{"lab": {"status": "current", "title": "Wei Xie, TSINGHUA", "@id": "/labs/wei-xie-lab/", "@type": ["Lab", "Item"], "uuid": "8c95312f-afa0-49ee-9d3c-e30849c74e50", "display_title": "Wei Xie, TSINGHUA", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8c95312f-afa0-49ee-9d3c-e30849c74e50"]}}, "award": {"@type": ["Award", "Item"], "center": "External", "status": "current", "display_title": "EXTERNAL AWARD", "center_title": "External", "description": "Funding source is from outside 4DN.", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "name": "external-award", "project": "External", "@id": "/awards/external-award/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "a80c6289032b42d55ef52fa6cf9619e4", "status": "released", "accession": "4DNFIFLS1BSB", "file_size": 4654568590, "file_type": "contact list-combined", "description": "This is an output file of the Hi-C processing pipeline", "extra_files": [{"href": "/files-processed/4DNFIFLS1BSB/@@download/4DNFIFLS1BSB.pairs.gz.px2", "uuid": "64417803-2951-46c8-abb7-907b5dac9d8d", "md5sum": "9961f5bc163b3d39b2fc7077ab5f3a9a", "status": "released", "filename": "4DNFIFLS1BSB", "accession": "4DNFIFLS1BSB", "file_size": 9243932, "upload_key": "64417803-2951-46c8-abb7-907b5dac9d8d/4DNFIFLS1BSB.pairs.gz.px2", "file_format": {"display_title": "pairs_px2", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs_px2/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"file_format": "pairs", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "display_title": "pairs", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2020-01-24T21:01:55.313815+00:00", "notes_to_tsv": ["WARNING: some distinct reads in this file may share the same identifier because the file was generated after merging fastq files with integer identifiers (eg. @1, @2) during processing."], "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-04-06T20:18:51.644854+00:00"}, "public_release": "2020-02-07", "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIFLS1BSB/pairsqc_report.html", "Short cis reads (<20kb)": 77376888, "@id": "/quality-metrics-pairsqc/949f74d7-1e43-4046-a97f-19f3e9f137d4/", "Total reads": 274689100, "Trans reads": 68396455, "uuid": "949f74d7-1e43-4046-a97f-19f3e9f137d4", "display_title": "QualityMetricPairsqc from 2020-01-25", "Cis reads (>20kb)": 128915757, "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "status": "released", "quality_metric_summary": [{"title": "Filtered Reads", "value": "274689100", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "46.932", "tooltip": "Percent of filtered reads (=128.92m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "28.169", "tooltip": "Percent of filtered reads (=77.38m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "24.9", "tooltip": "Percent of filtered reads (=68.4m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "3", "static_headers": [], "genome_assembly": "GRCm38", "project_release": "2020-02-07", "source_experiments": ["adff3ed9-5d76-42f1-afbe-0f22cb43c300", "9feab756-9dc5-40e9-a96a-ae48dc2721aa", "c53c4771-5da6-42e1-b838-9cce28145c98", "32c919ae-957b-448c-8b8c-f47f6009e234"], "file_classification": "processed file", "@id": "/files-processed/4DNFIFLS1BSB/", "@type": ["FileProcessed", "File", "Item"], "uuid": "64417803-2951-46c8-abb7-907b5dac9d8d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIFLS1BSB.pairs.gz", "external_references": [], "experiments": [], "file_type_detailed": "contact list-combined (pairs)", "track_and_facet_info": {"dataset": "sisHi-C during early embryonic development", "condition": "Late 2-cell embryos", "experimental_lab": "Wei Xie, TSINGHUA", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "MboI", "biosource_name": "Late 2-cell stage embryo", "lab_name": "Wei Xie, TSINGHUA"}, "title": "4DNFIFLS1BSB", "href": "/files-processed/4DNFIFLS1BSB/@@download/4DNFIFLS1BSB.pairs.gz", "upload_key": "64417803-2951-46c8-abb7-907b5dac9d8d/4DNFIFLS1BSB.