{"lab": {"correspondence": [{"contact_email": "emhhb2tAbmhsYmkubmloLmdvdg==", "@id": "/users/44d2c6b9-15a0-4991-b84e-601e432df30f/", "display_title": "Keji Zhao"}], "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "status": "current", "display_title": "Keji Zhao, NHLBI", "@type": ["Lab", "Item"], "title": "Keji Zhao, NHLBI", "@id": "/labs/keji-zhao-lab/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "tags": ["2018_01_internal"], "award": {"display_title": "DEVELOPMENT OF TRAC-LOOP, A NOVEL TECHNIQUE TO DETECT GENOME-WIDE CHROMATIN INTERACTIONS", "status": "current", "name": "TCPA-2017-08", "project": "4DN", "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.", "@type": ["Award", "Item"], "uuid": "0116e3c0-fb5a-491c-a9c2-8e17df70bfc1", "@id": "/awards/TCPA-2017-08/", "center_title": "TCPA - Zhao", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "pi": {"error": "no view permissions"}}, "status": "released", "aliases": ["zhaolab:Experiment_TrACloop_gm12878"], "accession": "4DNES5BDII8F", "description": "TrAC-loop on GM12878 cells- 4 biological replicates", "date_created": "2018-02-09T16:05:47.941107+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-01-28T21:46:17.119492+00:00"}, "public_release": "2025-01-28", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-seq/4DNEXE2EER1V/", "@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "uuid": "c7fb219b-d118-4c15-8855-e81767737edd", "accession": "4DNEXE2EER1V", "display_title": "TrAC-loop on GM12878 (Tier 1) - 4DNEXE2EER1V", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-seq/4DNEXAHVP5SD/", "@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "uuid": "f8f237cd-e14c-4ac0-abf7-872c6d4318d9", "accession": "4DNEXAHVP5SD", "display_title": "TrAC-loop on GM12878 (Tier 1) - 4DNEXAHVP5SD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 3, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-seq/4DNEX15HMJS9/", "@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "uuid": "41eb4f1b-ca6e-4dea-b2cd-5940276060cb", "accession": "4DNEX15HMJS9", "display_title": "TrAC-loop on GM12878 (Tier 1) - 4DNEX15HMJS9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 4, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-seq/4DNEXXRV8DHE/", "@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "uuid": "c6cf0e3c-e25a-49a6-a942-817b04bd78bc", "accession": "4DNEXXRV8DHE", "display_title": "TrAC-loop on GM12878 (Tier 1) - 4DNEXXRV8DHE", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"description": "4DNES5BDII8F (TrAC-loop on GM12878 cells- 4 biological replicates): 4DNFIUVXHNNB", "filetype": "HiglassViewConfig", "title": "4DNES5BDII8F - Processed files", "display_title": "4DNES5BDII8F - Processed files", "status": "released", "@id": "/higlass-view-configs/a32e9874-557c-4a91-8e78-c0289215b65f/", "uuid": "a32e9874-557c-4a91-8e78-c0289215b65f", "award": {"@id": "/awards/TCPA-2017-08/", "display_title": "DEVELOPMENT OF TRAC-LOOP, A NOVEL TECHNIQUE TO DETECT GENOME-WIDE CHROMATIN INTERACTIONS", "status": "current", "@type": ["Award", "Item"], "uuid": "0116e3c0-fb5a-491c-a9c2-8e17df70bfc1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Keji Zhao, NHLBI", "@id": "/labs/keji-zhao-lab/", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "@type": ["Lab", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "contributing_labs": [], "name": "a32e9874-557c-4a91-8e78-c0289215b65f", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}, "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/4DNFIZDCXIL7/@@download/4DNFIZDCXIL7.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c165d4cb-14b6-4bdf-ab0d-e6ee90699693/4DNFIZDCXIL7.pairs.gz", "file_classification": "processed file", "display_title": "4DNFIZDCXIL7.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": "c165d4cb-14b6-4bdf-ab0d-e6ee90699693/4DNFIZDCXIL7.pairs.gz", "genome_assembly": "GRCh38", "file_size": 1896296578, "status": "released", "file_type_detailed": "contact list-combined (pairs)", "accession": "4DNFIZDCXIL7", "@type": ["FileProcessed", "File", "Item"], "file_type": "contact list-combined", "uuid": "c165d4cb-14b6-4bdf-ab0d-e6ee90699693", "md5sum": "6ea8bcd08836ec59d7fdbce1a88682ba", "@id": "/files-processed/4DNFIZDCXIL7/", "extra_files": [{"href": "/files-processed/4DNFIZDCXIL7/@@download/4DNFIZDCXIL7.pairs.gz.px2", "file_size": 21347289, "md5sum": "4b4f2dce776886753dbb67c6a3e037b1", "file_format": {"status": "released", "file_format": "pairs_px2", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "display_title": "pairs_px2", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs_px2/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "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-pairsqc/40809586-90d3-458c-87ae-a6f93f4ee5f1/", "overall_quality_status": "PASS", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "display_title": "QualityMetricPairsqc from 2018-06-05", "uuid": "40809586-90d3-458c-87ae-a6f93f4ee5f1", "Total reads": 109520721, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIZDCXIL7/pairsqc_report.html", "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"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "contributing_labs": [{"status": "current", "name": "keji-zhao-lab", "display_title": "Keji Zhao, NHLBI", "@type": ["Lab", "Item"], "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "@id": "/labs/keji-zhao-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "TrAC-loop", "biosource_name": "GM12878 (Tier 1)", "lab_name": "4DN DCIC, HMS"}, "last_modified": {"date_modified": "2025-02-20T14:24:20.371619+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"href": "/files-processed/4DNFIMSECEES/@@download/4DNFIMSECEES.hic", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/b36b20bc-01d5-43f1-85ea-1694840b3de0/4DNFIMSECEES.hic", "file_classification": "processed file", "display_title": "4DNFIMSECEES.hic", "file_format": {"@id": "/file-formats/hic/", "status": "released", "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "hic", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "upload_key": "b36b20bc-01d5-43f1-85ea-1694840b3de0/4DNFIMSECEES.hic", "genome_assembly": "GRCh38", "file_size": 694914721, "status": "released", "file_type_detailed": "contact matrix (hic)", "accession": "4DNFIMSECEES", "@type": ["FileProcessed", "File", "Item"], "file_type": "contact matrix", "uuid": "b36b20bc-01d5-43f1-85ea-1694840b3de0", "md5sum": "f556cbf7fdaadda1717c89402b2a96d8", "@id": "/files-processed/4DNFIMSECEES/", "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"]}}, "external_references": [], "contributing_labs": [{"status": "current", "name": "keji-zhao-lab", "display_title": "Keji Zhao, NHLBI", "@type": ["Lab", "Item"], "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "@id": "/labs/keji-zhao-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "TrAC-loop", "biosource_name": "GM12878 (Tier 1)", "lab_name": "4DN DCIC, HMS"}, "last_modified": {"date_modified": "2025-02-20T14:24:09.105523+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"href": "/files-processed/4DNFIUVXHNNB/@@download/4DNFIUVXHNNB.mcool", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/6fd405fe-0795-4345-ac6e-e26017378614/4DNFIUVXHNNB.mcool", "file_classification": "processed file", "higlass_uid": "c1OxwyBZRSiTcfKfXwkUJA", "display_title": "4DNFIUVXHNNB.mcool", "file_format": {"@id": "/file-formats/mcool/", "status": "released", "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "mcool", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "upload_key": "6fd405fe-0795-4345-ac6e-e26017378614/4DNFIUVXHNNB.mcool", "genome_assembly": "GRCh38", "file_size": 571119510, "status": "released", "file_type_detailed": "contact matrix (mcool)", "accession": "4DNFIUVXHNNB", "@type": ["FileProcessed", "File", "Item"], "file_type": "contact matrix", "uuid": "6fd405fe-0795-4345-ac6e-e26017378614", "md5sum": "229402a53414a7ffb4b606c34b9408f5", "notes_to_tsv": ["WARNING - Due to a bug in the version of cooler (0.8.3) used in the current 4DN standard Hi-C processing pipeline some pixels may occur mulitple times at a single resolution with different counts being reported for each occurence.  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/4DNFIUVXHNNB/", "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/f04cc6b4-d7c6-4b43-9d89-31f1acda2b8b/", "overall_quality_status": "WARN", "@type": ["QualityMetricMcool", "QualityMetric", "Item"], "display_title": "QualityMetricMcool from 2021-05-21", "uuid": "f04cc6b4-d7c6-4b43-9d89-31f1acda2b8b", "quality_metric_summary": [{"title": "Failed Balancing", "value": "1000; 2000; 5000; 10000; 25000; 50000; 100000; 250000; 500000; 1000000; 2500000; 5000000; 10000000", "tooltip": "Resolutions where balancing failed", "numberType": "string"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@id": "/higlass-view-configs/102bf0de-3771-46ac-a87f-7ce5f71921ae/", "uuid": "102bf0de-3771-46ac-a87f-7ce5f71921ae", "status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIUVXHNNB - contact matrix for GM12878 (Tier 1) TrAC-loop", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "external_references": [], "contributing_labs": [{"status": "current", "name": "keji-zhao-lab", "display_title": "Keji Zhao, NHLBI", "@type": ["Lab", "Item"], "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "@id": "/labs/keji-zhao-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "TrAC-loop", "biosource_name": "GM12878 (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "contact matrix for GM12878 (Tier 1) TrAC-loop"}, "last_modified": {"date_modified": "2025-02-20T14:46:07.060901+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "project_release": "2018-02-15", "experiments_in_set": [{"files": [{"paired_end": "1", "upload_key": "0052c6e5-96aa-4ca4-b8cb-4c41f857e2fd/4DNFIPH8CKTY.fastq.gz", "@id": "/files-fastq/4DNFIPH8CKTY/", "file_classification": "raw file", "uuid": "0052c6e5-96aa-4ca4-b8cb-4c41f857e2fd", "status": "released", "file_size": 1324704647, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/0052c6e5-96aa-4ca4-b8cb-4c41f857e2fd/4DNFIPH8CKTY.