project": "4DN", "description": "TCPA: \u200bThere is a clear relationship between nuclear genome organization and the regulation of gene expression, and a great deal of effort has been dedicated to defining the effects of genome architecture on gene activity. Herein, we propose to complement this work by approaching the relationship from the other direction. We will ask: how does nascent RNA synthesis from enhancers and promoters impact genome organization? Our specific hypothesis is that nascent RNA plays a central role in stabilizing transient promoter-enhancer contacts that occur within topologically-associated domains (TADs), and thus facilitates the communication between distal cis-regulatory regions. This idea is supported by recent demonstrations that nascent RNA can serve as a platform for the recruitment and retention of transcription factors and epigenetic modifiers. Accordingly, several studies have suggested roles for specific enhancer RNAs in the establishment or maintenance of three-dimensional (3D) enhancer-promoter loops and associated gene activity. However, a full appreciation for the role of nascent RNA synthesis on \ngenome structure will require a more rigorous, coordinated and comprehensive approach than has been carried out to date. We therefore propose a collaborative project within the framework of the 4D Nucleome network to address how enhancer and gene transcription impact chromosome organization.", "@type": ["Award", "Item"], "uuid": "619535d9-ec49-4f36-9cad-a0887cf535cb", "@id": "/awards/TCPA-2017-01/", "center_title": "TCPA - Adelman", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "pi": {"error": "no view permissions"}}, "status": "released", "aliases": ["joanna-wysocka-lab:EpiLCdiff_HiChIP_SMC1A_48hr"], "accession": "4DNES5FOV49M", "condition": "48 h, SMC1A", "description": "SMC1A PLAC-seq time course of EpiLC differentiation in F121-9 mESCs, 48 h time point", "date_created": "2021-02-01T20:45:11.119465+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "PLAC-seq time course of EpiLC differentiation", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-06-30T20:46:01.971148+00:00"}, "public_release": "2023-06-30", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-chiapet/4DNEXL9FIDCY/", "@type": ["ExperimentChiapet", "Experiment", "Item"], "status": "released", "uuid": "f9437c23-464a-47ef-b78b-4d661040cf1f", "accession": "4DNEXL9FIDCY", "display_title": "PLAC-seq against Smc1a (mouse) on F121-9-CASTx129 (Tier 2) differentiated to epiblast cell - 4DNEXL9FIDCY", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-chiapet/4DNEXQ21PRZG/", "@type": ["ExperimentChiapet", "Experiment", "Item"], "status": "released", "uuid": "3f1ca50f-ef49-4250-b466-d78ce88c3837", "accession": "4DNEXQ21PRZG", "display_title": "PLAC-seq against Smc1a (mouse) on F121-9-CASTx129 (Tier 2) differentiated to epiblast cell - 4DNEXQ21PRZG", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 3, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-chiapet/4DNEXEPR9FMN/", "@type": ["ExperimentChiapet", "Experiment", "Item"], "status": "released", "uuid": "d35e1c17-e03a-46f1-b0c5-81a0d65c2854", "accession": "4DNEXEPR9FMN", "display_title": "PLAC-seq against Smc1a (mouse) on F121-9-CASTx129 (Tier 2) differentiated to epiblast cell - 4DNEXEPR9FMN", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"description": "4DNES5FOV49M (SMC1A PLAC-seq time course of EpiLC differentiation in F121-9 mESCs, 48 h time point): 4DNFIIW1EXIQ", "filetype": "HiglassViewConfig", "title": "4DNES5FOV49M - Processed files", "display_title": "4DNES5FOV49M - Processed files", "status": "released", "@id": "/higlass-view-configs/04a3c25b-025c-43af-ae10-9819ff330cd9/", "uuid": "04a3c25b-025c-43af-ae10-9819ff330cd9", "award": {"@id": "/awards/TCPA-2017-01/", "display_title": "ELUCIDATING THE ROLE OF NASCENT RNA IN ENHANCER-PROMOTER COMMUNICATION AND THREE-DIMENSIONAL GENOME ORGANIZATION", "status": "current", "@type": ["Award", "Item"], "uuid": "619535d9-ec49-4f36-9cad-a0887cf535cb", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Joanna Wysocka, STANFORD", "@id": "/labs/joanna-wysocka-lab/", "uuid": "88ba2aa9-321a-43a5-af1e-75fca4236907", "@type": ["Lab", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.88ba2aa9-321a-43a5-af1e-75fca4236907"]}}, "contributing_labs": [{"status": "current", "@id": "/labs/karen-adelman-lab/", "display_title": "Karen