{"lab": {"correspondence": [{"contact_email": "a2FyZW5fYWRlbG1hbkBobXMuaGFydmFyZC5lZHU=", "@id": "/users/59826b1d-7f8b-484f-bfba-8e29f57169d2/", "display_title": "Karen Adelman"}], "display_title": "Karen Adelman, HARVARD", "status": "current", "uuid": "0aae4b45-b6de-45da-84e6-738667c36f03", "@id": "/labs/karen-adelman-lab/", "@type": ["Lab", "Item"], "title": "Karen Adelman, HARVARD", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0aae4b45-b6de-45da-84e6-738667c36f03"]}}, "award": {"status": "current", "display_title": "ELUCIDATING THE ROLE OF NASCENT RNA IN ENHANCER-PROMOTER COMMUNICATION AND THREE-DIMENSIONAL GENOME ORGANIZATION", "@type": ["Award", "Item"], "name": "TCPA-2017-01", "project": "4DN", "uuid": "619535d9-ec49-4f36-9cad-a0887cf535cb", "@id": "/awards/TCPA-2017-01/", "center_title": "TCPA - Adelman", "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.", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "star_log_qc": {"Finished on": "Jan 27 15:46:47", "Started job on": "Jan 27 15:29:33", "Started mapping on": "Jan 27 15:29:54", "% of chimeric reads": "0.00%", "Average mapped length": "158.66", "Number of input reads": "60035458", "Deletion rate per base": "0.02%", "Deletion average length": "2.24", "Insertion rate per base": "0.02%", "Uniquely mapped reads %": "75.58%", "Insertion average length": "2.11", "Number of chimeric reads": "0", "Number of splices: AT/AC": "30596", "Number of splices: GC/AG": "271799", "Number of splices: GT/AG": "24363809", "Number of splices: Total": "24687011", "Average input read length": "160", "Mismatch rate per base, %": "0.57%", "% of reads unmapped: other": "0.34%", "Uniquely mapped reads number": "45374926", "% of reads unmapped: too short": "5.07%", "Number of splices: Non-canonical": "20807", "% of reads mapped to multiple loci": "18.81%", "% of reads mapped to too many loci": "0.20%", "Number of splices: Annotated (sjdb)": "24485904", "Number of reads mapped to multiple loci": "11291288", "Number of reads mapped to too many loci": "120311", "% of reads unmapped: too many mismatches": "0.00%", "Mapping speed, Million of reads per hour": "213.35"}, "date_created": "2021-01-27T17:38:07.885092+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-06-28T14:51:28.240823+00:00"}, "public_release": "2023-06-28", "schema_version": "1", "project_release": "2023-06-28", "contributing_labs": [{"correspondence": [{"contact_email": "d3lzb2NrYUBzdGFuZm9yZC5lZHU=", "@id": "/users/1cc9469d-ff0c-4ef0-b0c7-5ed4d0966a13/", "display_title": "Joanna Wysocka"}], "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"]}, "pi": {"error": "no view permissions"}}, {"correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}, "pi": {"error": "no view permissions"}}], "overall_quality_status": "PASS", "samtools_genome_flagstat": {"read1": 60035458, "read2": 60035458, "total": 164602186, "mapped": 157863698, "paired": 120070916, "duplicates": 0, "mapped_pct": 95.91, "singletons": 0, "diff_chroms": 0, "with_itself": 113332428, "singletons_pct": 0.0, "paired_properly": 113332428, "read1_qc_failed": 0, "read2_qc_failed": 0, "total_qc_failed": 0, "mapped_qc_failed": 0, "paired_qc_failed": 0, "paired_properly_pct": 94.39, "duplicates_qc_failed": 0, "singletons_qc_failed": 0, "diff_chroms_qc_failed": 0, "with_itself_qc_failed": 0, "paired_properly_qc_failed": 0}, "@id": "/quality-metrics-rnaseq/b84dc465-2d39-4c46-916c-c6504204b51a/", "@type": ["QualityMetricRnaseq", "QualityMetric", "Item"], "uuid": "b84dc465-2d39-4c46-916c-c6504204b51a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "QualityMetricRnaseq from 2021-01-27", "external_references": [], "quality_metric_summary": [{"title": "Total mapped reads (genome)", "value": "56666214", "numberType": "integer"}, {"title": "Total uniquely mapped reads (genome)", "value": "45374926", "numberType": "integer"}], "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}