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "241e807157e4ea0cac3be3bb85a85309", "file_type_detailed": "reads (fastq)", "display_title": "4DNFIPH8CKTY.fastq.gz", "accession": "4DNFIPH8CKTY", "href": "/files-fastq/4DNFIPH8CKTY/@@download/4DNFIPH8CKTY.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "2229080f-aa13-4e42-bb64-99954adc5a5c", "file_type": "reads", "@id": "/files-fastq/4DNFICQFPTFZ/", "accession": "4DNFICQFPTFZ", "display_title": "4DNFICQFPTFZ.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/eb3bd116-f4c3-472e-b465-50f6ca843733/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 41190590, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIPH8CKTY/fastqc_report.html", "uuid": "eb3bd116-f4c3-472e-b465-50f6ca843733", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "2", "upload_key": "2229080f-aa13-4e42-bb64-99954adc5a5c/4DNFICQFPTFZ.fastq.gz", "@id": "/files-fastq/4DNFICQFPTFZ/", "file_classification": "raw file", "uuid": "2229080f-aa13-4e42-bb64-99954adc5a5c", "status": "released", "file_size": 1546879916, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/2229080f-aa13-4e42-bb64-99954adc5a5c/4DNFICQFPTFZ.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "4030ca6950b6fb652a23eb809aa6c03f", "file_type_detailed": "reads (fastq)", "display_title": "4DNFICQFPTFZ.fastq.gz", "accession": "4DNFICQFPTFZ", "href": "/files-fastq/4DNFICQFPTFZ/@@download/4DNFICQFPTFZ.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "0052c6e5-96aa-4ca4-b8cb-4c41f857e2fd", "file_type": "reads", "@id": "/files-fastq/4DNFIPH8CKTY/", "accession": "4DNFIPH8CKTY", "display_title": "4DNFIPH8CKTY.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/5a5e490b-05cb-4046-9918-54dc2f9c6a3e/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 41190590, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFICQFPTFZ/fastqc_report.html", "uuid": "5a5e490b-05cb-4046-9918-54dc2f9c6a3e", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "1", "upload_key": "c8cc4834-bb7b-4b9d-bbb6-adefc28575cf/4DNFI6Z6ZR9X.fastq.gz", "@id": "/files-fastq/4DNFI6Z6ZR9X/", "file_classification": "raw file", "uuid": "c8cc4834-bb7b-4b9d-bbb6-adefc28575cf", "status": "released", "file_size": 1233212286, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/c8cc4834-bb7b-4b9d-bbb6-adefc28575cf/4DNFI6Z6ZR9X.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "0d59910a6ee489f0374caa0f06b1b296", "file_type_detailed": "reads (fastq)", "display_title": "4DNFI6Z6ZR9X.fastq.gz", "accession": "4DNFI6Z6ZR9X", "href": "/files-fastq/4DNFI6Z6ZR9X/@@download/4DNFI6Z6ZR9X.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "a8253986-ffcd-4817-bd2a-fa4eaa5bbbc2", "file_type": "reads", "@id": "/files-fastq/4DNFIV5H3RCO/", "accession": "4DNFIV5H3RCO", "display_title": "4DNFIV5H3RCO.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/84f2ae0b-ac9f-4bea-8664-c78de1b4d42d/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 37840312, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI6Z6ZR9X/fastqc_report.html", "uuid": "84f2ae0b-ac9f-4bea-8664-c78de1b4d42d", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "2", "upload_key": "a8253986-ffcd-4817-bd2a-fa4eaa5bbbc2/4DNFIV5H3RCO.fastq.gz", "@id": "/files-fastq/4DNFIV5H3RCO/", "file_classification": "raw file", "uuid": "a8253986-ffcd-4817-bd2a-fa4eaa5bbbc2", "status": "released", "file_size": 1418546634, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/a8253986-ffcd-4817-bd2a-fa4eaa5bbbc2/4DNFIV5H3RCO.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "96573e0bb49a27891efb07bb6ec55116", "file_type_detailed": "reads (fastq)", "display_title": "4DNFIV5H3RCO.fastq.gz", "accession": "4DNFIV5H3RCO", "href": "/files-fastq/4DNFIV5H3RCO/@@download/4DNFIV5H3RCO.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "c8cc4834-bb7b-4b9d-bbb6-adefc28575cf", "file_type": "reads", "@id": "/files-fastq/4DNFI6Z6ZR9X/", "accession": "4DNFI6Z6ZR9X", "display_title": "4DNFI6Z6ZR9X.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/878c1d9d-d79c-4d42-af66-bb5f69220b9f/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 37840312, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIV5H3RCO/fastqc_report.html", "uuid": "878c1d9d-d79c-4d42-af66-bb5f69220b9f", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "1", "upload_key": "950c6023-5be5-43a4-8bf3-685cad5b62f4/4DNFIFNFPWA8.fastq.gz", "@id": "/files-fastq/4DNFIFNFPWA8/", "file_classification": "raw file", "uuid": "950c6023-5be5-43a4-8bf3-685cad5b62f4", "status": "released", "file_size": 1091960183, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/950c6023-5be5-43a4-8bf3-685cad5b62f4/4DNFIFNFPWA8.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "8f4871223e7e88806626242ad3eba876", "file_type_detailed": "reads (fastq)", "display_title": "4DNFIFNFPWA8.fastq.gz", "accession": "4DNFIFNFPWA8", "href": "/files-fastq/4DNFIFNFPWA8/@@download/4DNFIFNFPWA8.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "2874e7be-6a35-42f0-ba7b-866463f13e22", "file_type": "reads", "@id": "/files-fastq/4DNFI4TZRR4Y/", "accession": "4DNFI4TZRR4Y", "display_title": "4DNFI4TZRR4Y.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/2537b792-159c-48ce-844f-ca64e81eb808/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 34309571, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIFNFPWA8/fastqc_report.html", "uuid": "2537b792-159c-48ce-844f-ca64e81eb808", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "2", "upload_key": "2874e7be-6a35-42f0-ba7b-866463f13e22/4DNFI4TZRR4Y.fastq.gz", "@id": "/files-fastq/4DNFI4TZRR4Y/", "file_classification": "raw file", "uuid": "2874e7be-6a35-42f0-ba7b-866463f13e22", "status": "released", "file_size": 1255614897, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/2874e7be-6a35-42f0-ba7b-866463f13e22/4DNFI4TZRR4Y.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "12f628f95231ea9ac9c5f3b662627683", "file_type_detailed": "reads (fastq)", "display_title": "4DNFI4TZRR4Y.fastq.gz", "accession": "4DNFI4TZRR4Y", "href": "/files-fastq/4DNFI4TZRR4Y/@@download/4DNFI4TZRR4Y.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "950c6023-5be5-43a4-8bf3-685cad5b62f4", "file_type": "reads", "@id": "/files-fastq/4DNFIFNFPWA8/", "accession": "4DNFIFNFPWA8", "display_title": "4DNFIFNFPWA8.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/eee2f4a5-adef-4584-827d-f8fc94372218/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 34309571, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI4TZRR4Y/fastqc_report.html", "uuid": "eee2f4a5-adef-4584-827d-f8fc94372218", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "1", "upload_key": "dedfc2bc-de07-4058-8763-a295f4c4362f/4DNFIQW39HC5.fastq.gz", "@id": "/files-fastq/4DNFIQW39HC5/", "file_classification": "raw file", "uuid": "dedfc2bc-de07-4058-8763-a295f4c4362f", "status": "released", "file_size": 1126258924, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/dedfc2bc-de07-4058-8763-a295f4c4362f/4DNFIQW39HC5.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "e84bd51be3ab2d8f04ec9980d0459140", "file_type_detailed": "reads (fastq)", "display_title": "4DNFIQW39HC5.fastq.gz", "accession": "4DNFIQW39HC5", "href": "/files-fastq/4DNFIQW39HC5/@@download/4DNFIQW39HC5.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "b11913c3-ad5d-4f62-b0e1-a17b0c05fdbc", "file_type": "reads", "@id": "/files-fastq/4DNFIEC2SIAM/", "accession": "4DNFIEC2SIAM", "display_title": "4DNFIEC2SIAM.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/080c5063-228f-402f-8d24-569f31af7b00/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 34730010, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIQW39HC5/fastqc_report.html", "uuid": "080c5063-228f-402f-8d24-569f31af7b00", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "2", "upload_key": "b11913c3-ad5d-4f62-b0e1-a17b0c05fdbc/4DNFIEC2SIAM.fastq.gz", "@id": "/files-fastq/4DNFIEC2SIAM/", "file_classification": "raw file", "uuid": "b11913c3-ad5d-4f62-b0e1-a17b0c05fdbc", "status": "released", "file_size": 1280112644, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/b11913c3-ad5d-4f62-b0e1-a17b0c05fdbc/4DNFIEC2SIAM.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "92115fe0ddbbbc5b70c1db99d620d14c", "file_type_detailed": "reads (fastq)", "display_title": "4DNFIEC2SIAM.fastq.gz", "accession": "4DNFIEC2SIAM", "href": "/files-fastq/4DNFIEC2SIAM/@@download/4DNFIEC2SIAM.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "dedfc2bc-de07-4058-8763-a295f4c4362f", "file_type": "reads", "@id": "/files-fastq/4DNFIQW39HC5/", "accession": "4DNFIQW39HC5", "display_title": "4DNFIQW39HC5.