Adelman, HARVARD", "uuid": "0aae4b45-b6de-45da-84e6-738667c36f03", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0aae4b45-b6de-45da-84e6-738667c36f03"]}}], "name": "04a3c25b-025c-43af-ae10-9819ff330cd9", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}, "location": "tab:processed-files", "description": "auto_generated_higlass_view_config"}], "static_headers": [{"lab": {"status": "current", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "\n**Data Use Guidelines:** This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) \nand the 4DN Data Portal paper \n([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).", "name": "item-page-headers.ExperimentSet.data-usage-guidelines", "award": {"@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@id": "/awards/1U01CA200059-01/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Data Usage Guidelines", "status": "released", "aliases": [], "options": {"filetype": "md", "title_icon": "exclamation-circle", "collapsible": false, "default_open": true}, "date_created": "2018-08-06T03:09:55.543206+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-05-09T09:31:34.537494+00:00"}, "schema_version": "2", "@id": "/static-sections/621e8359-3885-40ce-965d-91894aa7b758/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "621e8359-3885-40ce-965d-91894aa7b758", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267228139"]}, "display_title": "Data Usage Guidelines", "external_references": [], "content": "\n**Data Use Guidelines:** This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) \nand the 4DN Data Portal paper \n([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p><strong>Data Use Guidelines:</strong> This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n(<a href=\"https://doi.org/10.1038/nature23884\" rel=\"noopener noreferrer\" target=\"_blank\">doi:10.1038/nature23884</a>) \nand the 4DN Data Portal paper \n(<a href=\"https://doi.org/10.1038/s41467-022-29697-4\" rel=\"noopener noreferrer\" target=\"_blank\">doi:10.1038/s41467-022-29697-4</a>), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the <a href=\"mailto:support@4dnucleome.org\">Data Coordination and Integration Center</a>.</p></div>"}], "processed_files": [{"href": "/files-processed/4DNFILLL6EOQ/@@download/4DNFILLL6EOQ.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/689bc0dc-b3d3-433e-929c-0b8debeeabde/4DNFILLL6EOQ.pairs.gz", "file_classification": "processed file", "display_title": "4DNFILLL6EOQ.pairs.gz", "file_format": {"@id": "/file-formats/pairs/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "upload_key": "689bc0dc-b3d3-433e-929c-0b8debeeabde/4DNFILLL6EOQ.pairs.gz", "genome_assembly": "GRCm38", "file_size": 1305409913, "status": "released", "file_type_detailed": "contact list-combined (pairs)", "accession": "4DNFILLL6EOQ", "@type": ["FileProcessed", "File", 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This duplication does not affect the higlass display of these files, howevver, downstream analyses using this file may encounter issues due to this pixel duplication.  The counts from the duplicate pixels can be aggregated to determine the correct count value at that location. If this issue is problematic for your needs you should consider regenerating the matrices from the merged pairs file of the associated dataset using a more recent version of cooler.  We are working to update the pipeline but do not yet have a predicted date for when this issue will be resolved."], "@id": "/files-processed/4DNFIIW1EXIQ/", "lab": {"display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "quality_metric": {"status": "released", "@id": "/quality-metrics-mcool/810a32c4-ba51-4b87-864e-793669084cde/", "overall_quality_status": "WARN", "@type": ["QualityMetricMcool", "QualityMetric", "Item"], "display_title": "QualityMetricMcool from 2023-06-30", "uuid": "810a32c4-ba51-4b87-864e-793669084cde", "quality_metric_summary": [{"title": "Failed Balancing", "value": "1000; 2000; 5000; 10000; 25000; 50000; 100000; 250000; 500000; 1000000; 2500000; 5000000; 10000000", "tooltip": "Resolutions 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