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/64417803-2951-46c8-abb7-907b5dac9d8d/4DNFIFLS1BSB.pairs.gz", "tsv_notes": "WARNING: some distinct reads in this file may share the same identifier because the file was generated after merging fastq files with integer identifiers (eg. @1, @2) during processing.", "workflow_run_inputs": [{"display_title": "pairsqc-single 0.2.6 run 2020-01-25 05:01:13.235057", "uuid": "cebc6591-6d2c-4220-9619-eacd1c325a4d", "@id": "/workflow-runs-awsem/cebc6591-6d2c-4220-9619-eacd1c325a4d/", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "input_files": [{"workflow_argument_name": "chromsizes", "value": {"filename": "mm10.mainonly.chrom.sizes", "@type": ["FileReference", "File", "Item"], "status": "released", "uuid": "bd0784a5-2a3d-42f0-ba9c-d9b3dc0539c6", "display_title": "4DNFI3UBJ3HZ.chrom.sizes", "@id": "/files-reference/4DNFI3UBJ3HZ/", "accession": "4DNFI3UBJ3HZ", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/chromsizes/", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "file_format": "chromsizes", "display_title": "chromsizes", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"@type": ["FileProcessed", "File", "Item"], "status": "released", "uuid": "64417803-2951-46c8-abb7-907b5dac9d8d", "display_title": "4DNFIFLS1BSB.pairs.gz", "@id": "/files-processed/4DNFIFLS1BSB/", "accession": "4DNFIFLS1BSB", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "output_files": [{"workflow_argument_name": "report", "value_qc": {"display_title": "QualityMetricPairsqc from 2020-01-25", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIFLS1BSB/pairsqc_report.html", "uuid": "949f74d7-1e43-4046-a97f-19f3e9f137d4", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "@id": "/quality-metrics-pairsqc/949f74d7-1e43-4046-a97f-19f3e9f137d4/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"status": "released", "@id": "/workflows/4DNWFHB26CID/", "uuid": "b8c533e0-f8c0-4510-b4a1-ac35158e27c3", "display_title": "PairsQC 0.2.6 - 4DNWFHB26CID", "@type": ["Workflow", "Item"], "title": "PairsQC 0.2.6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [{"status": "released", "display_title": "hi-c-processing-pairs 0.2.7 run 2020-01-24 21:01:57.787374", "uuid": "2a95e024-a446-4ba4-a2ec-32e4d027ebda", "@id": "/workflow-runs-awsem/2a95e024-a446-4ba4-a2ec-32e4d027ebda/", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "workflow": {"@type": ["Workflow", "Item"], "status": "released", "title": "Generation of multiresolution Hi-C contact matrices from a set of contact lists 0.2.7", "uuid": "23bd6d73-4190-496d-837c-21bcdb3802ed", "@id": "/workflows/4DNWF2YBHXQM/", "display_title": "Generation of multiresolution Hi-C contact matrices from a set of contact lists 0.2.7 - 4DNWF2YBHXQM", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "merged_pairs", "value": {"uuid": "64417803-2951-46c8-abb7-907b5dac9d8d", "status": "released", "@id": "/files-processed/4DNFIFLS1BSB/", "accession": "4DNFIFLS1BSB", "display_title": "4DNFIFLS1BSB.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "file_format": {"display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "file_format": "pairs", "status": "released", "@id": "/file-formats/pairs/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "hic", "value": {"uuid": "cc2b78fd-52d4-4e0c-ac93-b84ee82daf7e", "status": "released", "@id": "/files-processed/4DNFICXCFGEI/", "accession": "4DNFICXCFGEI", "display_title": "4DNFICXCFGEI.hic", "@type": ["FileProcessed", "File", "Item"], "file_format": {"display_title": "hic", "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "@type": ["FileFormat", "Item"], "file_format": "hic", "status": "released", "@id": "/file-formats/hic/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "mcool", "value": {"uuid": "c04ceae2-51ac-4f7c-a7a1-1d401486e445", "status": "released", "@id": "/files-processed/4DNFIIWW8LIF/", "accession": "4DNFIIWW8LIF", "display_title": "4DNFIIWW8LIF.mcool