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/7dcf0489-6734-47c3-a042-09066611a8a5/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 34730010, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIEC2SIAM/fastqc_report.html", "uuid": "7dcf0489-6734-47c3-a042-09066611a8a5", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}], "@id": "/experiments-seq/4DNEXE2EER1V/", "status": "released", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "c7fb219b-d118-4c15-8855-e81767737edd", "accession": "4DNEXE2EER1V", "display_title": "TrAC-loop on GM12878 (Tier 1) - 4DNEXE2EER1V", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "processed_files": [{"md5sum": "d221719b4e28eedba09fc5c98c592f93", "@type": ["FileProcessed", "File", "Item"], "href": "/files-processed/4DNFIB1715GA/@@download/4DNFIB1715GA.bam", "upload_key": "48c540cb-9d64-4e35-9ef7-afaf43f0ba89/4DNFIB1715GA.bam", "genome_assembly": "GRCh38", "file_classification": "processed file", "file_size": 11003497742, "status": "released", "display_title": "4DNFIB1715GA.bam", "file_type_detailed": "alignments (bam)", "@id": "/files-processed/4DNFIB1715GA/", "file_type": "alignments", "uuid": "48c540cb-9d64-4e35-9ef7-afaf43f0ba89", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/48c540cb-9d64-4e35-9ef7-afaf43f0ba89/4DNFIB1715GA.bam", "accession": "4DNFIB1715GA", "contributing_labs": [{"@id": "/labs/keji-zhao-lab/", "name": "keji-zhao-lab", "status": "current", "display_title": "Keji Zhao, NHLBI", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}], "quality_metric": {"overall_quality_status": "PASS", "uuid": "75ae6e50-5b4c-4c84-9840-81f0fbab0605", "status": "released", "display_title": "QualityMetricBamqc from 2019-12-20", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "@id": "/quality-metrics-bamqc/75ae6e50-5b4c-4c84-9840-81f0fbab0605/", "quality_metric_summary": [{"title": "Total Reads", "value": "148070483", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "3.572", "tooltip": "Percent of total reads (=5.29m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "28.159", "tooltip": "Percent of total reads (=41.7m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "43.265", "tooltip": "Percent of total reads (=64.06m)", "numberType": "percent"}, {"title": "Walks", "value": "0.003", "tooltip": "Percent of total reads (=0.0m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "7.39", "tooltip": "Percent of total reads (=10.94m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "processed file", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "last_modified": {"date_modified": "2025-02-20T14:27:40.862474+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "c89594e8fe07e2752cb015e0386ca826", "@type": ["FileProcessed", "File", "Item"], "href": "/files-processed/4DNFIF4ROSFQ/@@download/4DNFIF4ROSFQ.pairs.gz", "upload_key": "d667b385-ac14-4879-a491-c88c78ea432f/4DNFIF4ROSFQ.pairs.gz", "genome_assembly": "GRCh38", "file_classification": "processed file", "file_size": 705852065, "status": "released", "display_title": "4DNFIF4ROSFQ.pairs.gz", "file_type_detailed": "contact list-replicate (pairs)", "@id": "/files-processed/4DNFIF4ROSFQ/", "file_type": "contact list-replicate", "uuid": "d667b385-ac14-4879-a491-c88c78ea432f", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/d667b385-ac14-4879-a491-c88c78ea432f/4DNFIF4ROSFQ.pairs.gz", "accession": "4DNFIF4ROSFQ", "contributing_labs": [{"@id": "/labs/keji-zhao-lab/", "name": "keji-zhao-lab", "status": "current", "display_title": "Keji Zhao, NHLBI", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}], "quality_metric": {"overall_quality_status": "PASS", "uuid": "92525f18-f08a-4879-9e8a-456b18a3e833", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIF4ROSFQ/pairsqc_report.html", "status": "released", "Total reads": 37020225, "display_title": "QualityMetricPairsqc from 2018-06-22", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "@id": "/quality-metrics-pairsqc/92525f18-f08a-4879-9e8a-456b18a3e833/", "quality_metric_summary": [{"title": "Filtered Reads", "value": "37020225", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "15.138", "tooltip": "Percent of filtered reads (=5.6m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "72.834", "tooltip": "Percent of filtered reads (=26.96m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "12.029", "tooltip": "Percent of filtered reads (=4.45m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "extra_files": [{"href": "/files-processed/4DNFIF4ROSFQ/@@download/4DNFIF4ROSFQ.pairs.gz.px2", "file_size": 17359027, "md5sum": "6c184f672c0ec0ec77bb37d901de8192", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "display_title": "pairs_px2", "@id": "/file-formats/pairs_px2/", "@type": ["FileFormat", "Item"], "file_format": "pairs_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "processed file", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "last_modified": {"date_modified": "2025-02-20T14:26:45.907465+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosample": {"accession": "4DNBS8A4V1B2", "biosource_summary": "GM12878 (Tier 1)", "treatments_summary": "None", "@id": "/biosamples/4DNBS8A4V1B2/", "uuid": "56a4c7da-7d45-4dd5-92e8-7e6024851186", "@type": ["Biosample", "Item"], "biosample_type": "immortalized cells", "biosample_category": ["GM12878", "1000 genomes/Hap Map"], "display_title": "4DNBS8A4V1B2", "modifications_summary": "None", "status": "released", "biosource": [{"uuid": "c9affe27-c09e-46be-ac1c-a614df02587a", "biosource_type": "immortalized cell line", "cell_line_tier": "Tier 1", "accession": "4DNSRH17RFKR", "@type": ["Biosource", "Item"], "display_title": "GM12878 (Tier 1) - 4DNSRH17RFKR", "status": "released", "@id": "/biosources/4DNSRH17RFKR/", "cell_line": {"term_id": "EFO:0002784", "status": "released", "uuid": "b9668b9a-be39-47de-8eab-5bf1b0854417", "@id": "/ontology-terms/EFO:0002784/", "@type": ["OntologyTerm", "Item"], "preferred_name": "GM12878", "display_title": "GM12878", "term_name": "GM12878", "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"preferred_name": "B-lymphocyte", "@id": "/ontology-terms/CL:0000945/", "@type": ["OntologyTerm", "Item"], "term_name": "lymphocyte of B lineage", "status": "released", "display_title": "B-lymphocyte", "uuid": "0c98ef0b-9a03-43f3-b409-fb091e62e2f8", "term_id": "CL:0000945", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0002405/", "display_title": "immune system", "uuid": "111133bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "current", "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"status": "released", "@id": "/organisms/9606/", "display_title": "H. sapiens", "@type": ["Organism", "Item"], "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "scientific_name": "Homo sapiens", "name": "human", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"display_title": "BiosampleCellCulture from 2018-02-09", "in_vitro_differentiated": "No", "status": "released", "@id": "/biosample-cell-cultures/f39462a5-cced-4c2d-9ef6-71c3faf63591/", "uuid": "f39462a5-cced-4c2d-9ef6-71c3faf63591", "@type": ["BiosampleCellCulture", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample missing doubling_number", "Biosample missing morphology_image"], "badge": {"display_title": "Biosample Metadata Incomplete", "badge_classification": "Warning", "badge_icon": "/static/img/badges/biosample-icon.svg", "@type": ["Badge", "Item"], "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "warning": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "tissue_organ_info": {"organ_system": ["immune system"], "tissue_source": "B-lymphocyte"}}, "experiment_type": {"assay_subclass_short": "Ligation-free 3C", "status": "released", "other_tags": ["DNA-DNA", "3D", "Pairwise"], "title": "TrAC-loop", "display_title": "TrAC-loop", "@id": "/experiment-types/trac-loop/", "@type": ["ExperimentType", "Item"], "uuid": "13fc76db-939a-4b92-b076-2caa7525b5c9", "experiment_category": "Sequencing", "assay_classification": "Ligation-free 3C", "assay_subclassification": "DNA-DNA Pairwise Interactions", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"field": "Default"}, "last_modified": {"date_modified": "2025-01-28T20:59:18.046033+00:00"}, "external_references": []}, {"files": [{"paired_end": "1", "upload_key": "3219f98f-ddc2-4351-8033-738cc1b1de78/4DNFIX2YU76H.fastq.gz", "@id": "/files-fastq/4DNFIX2YU76H/", "file_classification": "raw file", "uuid": "3219f98f-ddc2-4351-8033-738cc1b1de78", "status": "released", "file_size": 1163399917, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/3219f98f-ddc2-4351-8033-738cc1b1de78/4DNFIX2YU76H.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "45c46f7e8956af881c8f2a8c5745f4c6", "file_type_detailed": "reads (fastq)", "display_title": "4DNFIX2YU76H.fastq.gz", "accession": "4DNFIX2YU76H", "href": "/files-fastq/4DNFIX2YU76H/@@download/4DNFIX2YU76H.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "a41ce2ba-6ccd-41b4-88f2-ede14d04d584", "file_type": "reads", "@id": "/files-fastq/4DNFI3AF2455/", "accession": "4DNFI3AF2455", "display_title": "4DNFI3AF2455.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/43e9d4e8-50c2-427e-b125-4b1cd4206ffc/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 36831055, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIX2YU76H/fastqc_report.html", "uuid": "43e9d4e8-50c2-427e-b125-4b1cd4206ffc", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "2", "upload_key": "a41ce2ba-6ccd-41b4-88f2-ede14d04d584/4DNFI3AF2455.fastq.gz", "@id": "/files-fastq/4DNFI3AF2455/", "file_classification": "raw file", "uuid": "a41ce2ba-6ccd-41b4-88f2-ede14d04d584", "status": "released", "file_size": 1311830988, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/a41ce2ba-6ccd-41b4-88f2-ede14d04d584/4DNFI3AF2455.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "24623c57a2593d2ae566d1c66db4d7aa", "file_type_detailed": "reads (fastq)", "display_title": "4DNFI3AF2455.fastq.gz", "accession": "4DNFI3AF2455", "href": "/files-fastq/4DNFI3AF2455/@@download/4DNFI3AF2455.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "3219f98f-ddc2-4351-8033-738cc1b1de78", "file_type": "reads", "@id": "/files-fastq/4DNFIX2YU76H/", "accession": "4DNFIX2YU76H", "display_title": "4DNFIX2YU76H.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/40c4f2a8-b76e-4d3e-a35c-b4c30b282265/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 36831055, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI3AF2455/fastqc_report.html", "uuid": "40c4f2a8-b76e-4d3e-a35c-b4c30b282265", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "1", "upload_key": "56a92625-62ab-42c3-857a-b8e7419b12f4/4DNFI53E3GJJ.fastq.gz", "@id": "/files-fastq/4DNFI53E3GJJ/", "file_classification": "raw file", "uuid": "56a92625-62ab-42c3-857a-b8e7419b12f4", "status": "released", "file_size": 1133770742, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/56a92625-62ab-42c3-857a-b8e7419b12f4/4DNFI53E3GJJ.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "0b6a3799911fd5365d5e5665bec7b1ce", "file_type_detailed": "reads (fastq)", "display_title": "4DNFI53E3GJJ.fastq.gz", "accession": "4DNFI53E3GJJ", "href": "/files-fastq/4DNFI53E3GJJ/@@download/4DNFI53E3GJJ.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "0ba091ed-5fb0-4185-8fb1-6b5aadbbdd99", "file_type": "reads", "@id": "/files-fastq/4DNFITM3L7ZQ/", "accession": "4DNFITM3L7ZQ", "display_title": "4DNFITM3L7ZQ.