{"lab": {"title": "Keji Zhao, NHLBI", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "@id": "/labs/keji-zhao-lab/", "correspondence": [{"contact_email": "emhhb2tAbmhsYmkubmloLmdvdg==", "@id": "/users/44d2c6b9-15a0-4991-b84e-601e432df30f/", "display_title": "Keji Zhao"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIZDCXIL7/pairsqc_report.html", "award": {"@id": "/awards/TCPA-2017-08/", "display_title": "DEVELOPMENT OF TRAC-LOOP, A NOVEL TECHNIQUE TO DETECT GENOME-WIDE CHROMATIN INTERACTIONS", "uuid": "0116e3c0-fb5a-491c-a9c2-8e17df70bfc1", "status": "current", "description": "TCPA: Most current techniques for genome-wide analysis of chromatin interactions are based on the \nchromosome conformation capture (3C) technique. Because the traditional Hi-C technique uses a 6-bp restriction enzyme to cut chromatin, which usually finds one cleavage site every 5000bp in the genome, it does not have sufficient resolution for identification of enhancer-promoter interactions. Significant improvement has been achieved by the in situ Hi-C protocol, which uses a 4-bp cutter enzyme and reaches a resolution of about 1kb, thus enabling identification of specific enhancer-promoter interactions at high-resolution. However, this method requires a costly sequencing depth of 5 to 10 billions of paired-end tags (PETs) per library, which prohibits its application to a large number of samples. Other 3C-based techniques have been developed to focus on interactions at selected regions by capture Hi-C or tethered through specific proteins by ChIA-PET have helped to increase resolution by focusing on potential regulatory regions of the genome. However, a recent study compared \nchromatin interactions detected by fluorescence in situ hybridization (FISH) and 3C-based assays and found a high degree of discrepancy between the two techniques, suggesting that cross-validation of interaction data using different strategies is critical. \nWe propose to develop a novel technique, TrAC-loop, for Transposition-mediated Analysis of \nChromatin loops in the genome. The method does not require SDS-mediated partial decondensation of chromatin, restriction enzyme digestion, or proximity-based ligation of chromatin fragments. TrAC-loop directly captures interacting chromatin regions by Tn5-mediated transposition of a bivalent ME (mosaic end) linker without disrupting the nuclear structure. Thus, this novel strategy avoids potential artifacts derived from SDS-mediated partial decondensation of chromatin, restriction enzyme digestion and proximity-based re-ligation of chromatin fragments that are used in the 3C assays. Our strategy represents a shift in paradigm. All other genome-wide methods of mapping chromatin interactions use 3C-based techniques, whereas ours use transposition. Although transposition has been used to tag \nchromatin, this is the first time it is used to join chromatin segments.", "center_title": "TCPA - Zhao", "name": "TCPA-2017-08", "@type": ["Award", "Item"], "project": "4DN", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "slope": -1.16, "status": "released", "aliases": [], "Total reads": 109520721, "Trans reads": 10499053, "convergence": "Not converged", "date_created": "2018-06-05T20:32:02.376957+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-01-28T21:00:39.199860+00:00"}, "public_release": "2025-01-28", "schema_version": "1", "Cis/Trans ratio": 54.563, "project_release": "2018-11-05", "Cis reads (>20kb)": 12607650, "contributing_labs": [{"@type": ["Lab", "Item"], "correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}], "overall_quality_status": "PASS", "Short cis reads (<20kb)": 86414018, "% Long-range intrachromosomal reads": 11.512, "@id": "/quality-metrics-pairsqc/40809586-90d3-458c-87ae-a6f93f4ee5f1/", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "uuid": "40809586-90d3-458c-87ae-a6f93f4ee5f1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "QualityMetricPairsqc from 2018-06-05", "external_references": [], "quality_metric_summary": [{"title": "Filtered Reads", "value": "109520721", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "11.512", "tooltip": "Percent of filtered reads (=12.61m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "78.902", "tooltip": "Percent of filtered reads (=86.41m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "9.586", "tooltip": "Percent of filtered reads (=10.5m)", "numberType": "percent"}], "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}