", "@type": ["FileProcessed", "File", "Item"], "file_format": {"display_title": "mcool", "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "@type": ["FileFormat", "Item"], "file_format": "mcool", "status": "released", "@id": "/file-formats/mcool/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "chromsizes", "value": {"accession": "4DNFI3UBJ3HZ", "@type": ["FileReference", "File", "Item"], "uuid": "bd0784a5-2a3d-42f0-ba9c-d9b3dc0539c6", "display_title": "4DNFI3UBJ3HZ.chrom.sizes", "filename": "mm10.mainonly.chrom.sizes", "@id": "/files-reference/4DNFI3UBJ3HZ/", "status": "released", "file_format": {"@id": "/file-formats/chromsizes/", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "display_title": "chromsizes", "status": "released", "file_format": "chromsizes", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"accession": "4DNFIPLGJJ91", "@type": ["FileProcessed", "File", "Item"], "uuid": "49ad7ee9-4933-4bb1-8edd-49006401f6d2", "display_title": "4DNFIPLGJJ91.pairs.gz", "@id": "/files-processed/4DNFIPLGJJ91/", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "pairs", "status": "released", "file_format": "pairs", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"accession": "4DNFI1JB7E6J", "@type": ["FileProcessed", "File", "Item"], "uuid": "4af9078e-e256-4c42-986b-f938e34bc711", "display_title": "4DNFI1JB7E6J.pairs.gz", "@id": "/files-processed/4DNFI1JB7E6J/", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "pairs", "status": "released", "file_format": "pairs", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"accession": "4DNFIU7DL977", "@type": ["FileProcessed", "File", "Item"], "uuid": "670423d8-0688-4389-9761-52f99ab769eb", "display_title": "4DNFIU7DL977.pairs.gz", "@id": "/files-processed/4DNFIU7DL977/", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "pairs", "status": "released", "file_format": "pairs", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"accession": "4DNFILEFNUZY", "@type": ["FileProcessed", "File", "Item"], "uuid": "6f63acdf-5055-40f0-a657-741bc9925dad", "display_title": "4DNFILEFNUZY.pairs.gz", "@id": "/files-processed/4DNFILEFNUZY/", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "pairs", "status": "released", "file_format": "pairs", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "restriction_file", "value": {"accession": "4DNFIONK4G14", "@type": ["FileReference", "File", "Item"], "uuid": "cb3c293b-b5fe-4f47-9373-a29399ea1edc", "display_title": "4DNFIONK4G14.txt", "filename": "mm10_MboI.txt", "@id": "/files-reference/4DNFIONK4G14/", "status": "released", "file_format": {"@id": "/file-formats/juicer_format_restriction_site_file/", "uuid": "d13d06cf-218e-4f61-55f0-94f226248b2c", "display_title": "juicer_format_restriction_site_file", "status": "released", "file_format": "juicer_format_restriction_site_file", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_sets": [{"uuid": "483d941f-bcd9-4fef-a7e0-9d3e2f1c215d", "status": "released", "@id": "/experiment-set-replicates/4DNESXZHIUAU/", "accession": "4DNESXZHIUAU", "display_title": "4DNESXZHIUAU", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "last_modified": {"date_modified": "2024-07-31T14:46:36.036878+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "pairsqc_table": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIFLS1BSB/4DNFIFLS1BSB.plot_table.out", "source_experiment_sets": [{"@id": "/experiment-set-replicates/4DNESXZHIUAU/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "483d941f-bcd9-4fef-a7e0-9d3e2f1c215d", "status": "released", "display_title": "4DNESXZHIUAU", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiment-set-replicates/4DNESXZHIUAU/", "embedded_path": "experiment_sets.last_modified", "item": {"date_modified": "2024-07-31T14:46:36.036878+00:00"}}, {"parent": "/files-processed/4DNFIFLS1BSB/", "embedded_path": "last_modified", "item": {"date_modified": "2021-04-06T20:18:51.644854+00:00"}}]}, "validation-errors": []}