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/c9f14cbb-0b56-44f8-99e2-327799a73220/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 34966819, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI53E3GJJ/fastqc_report.html", "uuid": "c9f14cbb-0b56-44f8-99e2-327799a73220", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "2", "upload_key": "0ba091ed-5fb0-4185-8fb1-6b5aadbbdd99/4DNFITM3L7ZQ.fastq.gz", "@id": "/files-fastq/4DNFITM3L7ZQ/", "file_classification": "raw file", "uuid": "0ba091ed-5fb0-4185-8fb1-6b5aadbbdd99", "status": "released", "file_size": 1264095483, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/0ba091ed-5fb0-4185-8fb1-6b5aadbbdd99/4DNFITM3L7ZQ.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "7985ea99478c2505659397e946399a97", "file_type_detailed": "reads (fastq)", "display_title": "4DNFITM3L7ZQ.fastq.gz", "accession": "4DNFITM3L7ZQ", "href": "/files-fastq/4DNFITM3L7ZQ/@@download/4DNFITM3L7ZQ.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "56a92625-62ab-42c3-857a-b8e7419b12f4", "file_type": "reads", "@id": "/files-fastq/4DNFI53E3GJJ/", "accession": "4DNFI53E3GJJ", "display_title": "4DNFI53E3GJJ.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/b06bf038-3e1f-4e5c-b2fd-95a7d937d5e7/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 34966819, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFITM3L7ZQ/fastqc_report.html", "uuid": "b06bf038-3e1f-4e5c-b2fd-95a7d937d5e7", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "1", "upload_key": "589b266c-81a0-45e7-89a2-2e5e9c2df140/4DNFID1E7NDD.fastq.gz", "@id": "/files-fastq/4DNFID1E7NDD/", "file_classification": "raw file", "uuid": "589b266c-81a0-45e7-89a2-2e5e9c2df140", "status": "released", "file_size": 1268288712, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/589b266c-81a0-45e7-89a2-2e5e9c2df140/4DNFID1E7NDD.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "e0b88748a592654b3878c3ff07cde85c", "file_type_detailed": "reads (fastq)", "display_title": "4DNFID1E7NDD.fastq.gz", "accession": "4DNFID1E7NDD", "href": "/files-fastq/4DNFID1E7NDD/@@download/4DNFID1E7NDD.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "ec8582bc-1139-44df-80ad-6d02ffe726d9", "file_type": "reads", "@id": "/files-fastq/4DNFITCJ4CB7/", "accession": "4DNFITCJ4CB7", "display_title": "4DNFITCJ4CB7.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/c09ec26e-3606-46ad-971c-957fa75c18a2/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 40229514, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFID1E7NDD/fastqc_report.html", "uuid": "c09ec26e-3606-46ad-971c-957fa75c18a2", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "2", "upload_key": "ec8582bc-1139-44df-80ad-6d02ffe726d9/4DNFITCJ4CB7.fastq.gz", "@id": "/files-fastq/4DNFITCJ4CB7/", "file_classification": "raw file", "uuid": "ec8582bc-1139-44df-80ad-6d02ffe726d9", "status": "released", "file_size": 1404012060, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/ec8582bc-1139-44df-80ad-6d02ffe726d9/4DNFITCJ4CB7.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "4388bcb7886075e33da2ac778fcae622", "file_type_detailed": "reads (fastq)", "display_title": "4DNFITCJ4CB7.fastq.gz", "accession": "4DNFITCJ4CB7", "href": "/files-fastq/4DNFITCJ4CB7/@@download/4DNFITCJ4CB7.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "589b266c-81a0-45e7-89a2-2e5e9c2df140", "file_type": "reads", "@id": "/files-fastq/4DNFID1E7NDD/", "accession": "4DNFID1E7NDD", "display_title": "4DNFID1E7NDD.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/f3235ad5-6947-4db6-8330-3671b8eea938/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 40229514, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFITCJ4CB7/fastqc_report.html", "uuid": "f3235ad5-6947-4db6-8330-3671b8eea938", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "1", "upload_key": "38384c50-cca2-4bbe-9841-e09d833b46e8/4DNFIVXSZD4Q.fastq.gz", "@id": "/files-fastq/4DNFIVXSZD4Q/", "file_classification": "raw file", "uuid": "38384c50-cca2-4bbe-9841-e09d833b46e8", "status": "released", "file_size": 1337672344, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/38384c50-cca2-4bbe-9841-e09d833b46e8/4DNFIVXSZD4Q.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "86c9344f7f91b7cff4b83ff939363e96", "file_type_detailed": "reads (fastq)", "display_title": "4DNFIVXSZD4Q.fastq.gz", "accession": "4DNFIVXSZD4Q", "href": "/files-fastq/4DNFIVXSZD4Q/@@download/4DNFIVXSZD4Q.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "233d59fd-6b5b-46ab-a918-49249b47cc71", "file_type": "reads", "@id": "/files-fastq/4DNFIKJUE8V9/", "accession": "4DNFIKJUE8V9", "display_title": "4DNFIKJUE8V9.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/87af1ab8-4264-4a7f-9ed5-0aa91898dff0/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 41266183, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIVXSZD4Q/fastqc_report.html", "uuid": "87af1ab8-4264-4a7f-9ed5-0aa91898dff0", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "2", "upload_key": "233d59fd-6b5b-46ab-a918-49249b47cc71/4DNFIKJUE8V9.fastq.gz", "@id": "/files-fastq/4DNFIKJUE8V9/", "file_classification": "raw file", "uuid": "233d59fd-6b5b-46ab-a918-49249b47cc71", "status": "released", "file_size": 1483530905, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/233d59fd-6b5b-46ab-a918-49249b47cc71/4DNFIKJUE8V9.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "0e43de08e3f04f9a7a259ad47e25e523", "file_type_detailed": "reads (fastq)", "display_title": "4DNFIKJUE8V9.fastq.gz", "accession": "4DNFIKJUE8V9", "href": "/files-fastq/4DNFIKJUE8V9/@@download/4DNFIKJUE8V9.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "38384c50-cca2-4bbe-9841-e09d833b46e8", "file_type": "reads", "@id": "/files-fastq/4DNFIVXSZD4Q/", "accession": "4DNFIVXSZD4Q", "display_title": "4DNFIVXSZD4Q.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/e6a118a7-22e1-44f9-be03-3a2ffe56e72a/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 41266183, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIKJUE8V9/fastqc_report.html", "uuid": "e6a118a7-22e1-44f9-be03-3a2ffe56e72a", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}], "@id": "/experiments-seq/4DNEXAHVP5SD/", "status": "released", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "f8f237cd-e14c-4ac0-abf7-872c6d4318d9", "accession": "4DNEXAHVP5SD", "display_title": "TrAC-loop on GM12878 (Tier 1) - 4DNEXAHVP5SD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "processed_files": [{"md5sum": "e92869db9323363aba2716e8e422c922", "@type": ["FileProcessed", "File", "Item"], "href": "/files-processed/4DNFIGDGGOKK/@@download/4DNFIGDGGOKK.bam", "upload_key": "876d6496-fa72-4f95-9879-a09c72e1f5c7/4DNFIGDGGOKK.bam", "genome_assembly": "GRCh38", "file_classification": "processed file", "file_size": 10851852492, "status": "released", "display_title": "4DNFIGDGGOKK.bam", "file_type_detailed": "alignments (bam)", "@id": "/files-processed/4DNFIGDGGOKK/", "file_type": "alignments", "uuid": "876d6496-fa72-4f95-9879-a09c72e1f5c7", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/876d6496-fa72-4f95-9879-a09c72e1f5c7/4DNFIGDGGOKK.bam", "accession": "4DNFIGDGGOKK", "contributing_labs": [{"@id": "/labs/keji-zhao-lab/", "name": "keji-zhao-lab", "status": "current", "display_title": "Keji Zhao, NHLBI", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}], "quality_metric": {"overall_quality_status": "PASS", "uuid": "430c2e53-1b76-4a2f-bfac-2316b9c06b17", "status": "released", "display_title": "QualityMetricBamqc from 2019-12-20", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "@id": "/quality-metrics-bamqc/430c2e53-1b76-4a2f-bfac-2316b9c06b17/", "quality_metric_summary": [{"title": "Total Reads", "value": "153293571", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "3.692", "tooltip": "Percent of total reads (=5.66m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "25.396", "tooltip": "Percent of total reads (=38.93m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "47.214", "tooltip": "Percent of total reads (=72.38m)", "numberType": "percent"}, {"title": "Walks", "value": "0.003", "tooltip": "Percent of total reads (=0.0m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "6.188", "tooltip": "Percent of total reads (=9.49m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "processed file", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "last_modified": {"date_modified": "2025-02-20T14:26:39.100054+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "f0b5bd6b699565f68d8d472e815dfaac", "@type": ["FileProcessed", "File", "Item"], "href": "/files-processed/4DNFI2ZOWMSI/@@download/4DNFI2ZOWMSI.pairs.gz", "upload_key": "263dcdac-0a0d-4b03-8c16-cef2712028cb/4DNFI2ZOWMSI.pairs.gz", "genome_assembly": "GRCh38", "file_classification": "processed file", "file_size": 678960106, "status": "released", "display_title": "4DNFI2ZOWMSI.pairs.gz", "file_type_detailed": "contact list-replicate (pairs)", "@id": "/files-processed/4DNFI2ZOWMSI/", "file_type": "contact list-replicate", "uuid": "263dcdac-0a0d-4b03-8c16-cef2712028cb", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/263dcdac-0a0d-4b03-8c16-cef2712028cb/4DNFI2ZOWMSI.pairs.gz", "accession": "4DNFI2ZOWMSI", "contributing_labs": [{"@id": "/labs/keji-zhao-lab/", "name": "keji-zhao-lab", "status": "current", "display_title": "Keji Zhao, NHLBI", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}], "quality_metric": {"overall_quality_status": "PASS", "uuid": "0002ac8c-3e65-4919-8efa-6f66a94b8b0d", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI2ZOWMSI/pairsqc_report.html", "status": "released", "Total reads": 36323292, "display_title": "QualityMetricPairsqc from 2018-06-22", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "@id": "/quality-metrics-pairsqc/0002ac8c-3e65-4919-8efa-6f66a94b8b0d/", "quality_metric_summary": [{"title": "Filtered Reads", "value": "36323292", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "10.396", "tooltip": "Percent of filtered reads (=3.78m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "80.597", "tooltip": "Percent of filtered reads (=29.28m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "9.007", "tooltip": "Percent of filtered reads (=3.27m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "extra_files": [{"href": "/files-processed/4DNFI2ZOWMSI/@@download/4DNFI2ZOWMSI.pairs.gz.px2", "file_size": 15558597, "md5sum": "b21ade70b38bf080f7019191dd32204b", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "display_title": "pairs_px2", "@id": "/file-formats/pairs_px2/", "@type": ["FileFormat", "Item"], "file_format": "pairs_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "processed file", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "last_modified": {"date_modified": "2025-02-20T14:25:39.347692+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosample": {"accession": "4DNBSSWGVKEQ", "biosource_summary": "GM12878 (Tier 1)", "treatments_summary": "None", "@id": "/biosamples/4DNBSSWGVKEQ/", "uuid": "90eb59dc-7d6f-42cc-b11d-caec1ce18da6", "@type": ["Biosample", "Item"], "biosample_type": "immortalized cells", "biosample_category": ["GM12878", "1000 genomes/Hap Map"], "display_title": "4DNBSSWGVKEQ", "modifications_summary": "None", "status": "released", "biosource": [{"uuid": "c9affe27-c09e-46be-ac1c-a614df02587a", "biosource_type": "immortalized cell line", "cell_line_tier": "Tier 1", "accession": "4DNSRH17RFKR", "@type": ["Biosource", "Item"], "display_title": "GM12878 (Tier 1) - 4DNSRH17RFKR", "status": "released", "@id": "/biosources/4DNSRH17RFKR/", "cell_line": {"term_id": "EFO:0002784", "status": "released", "uuid": "b9668b9a-be39-47de-8eab-5bf1b0854417", "@id": "/ontology-terms/EFO:0002784/", "@type": ["OntologyTerm", "Item"], "preferred_name": "GM12878", "display_title": "GM12878", "term_name": "GM12878", "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"preferred_name": "B-lymphocyte", "@id": "/ontology-terms/CL:0000945/", "@type": ["OntologyTerm", "Item"], "term_name": "lymphocyte of B lineage", "status": "released", "display_title": "B-lymphocyte", "uuid": "0c98ef0b-9a03-43f3-b409-fb091e62e2f8", "term_id": "CL:0000945", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0002405/", "display_title": "immune system", "uuid": "111133bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "current", "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"status": "released", "@id": "/organisms/9606/", "display_title": "H. sapiens", "@type": ["Organism", "Item"], "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "scientific_name": "Homo sapiens", "name": "human", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"display_title": "BiosampleCellCulture from 2018-02-09", "in_vitro_differentiated": "No", "status": "released", "@id": "/biosample-cell-cultures/2bc70bb1-c9fd-47ac-acb4-03676fc57530/", "uuid": "2bc70bb1-c9fd-47ac-acb4-03676fc57530", "@type": ["BiosampleCellCulture", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample missing doubling_number", "Biosample missing morphology_image"], "badge": {"display_title": "Biosample Metadata Incomplete", "badge_classification": "Warning", "badge_icon": "/static/img/badges/biosample-icon.svg", "@type": ["Badge", "Item"], "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "warning": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "tissue_organ_info": {"organ_system": ["immune system"], "tissue_source": "B-lymphocyte"}}, "experiment_type": {"assay_subclass_short": "Ligation-free 3C", "status": "released", "other_tags": ["DNA-DNA", "3D", "Pairwise"], "title": "TrAC-loop", "display_title": "TrAC-loop", "@id": "/experiment-types/trac-loop/", "@type": ["ExperimentType", "Item"], "uuid": "13fc76db-939a-4b92-b076-2caa7525b5c9", "experiment_category": "Sequencing", "assay_classification": "Ligation-free 3C", "assay_subclassification": "DNA-DNA Pairwise Interactions", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"field": "Default"}, "last_modified": {"date_modified": "2025-01-28T20:59:17.709018+00:00"}, "external_references": []}, {"files": [{"paired_end": "1", "upload_key": "60751a1f-51b3-4e2e-a271-f03287535c44/4DNFI75SPZAN.fastq.gz", "@id": "/files-fastq/4DNFI75SPZAN/", "file_classification": "raw file", "uuid": "60751a1f-51b3-4e2e-a271-f03287535c44", "status": "released", "file_size": 971598493, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/60751a1f-51b3-4e2e-a271-f03287535c44/4DNFI75SPZAN.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "6a0eb5b6e7821c5d05c903aa6ebc225b", "file_type_detailed": "reads (fastq)", "display_title": "4DNFI75SPZAN.fastq.gz", "accession": "4DNFI75SPZAN", "href": "/files-fastq/4DNFI75SPZAN/@@download/4DNFI75SPZAN.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "839af0af-9359-46f8-93af-053edcc986fa", "file_type": "reads", "@id": "/files-fastq/4DNFI38DCAR2/", "accession": "4DNFI38DCAR2", "display_title": "4DNFI38DCAR2.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/7c4280f3-f26e-4647-8ee1-0edf79810530/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 31434227, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI75SPZAN/fastqc_report.html", "uuid": "7c4280f3-f26e-4647-8ee1-0edf79810530", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "2", "upload_key": "839af0af-9359-46f8-93af-053edcc986fa/4DNFI38DCAR2.fastq.gz", "@id": "/files-fastq/4DNFI38DCAR2/", "file_classification": "raw file", "uuid": "839af0af-9359-46f8-93af-053edcc986fa", "status": "released", "file_size": 1066948080, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/839af0af-9359-46f8-93af-053edcc986fa/4DNFI38DCAR2.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "fec9e6434d0282b4d27f2f2ac6f8d7d0", "file_type_detailed": "reads (fastq)", "display_title": "4DNFI38DCAR2.fastq.gz", "accession": "4DNFI38DCAR2", "href": "/files-fastq/4DNFI38DCAR2/@@download/4DNFI38DCAR2.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "60751a1f-51b3-4e2e-a271-f03287535c44", "file_type": "reads", "@id": "/files-fastq/4DNFI75SPZAN/", "accession": "4DNFI75SPZAN", "display_title": "4DNFI75SPZAN.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/c50acce1-edc2-4fa8-ab50-3fbe680546a4/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 31434227, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI38DCAR2/fastqc_report.html", "uuid": "c50acce1-edc2-4fa8-ab50-3fbe680546a4", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "1", "upload_key": "983eb20a-db6b-44ed-87f1-be16f702b927/4DNFIASBU8FG.fastq.gz", "@id": "/files-fastq/4DNFIASBU8FG/", "file_classification": "raw file", "uuid": "983eb20a-db6b-44ed-87f1-be16f702b927", "status": "released", "file_size": 992947766, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/983eb20a-db6b-44ed-87f1-be16f702b927/4DNFIASBU8FG.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "a1a609782aee769de6a717c5d2381de5", "file_type_detailed": "reads (fastq)", "display_title": "4DNFIASBU8FG.fastq.gz", "accession": "4DNFIASBU8FG", "href": "/files-fastq/4DNFIASBU8FG/@@download/4DNFIASBU8FG.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "e19617dc-1672-42a4-b607-fda54819e401", "file_type": "reads", "@id": "/files-fastq/4DNFIT2BW6NR/", "accession": "4DNFIT2BW6NR", "display_title": "4DNFIT2BW6NR.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/5570f966-e67e-4bf5-8565-bb4710e45495/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 31765355, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIASBU8FG/fastqc_report.html", "uuid": "5570f966-e67e-4bf5-8565-bb4710e45495", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "2", "upload_key": "e19617dc-1672-42a4-b607-fda54819e401/4DNFIT2BW6NR.fastq.gz", "@id": "/files-fastq/4DNFIT2BW6NR/", "file_classification": "raw file", "uuid": "e19617dc-1672-42a4-b607-fda54819e401", "status": "released", "file_size": 1088300423, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/e19617dc-1672-42a4-b607-fda54819e401/4DNFIT2BW6NR.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "07ce7bfeaf84aeaa2fc2e394eb2edcf5", "file_type_detailed": "reads (fastq)", "display_title": "4DNFIT2BW6NR.fastq.gz", "accession": "4DNFIT2BW6NR", "href": "/files-fastq/4DNFIT2BW6NR/@@download/4DNFIT2BW6NR.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "983eb20a-db6b-44ed-87f1-be16f702b927", "file_type": "reads", "@id": "/files-fastq/4DNFIASBU8FG/", "accession": "4DNFIASBU8FG", "display_title": "4DNFIASBU8FG.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/c3ce8bc9-7001-44ce-8f05-46aec45c015b/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 31765355, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIT2BW6NR/fastqc_report.html", "uuid": "c3ce8bc9-7001-44ce-8f05-46aec45c015b", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "1", "upload_key": "4e088990-1803-4214-98d1-568e76f0ec86/4DNFIPK17VRO.fastq.gz", "@id": "/files-fastq/4DNFIPK17VRO/", "file_classification": "raw file", "uuid": "4e088990-1803-4214-98d1-568e76f0ec86", "status": "released", "file_size": 1034889339, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/4e088990-1803-4214-98d1-568e76f0ec86/4DNFIPK17VRO.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "ec966e589b4fb703ecdf7dcf33a40df1", "file_type_detailed": "reads (fastq)", "display_title": "4DNFIPK17VRO.fastq.gz", "accession": "4DNFIPK17VRO", "href": "/files-fastq/4DNFIPK17VRO/@@download/4DNFIPK17VRO.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "21e4cbc0-6d3a-4186-95ac-fe1ff2885a9d", "file_type": "reads", "@id": "/files-fastq/4DNFIDF8KKKH/", "accession": "4DNFIDF8KKKH", "display_title": "4DNFIDF8KKKH.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/1551f49b-b3b9-4e6f-aaf0-1ece192660a1/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 33603571, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIPK17VRO/fastqc_report.html", "uuid": "1551f49b-b3b9-4e6f-aaf0-1ece192660a1", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "2", "upload_key": "21e4cbc0-6d3a-4186-95ac-fe1ff2885a9d/4DNFIDF8KKKH.fastq.gz", "@id": "/files-fastq/4DNFIDF8KKKH/", "file_classification": "raw file", "uuid": "21e4cbc0-6d3a-4186-95ac-fe1ff2885a9d", "status": "released", "file_size": 1102973453, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/21e4cbc0-6d3a-4186-95ac-fe1ff2885a9d/4DNFIDF8KKKH.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "b741c74989613dd7d357f511e7139dd5", "file_type_detailed": "reads (fastq)", "display_title": "4DNFIDF8KKKH.fastq.gz", "accession": "4DNFIDF8KKKH", "href": "/files-fastq/4DNFIDF8KKKH/@@download/4DNFIDF8KKKH.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "4e088990-1803-4214-98d1-568e76f0ec86", "file_type": "reads", "@id": "/files-fastq/4DNFIPK17VRO/", "accession": "4DNFIPK17VRO", "display_title": "4DNFIPK17VRO.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/deccf2c9-a6e6-42d3-ac97-21b3cd69d541/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 33603571, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIDF8KKKH/fastqc_report.html", "uuid": "deccf2c9-a6e6-42d3-ac97-21b3cd69d541", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "1", "upload_key": "4d850cee-dd02-4354-80e9-29637c9c6ca7/4DNFIZ8WVUPQ.fastq.gz", "@id": "/files-fastq/4DNFIZ8WVUPQ/", "file_classification": "raw file", "uuid": "4d850cee-dd02-4354-80e9-29637c9c6ca7", "status": "released", "file_size": 1044456600, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/4d850cee-dd02-4354-80e9-29637c9c6ca7/4DNFIZ8WVUPQ.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "7e139de1fd9b333d1a513a7466ec4b4e", "file_type_detailed": "reads (fastq)", "display_title": "4DNFIZ8WVUPQ.fastq.gz", "accession": "4DNFIZ8WVUPQ", "href": "/files-fastq/4DNFIZ8WVUPQ/@@download/4DNFIZ8WVUPQ.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "f6631cc2-fca1-480d-98c0-5456a5cc3e13", "file_type": "reads", "@id": "/files-fastq/4DNFI1ZF86A3/", "accession": "4DNFI1ZF86A3", "display_title": "4DNFI1ZF86A3.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/f9dc2abc-ce01-4e0e-8f5d-878ccd6fc53c/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 33613870, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIZ8WVUPQ/fastqc_report.html", "uuid": "f9dc2abc-ce01-4e0e-8f5d-878ccd6fc53c", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "2", "upload_key": "f6631cc2-fca1-480d-98c0-5456a5cc3e13/4DNFI1ZF86A3.fastq.gz", "@id": "/files-fastq/4DNFI1ZF86A3/", "file_classification": "raw file", "uuid": "f6631cc2-fca1-480d-98c0-5456a5cc3e13", "status": "released", "file_size": 1111717342, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/f6631cc2-fca1-480d-98c0-5456a5cc3e13/4DNFI1ZF86A3.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "fb6c6b0cd3fc3ff001ad6e8d7bc83e5d", "file_type_detailed": "reads (fastq)", "display_title": "4DNFI1ZF86A3.fastq.gz", "accession": "4DNFI1ZF86A3", "href": "/files-fastq/4DNFI1ZF86A3/@@download/4DNFI1ZF86A3.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "4d850cee-dd02-4354-80e9-29637c9c6ca7", "file_type": "reads", "@id": "/files-fastq/4DNFIZ8WVUPQ/", "accession": "4DNFIZ8WVUPQ", "display_title": "4DNFIZ8WVUPQ.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/512ffd6c-7549-484a-93c2-5866af6c5fc0/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 33613870, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI1ZF86A3/fastqc_report.html", "uuid": "512ffd6c-7549-484a-93c2-5866af6c5fc0", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}], "@id": "/experiments-seq/4DNEX15HMJS9/", "status": "released", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "41eb4f1b-ca6e-4dea-b2cd-5940276060cb", "accession": "4DNEX15HMJS9", "display_title": "TrAC-loop on GM12878 (Tier 1) - 4DNEX15HMJS9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "processed_files": [{"md5sum": "7e89c4b1bc7570fac6f5450574ddbb84", "@type": ["FileProcessed", "File", "Item"], "href": "/files-processed/4DNFIHHRIQLR/@@download/4DNFIHHRIQLR.bam", "upload_key": "ecda6b42-c093-4cf0-8104-c05d4e5055ee/4DNFIHHRIQLR.bam", "genome_assembly": "GRCh38", "file_classification": "processed file", "file_size": 8039599986, "status": "released", "display_title": "4DNFIHHRIQLR.bam", "file_type_detailed": "alignments (bam)", "@id": "/files-processed/4DNFIHHRIQLR/", "file_type": "alignments", "uuid": "ecda6b42-c093-4cf0-8104-c05d4e5055ee", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ecda6b42-c093-4cf0-8104-c05d4e5055ee/4DNFIHHRIQLR.bam", "accession": "4DNFIHHRIQLR", "contributing_labs": [{"@id": "/labs/keji-zhao-lab/", "name": "keji-zhao-lab", "status": "current", "display_title": "Keji Zhao, NHLBI", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}], "quality_metric": {"overall_quality_status": "PASS", "uuid": "8bbb057a-2d36-4d4b-aeed-3cea33914b65", "status": "released", "display_title": "QualityMetricBamqc from 2019-12-20", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "@id": "/quality-metrics-bamqc/8bbb057a-2d36-4d4b-aeed-3cea33914b65/", "quality_metric_summary": [{"title": "Total Reads", "value": "130417023", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "7.518", "tooltip": "Percent of total reads (=9.8m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "19.154", "tooltip": "Percent of total reads (=24.98m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "59.043", "tooltip": "Percent of total reads (=77.0m)", "numberType": "percent"}, {"title": "Walks", "value": "0.001", "tooltip": "Percent of total reads (=0.0m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "3.357", "tooltip": "Percent of total reads (=4.38m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "processed file", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "last_modified": {"date_modified": "2025-02-20T14:28:29.617136+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "da513c28ac1505b01bfa4a96511ec802", "@type": ["FileProcessed", "File", "Item"], "href": "/files-processed/4DNFIPD15L7F/@@download/4DNFIPD15L7F.pairs.gz", "upload_key": "77bdc345-4396-4daf-a58d-5c6bc5dde0b1/4DNFIPD15L7F.pairs.gz", "genome_assembly": "GRCh38", "file_classification": "processed file", "file_size": 343616164, "status": "released", "display_title": "4DNFIPD15L7F.pairs.gz", "file_type_detailed": "contact list-replicate (pairs)", "@id": "/files-processed/4DNFIPD15L7F/", "file_type": "contact list-replicate", "uuid": "77bdc345-4396-4daf-a58d-5c6bc5dde0b1", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/77bdc345-4396-4daf-a58d-5c6bc5dde0b1/4DNFIPD15L7F.pairs.gz", "accession": "4DNFIPD15L7F", "contributing_labs": [{"@id": "/labs/keji-zhao-lab/", "name": "keji-zhao-lab", "status": "current", "display_title": "Keji Zhao, NHLBI", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}], "quality_metric": {"overall_quality_status": "PASS", "uuid": "fd401e81-1ecd-4163-b244-40dcbd6e9d73", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIPD15L7F/pairsqc_report.html", "status": "released", "Total reads": 18627328, "display_title": "QualityMetricPairsqc from 2018-06-22", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "@id": "/quality-metrics-pairsqc/fd401e81-1ecd-4163-b244-40dcbd6e9d73/", "quality_metric_summary": [{"title": "Filtered Reads", "value": "18627328", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "7.677", "tooltip": "Percent of filtered reads (=1.43m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "85.624", "tooltip": "Percent of filtered reads (=15.95m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "6.699", "tooltip": "Percent of filtered reads (=1.25m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "extra_files": [{"href": "/files-processed/4DNFIPD15L7F/@@download/4DNFIPD15L7F.pairs.gz.px2", "file_size": 10167670, "md5sum": "4e942ef603cdda663fcc7a0ef5d2f23e", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "display_title": "pairs_px2", "@id": "/file-formats/pairs_px2/", "@type": ["FileFormat", "Item"], "file_format": "pairs_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "processed file", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "last_modified": {"date_modified": "2025-02-20T14:27:46.543127+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosample": {"accession": "4DNBS4Z97V85", "biosource_summary": "GM12878 (Tier 1)", "treatments_summary": "None", "@id": "/biosamples/4DNBS4Z97V85/", "uuid": "10777498-f5ba-49d0-98b9-3c690c156c43", "@type": ["Biosample", "Item"], "biosample_type": "immortalized cells", "biosample_category": ["GM12878", "1000 genomes/Hap Map"], "display_title": "4DNBS4Z97V85", "modifications_summary": "None", "status": "released", "biosource": [{"uuid": "c9affe27-c09e-46be-ac1c-a614df02587a", "biosource_type": "immortalized cell line", "cell_line_tier": "Tier 1", "accession": "4DNSRH17RFKR", "@type": ["Biosource", "Item"], "display_title": "GM12878 (Tier 1) - 4DNSRH17RFKR", "status": "released", "@id": "/biosources/4DNSRH17RFKR/", "cell_line": {"term_id": "EFO:0002784", "status": "released", "uuid": "b9668b9a-be39-47de-8eab-5bf1b0854417", "@id": "/ontology-terms/EFO:0002784/", "@type": ["OntologyTerm", "Item"], "preferred_name": "GM12878", "display_title": "GM12878", "term_name": "GM12878", "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"preferred_name": "B-lymphocyte", "@id": "/ontology-terms/CL:0000945/", "@type": ["OntologyTerm", "Item"], "term_name": "lymphocyte of B lineage", "status": "released", "display_title": "B-lymphocyte", "uuid": "0c98ef0b-9a03-43f3-b409-fb091e62e2f8", "term_id": "CL:0000945", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0002405/", "display_title": "immune system", "uuid": "111133bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "current", "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"status": "released", "@id": "/organisms/9606/", "display_title": "H. sapiens", "@type": ["Organism", "Item"], "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "scientific_name": "Homo sapiens", "name": "human", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"display_title": "BiosampleCellCulture from 2018-02-09", "in_vitro_differentiated": "No", "status": "released", "@id": "/biosample-cell-cultures/1db12513-e595-4e60-a3d5-74060436bc9a/", "uuid": "1db12513-e595-4e60-a3d5-74060436bc9a", "@type": ["BiosampleCellCulture", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample missing doubling_number", "Biosample missing morphology_image"], "badge": {"display_title": "Biosample Metadata Incomplete", "badge_classification": "Warning", "badge_icon": "/static/img/badges/biosample-icon.svg", "@type": ["Badge", "Item"], "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "warning": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "tissue_organ_info": {"organ_system": ["immune system"], "tissue_source": "B-lymphocyte"}}, "experiment_type": {"assay_subclass_short": "Ligation-free 3C", "status": "released", "other_tags": ["DNA-DNA", "3D", "Pairwise"], "title": "TrAC-loop", "display_title": "TrAC-loop", "@id": "/experiment-types/trac-loop/", "@type": ["ExperimentType", "Item"], "uuid": "13fc76db-939a-4b92-b076-2caa7525b5c9", "experiment_category": "Sequencing", "assay_classification": "Ligation-free 3C", "assay_subclassification": "DNA-DNA Pairwise Interactions", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"field": "Default"}, "last_modified": {"date_modified": "2025-01-28T20:59:20.185377+00:00"}, "external_references": []}, {"files": [{"paired_end": "1", "upload_key": "db0e45c1-a003-4644-806d-5939957de5b8/4DNFIGU4WV7D.fastq.gz", "@id": "/files-fastq/4DNFIGU4WV7D/", "file_classification": "raw file", "uuid": "db0e45c1-a003-4644-806d-5939957de5b8", "status": "released", "file_size": 789679886, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/db0e45c1-a003-4644-806d-5939957de5b8/4DNFIGU4WV7D.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "67757d5bd027345c177a0a6dddddd387", "file_type_detailed": "reads (fastq)", "display_title": "4DNFIGU4WV7D.fastq.gz", "accession": "4DNFIGU4WV7D", "href": "/files-fastq/4DNFIGU4WV7D/@@download/4DNFIGU4WV7D.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "59923f87-93ca-491d-8c71-9dcd7a877053", "file_type": "reads", "@id": "/files-fastq/4DNFIOXRTFJM/", "accession": "4DNFIOXRTFJM", "display_title": "4DNFIOXRTFJM.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/461eedc2-8681-4d34-88a8-427170f4e0ae/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 24973588, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIGU4WV7D/fastqc_report.html", "uuid": "461eedc2-8681-4d34-88a8-427170f4e0ae", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 4, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "2", "upload_key": "59923f87-93ca-491d-8c71-9dcd7a877053/4DNFIOXRTFJM.fastq.gz", "@id": "/files-fastq/4DNFIOXRTFJM/", "file_classification": "raw file", "uuid": "59923f87-93ca-491d-8c71-9dcd7a877053", "status": "released", "file_size": 873540365, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/59923f87-93ca-491d-8c71-9dcd7a877053/4DNFIOXRTFJM.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "5134baf380e053ded63012d6c8b820de", "file_type_detailed": "reads (fastq)", "display_title": "4DNFIOXRTFJM.fastq.gz", "accession": "4DNFIOXRTFJM", "href": "/files-fastq/4DNFIOXRTFJM/@@download/4DNFIOXRTFJM.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "db0e45c1-a003-4644-806d-5939957de5b8", "file_type": "reads", "@id": "/files-fastq/4DNFIGU4WV7D/", "accession": "4DNFIGU4WV7D", "display_title": "4DNFIGU4WV7D.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/351b9f07-4040-4b0d-b7be-3a0dd92f19b4/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 24973588, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIOXRTFJM/fastqc_report.html", "uuid": "351b9f07-4040-4b0d-b7be-3a0dd92f19b4", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 4, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "1", "upload_key": "69d0190f-0f14-49ff-85cd-0373ab156b06/4DNFIBL3JC41.fastq.gz", "@id": "/files-fastq/4DNFIBL3JC41/", "file_classification": "raw file", "uuid": "69d0190f-0f14-49ff-85cd-0373ab156b06", "status": "released", "file_size": 811175305, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/69d0190f-0f14-49ff-85cd-0373ab156b06/4DNFIBL3JC41.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "489ec8aba3c549965b22eea7d4c7e4ff", "file_type_detailed": "reads (fastq)", "display_title": "4DNFIBL3JC41.fastq.gz", "accession": "4DNFIBL3JC41", "href": "/files-fastq/4DNFIBL3JC41/@@download/4DNFIBL3JC41.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "7ff9e8f0-095c-4d99-a19c-b38ffa553d28", "file_type": "reads", "@id": "/files-fastq/4DNFIK5QD352/", "accession": "4DNFIK5QD352", "display_title": "4DNFIK5QD352.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/9b6ed30b-aedc-4f65-9e42-64c95d992ce6/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 25395691, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIBL3JC41/fastqc_report.html", "uuid": "9b6ed30b-aedc-4f65-9e42-64c95d992ce6", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 4, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "2", "upload_key": "7ff9e8f0-095c-4d99-a19c-b38ffa553d28/4DNFIK5QD352.fastq.gz", "@id": "/files-fastq/4DNFIK5QD352/", "file_classification": "raw file", "uuid": "7ff9e8f0-095c-4d99-a19c-b38ffa553d28", "status": "released", "file_size": 898819038, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/7ff9e8f0-095c-4d99-a19c-b38ffa553d28/4DNFIK5QD352.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "a23c1758768e1181c9d620b9a0c40f07", "file_type_detailed": "reads (fastq)", "display_title": "4DNFIK5QD352.fastq.gz", "accession": "4DNFIK5QD352", "href": "/files-fastq/4DNFIK5QD352/@@download/4DNFIK5QD352.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "69d0190f-0f14-49ff-85cd-0373ab156b06", "file_type": "reads", "@id": "/files-fastq/4DNFIBL3JC41/", "accession": "4DNFIBL3JC41", "display_title": "4DNFIBL3JC41.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/877c0764-aede-4251-8231-30e39674e628/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 25395691, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIK5QD352/fastqc_report.html", "uuid": "877c0764-aede-4251-8231-30e39674e628", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 4, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "1", "upload_key": "5c874788-96ce-44a5-bbf3-f4685cc6ca23/4DNFI3JG5GE9.fastq.gz", "@id": "/files-fastq/4DNFI3JG5GE9/", "file_classification": "raw file", "uuid": "5c874788-96ce-44a5-bbf3-f4685cc6ca23", "status": "released", "file_size": 882839986, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/5c874788-96ce-44a5-bbf3-f4685cc6ca23/4DNFI3JG5GE9.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "a3bf1d4e633ca25e8f475a25b7c096f5", "file_type_detailed": "reads (fastq)", "display_title": "4DNFI3JG5GE9.fastq.gz", "accession": "4DNFI3JG5GE9", "href": "/files-fastq/4DNFI3JG5GE9/@@download/4DNFI3JG5GE9.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "a5abfd12-045a-44f1-8a2e-3a21062fa60a", "file_type": "reads", "@id": "/files-fastq/4DNFI84Y6SH5/", "accession": "4DNFI84Y6SH5", "display_title": "4DNFI84Y6SH5.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/afe55a9b-37ac-4ba0-8951-f5e23e139e2f/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 28342161, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI3JG5GE9/fastqc_report.html", "uuid": "afe55a9b-37ac-4ba0-8951-f5e23e139e2f", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 4, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "2", "upload_key": "a5abfd12-045a-44f1-8a2e-3a21062fa60a/4DNFI84Y6SH5.fastq.gz", "@id": "/files-fastq/4DNFI84Y6SH5/", "file_classification": "raw file", "uuid": "a5abfd12-045a-44f1-8a2e-3a21062fa60a", "status": "released", "file_size": 960885029, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/a5abfd12-045a-44f1-8a2e-3a21062fa60a/4DNFI84Y6SH5.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "8b6b14948e6dc7c4130b9430bf3bf0da", "file_type_detailed": "reads (fastq)", "display_title": "4DNFI84Y6SH5.fastq.gz", "accession": "4DNFI84Y6SH5", "href": "/files-fastq/4DNFI84Y6SH5/@@download/4DNFI84Y6SH5.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "5c874788-96ce-44a5-bbf3-f4685cc6ca23", "file_type": "reads", "@id": "/files-fastq/4DNFI3JG5GE9/", "accession": "4DNFI3JG5GE9", "display_title": "4DNFI3JG5GE9.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/89c9d37c-673f-406c-81c2-f03070d1c1cd/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 28342161, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI84Y6SH5/fastqc_report.html", "uuid": "89c9d37c-673f-406c-81c2-f03070d1c1cd", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 4, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "1", "upload_key": "430edc3e-147b-4311-b7d8-617483591822/4DNFIP83XFRA.fastq.gz", "@id": "/files-fastq/4DNFIP83XFRA/", "file_classification": "raw file", "uuid": "430edc3e-147b-4311-b7d8-617483591822", "status": "released", "file_size": 899571878, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/430edc3e-147b-4311-b7d8-617483591822/4DNFIP83XFRA.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "f9fb7a3405587a6240adbe3410ee8742", "file_type_detailed": "reads (fastq)", "display_title": "4DNFIP83XFRA.fastq.gz", "accession": "4DNFIP83XFRA", "href": "/files-fastq/4DNFIP83XFRA/@@download/4DNFIP83XFRA.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "3e7a9f9a-f80a-4e83-8b04-8417bc949b74", "file_type": "reads", "@id": "/files-fastq/4DNFIFUKP1IJ/", "accession": "4DNFIFUKP1IJ", "display_title": "4DNFIFUKP1IJ.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/ee38e0e7-bdf6-418c-83e5-bfc0ffacb19c/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 28565251, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIP83XFRA/fastqc_report.html", "uuid": "ee38e0e7-bdf6-418c-83e5-bfc0ffacb19c", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 4, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}, {"paired_end": "2", "upload_key": "3e7a9f9a-f80a-4e83-8b04-8417bc949b74/4DNFIFUKP1IJ.fastq.gz", "@id": "/files-fastq/4DNFIFUKP1IJ/", "file_classification": "raw file", "uuid": "3e7a9f9a-f80a-4e83-8b04-8417bc949b74", "status": "released", "file_size": 979203520, "file_type": "reads", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/3e7a9f9a-f80a-4e83-8b04-8417bc949b74/4DNFIFUKP1IJ.fastq.gz", "@type": ["FileFastq", "File", "Item"], "md5sum": "eebbd8837ce9a458015d7d9fcf42dd26", "file_type_detailed": "reads (fastq)", "display_title": "4DNFIFUKP1IJ.fastq.gz", "accession": "4DNFIFUKP1IJ", "href": "/files-fastq/4DNFIFUKP1IJ/@@download/4DNFIFUKP1IJ.fastq.gz", "extra_files": [], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "430edc3e-147b-4311-b7d8-617483591822", "file_type": "reads", "@id": "/files-fastq/4DNFIP83XFRA/", "accession": "4DNFIP83XFRA", "display_title": "4DNFIP83XFRA.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/f10df7d8-544e-488a-9173-ec7e640bf49c/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 28565251, "display_title": "QualityMetricFastqc from 2018-02-11", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIFUKP1IJ/fastqc_report.html", "uuid": "f10df7d8-544e-488a-9173-ec7e640bf49c", "Sequence length": "50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/keji-zhao-lab/", "display_title": "Keji Zhao, NHLBI", "status": "current", "@type": ["Lab", "Item"], "name": "keji-zhao-lab", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}, "file_format": {"display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "raw file", "replicate_info": "Biorep 4, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "Keji Zhao, NHLBI"}}], "@id": "/experiments-seq/4DNEXXRV8DHE/", "status": "released", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "c6cf0e3c-e25a-49a6-a942-817b04bd78bc", "accession": "4DNEXXRV8DHE", "display_title": "TrAC-loop on GM12878 (Tier 1) - 4DNEXXRV8DHE", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "processed_files": [{"md5sum": "91cbb87cf2d381e058d1cd9a43aa6f5e", "@type": ["FileProcessed", "File", "Item"], "href": "/files-processed/4DNFINM4O27E/@@download/4DNFINM4O27E.bam", "upload_key": "b0606a69-6045-4531-8c10-ea5ee129675b/4DNFINM4O27E.bam", "genome_assembly": "GRCh38", "file_classification": "processed file", "file_size": 7003355493, "status": "released", "display_title": "4DNFINM4O27E.bam", "file_type_detailed": "alignments (bam)", "@id": "/files-processed/4DNFINM4O27E/", "file_type": "alignments", "uuid": "b0606a69-6045-4531-8c10-ea5ee129675b", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/b0606a69-6045-4531-8c10-ea5ee129675b/4DNFINM4O27E.bam", "accession": "4DNFINM4O27E", "contributing_labs": [{"@id": "/labs/keji-zhao-lab/", "name": "keji-zhao-lab", "status": "current", "display_title": "Keji Zhao, NHLBI", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}], "quality_metric": {"overall_quality_status": "PASS", "uuid": "16e7e581-6360-41fe-b2ff-ea9609d04625", "status": "released", "display_title": "QualityMetricBamqc from 2019-12-20", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "@id": "/quality-metrics-bamqc/16e7e581-6360-41fe-b2ff-ea9609d04625/", "quality_metric_summary": [{"title": "Total Reads", "value": "107276691", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "5.556", "tooltip": "Percent of total reads (=5.96m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "22.9", "tooltip": "Percent of total reads (=24.57m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "55.183", "tooltip": "Percent of total reads (=59.2m)", "numberType": "percent"}, {"title": "Walks", "value": "0.002", "tooltip": "Percent of total reads (=0.0m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "4.979", "tooltip": "Percent of total reads (=5.34m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "processed file", "replicate_info": "Biorep 4, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "last_modified": {"date_modified": "2025-02-20T14:25:33.336178+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "ec448620ddf25de6b99f35579ed80aae", "@type": ["FileProcessed", "File", "Item"], "href": "/files-processed/4DNFIXB7BSRD/@@download/4DNFIXB7BSRD.pairs.gz", "upload_key": "aa2b1565-f409-4c89-afc6-9ceaeea8623f/4DNFIXB7BSRD.pairs.gz", "genome_assembly": "GRCh38", "file_classification": "processed file", "file_size": 329887063, "status": "released", "display_title": "4DNFIXB7BSRD.pairs.gz", "file_type_detailed": "contact list-replicate (pairs)", "@id": "/files-processed/4DNFIXB7BSRD/", "file_type": "contact list-replicate", "uuid": "aa2b1565-f409-4c89-afc6-9ceaeea8623f", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/aa2b1565-f409-4c89-afc6-9ceaeea8623f/4DNFIXB7BSRD.pairs.gz", "accession": "4DNFIXB7BSRD", "contributing_labs": [{"@id": "/labs/keji-zhao-lab/", "name": "keji-zhao-lab", "status": "current", "display_title": "Keji Zhao, NHLBI", "uuid": "8017f1c9-8877-43b4-8cd5-c695621e78e5", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8017f1c9-8877-43b4-8cd5-c695621e78e5"]}}], "quality_metric": {"overall_quality_status": "PASS", "uuid": "99f3af58-dd72-4faf-8c24-b990c790c1ef", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIXB7BSRD/pairsqc_report.html", "status": "released", "Total reads": 17549876, "display_title": "QualityMetricPairsqc from 2018-06-22", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "@id": "/quality-metrics-pairsqc/99f3af58-dd72-4faf-8c24-b990c790c1ef/", "quality_metric_summary": [{"title": "Filtered Reads", "value": "17549876", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "10.242", "tooltip": "Percent of filtered reads (=1.8m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "81.06", "tooltip": "Percent of filtered reads (=14.23m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "8.698", "tooltip": "Percent of filtered reads (=1.53m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "extra_files": [{"href": "/files-processed/4DNFIXB7BSRD/@@download/4DNFIXB7BSRD.pairs.gz.px2", "file_size": 11186610, "md5sum": "23b6872304c38b3c586c7b3222fb486b", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "display_title": "pairs_px2", "@id": "/file-formats/pairs_px2/", "@type": ["FileFormat", "Item"], "file_format": "pairs_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Keji Zhao, NHLBI", "experiment_type": "TrAC-loop", "experiment_bucket": "processed file", "replicate_info": "Biorep 4, Techrep 1", "biosource_name": "GM12878 (Tier 1)", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "last_modified": {"date_modified": "2025-02-20T14:24:56.586047+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosample": {"accession": "4DNBS2N5P2DR", "biosource_summary": "GM12878 (Tier 1)", "treatments_summary": "None", "@id": "/biosamples/4DNBS2N5P2DR/", "uuid": "e82c367d-66ea-40ad-b891-e06176f1fa15", "@type": ["Biosample", "Item"], "biosample_type": "immortalized cells", "biosample_category": ["GM12878", "1000 genomes/Hap Map"], "display_title": "4DNBS2N5P2DR", "modifications_summary": "None", "status": "released", "biosource": [{"uuid": "c9affe27-c09e-46be-ac1c-a614df02587a", "biosource_type": "immortalized cell line", "cell_line_tier": "Tier 1", "accession": "4DNSRH17RFKR", "@type": ["Biosource", "Item"], "display_title": "GM12878 (Tier 1) - 4DNSRH17RFKR", "status": "released", "@id": "/biosources/4DNSRH17RFKR/", "cell_line": {"term_id": "EFO:0002784", "status": "released", "uuid": "b9668b9a-be39-47de-8eab-5bf1b0854417", "@id": "/ontology-terms/EFO:0002784/", "@type": ["OntologyTerm", "Item"], "preferred_name": "GM12878", "display_title": "GM12878", "term_name": "GM12878", "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"preferred_name": "B-lymphocyte", "@id": "/ontology-terms/CL:0000945/", "@type": ["OntologyTerm", "Item"], "term_name": "lymphocyte of B lineage", "status": "released", "display_title": "B-lymphocyte", "uuid": "0c98ef0b-9a03-43f3-b409-fb091e62e2f8", "term_id": "CL:0000945", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0002405/", "display_title": "immune system", "uuid": "111133bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "current", "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"status": "released", "@id": "/organisms/9606/", "display_title": "H. sapiens", "@type": ["Organism", "Item"], "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "scientific_name": "Homo sapiens", "name": "human", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"display_title": "BiosampleCellCulture from 2018-02-09", "in_vitro_differentiated": "No", "status": "released", "@id": "/biosample-cell-cultures/a12b8ef7-761a-4841-b7ba-11a3d96f6ecc/", "uuid": "a12b8ef7-761a-4841-b7ba-11a3d96f6ecc", "@type": ["BiosampleCellCulture", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample missing doubling_number", "Biosample missing morphology_image"], "badge": {"display_title": "Biosample Metadata Incomplete", "badge_classification": "Warning", "badge_icon": "/static/img/badges/biosample-icon.svg", "@type": ["Badge", "Item"], "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "warning": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "tissue_organ_info": {"organ_system": ["immune system"], "tissue_source": "B-lymphocyte"}}, "experiment_type": {"assay_subclass_short": "Ligation-free 3C", "status": "released", "other_tags": ["DNA-DNA", "3D", "Pairwise"], "title": "TrAC-loop", "display_title": "TrAC-loop", "@id": "/experiment-types/trac-loop/", "@type": ["ExperimentType", "Item"], "uuid": "13fc76db-939a-4b92-b076-2caa7525b5c9", "experiment_category": "Sequencing", "assay_classification": "Ligation-free 3C", "assay_subclassification": "DNA-DNA Pairwise Interactions", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"field": "Default"}, "last_modified": {"date_modified": "2025-01-28T20:59:18.569438+00:00"}, "external_references": []}], "experimentset_type": "replicate", "completed_processes": ["HiC_Pipeline_0.2.6"], "@id": "/experiment-set-replicates/4DNES5BDII8F/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "c5db8085-92bd-4d06-a22c-7958e4a78e19", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNES5BDII8F", "external_references": [], "pubs_using": [], "publications_of_set": [], "number_of_experiments": 4, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBS8A4V1B2/", "embedded_path": "experiments_in_set.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."}}}, {"parent": "/biosamples/4DNBSSWGVKEQ/", "embedded_path": "experiments_in_set.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."}}}, {"parent": "/biosamples/4DNBS4Z97V85/", "embedded_path": "experiments_in_set.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."}}}, {"parent": "/biosamples/4DNBS2N5P2DR/", "embedded_path": "experiments_in_set.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": []}