{"lab": {"status": "current", "@id": "/labs/wei-xie-lab/", "title": "Wei Xie, TSINGHUA", "@type": ["Lab", "Item"], "display_title": "Wei Xie, TSINGHUA", "uuid": "8c95312f-afa0-49ee-9d3c-e30849c74e50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8c95312f-afa0-49ee-9d3c-e30849c74e50"]}}, "award": {"@id": "/awards/external-award/", "display_title": "EXTERNAL AWARD", "status": "current", "center": "External", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "description": "Funding source is from outside 4DN.", "project": "External", "name": "external-award", "center_title": "External", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "396bc59b70f45853e3268660734ff3fc", "status": "released", "accession": "4DNFIJFSJMRQ", "file_size": 469249623, "file_type": "contact list-replicate", "description": "This is an output file of the Hi-C processing pipeline", "extra_files": [{"href": "/files-processed/4DNFIJFSJMRQ/@@download/4DNFIJFSJMRQ.pairs.gz.px2", "uuid": "f6c0f995-bbfb-4400-a713-1c40df638d6b", "md5sum": "01a6c56c4eed056f6a800234952b26bc", "status": "released", "filename": "4DNFIJFSJMRQ", "accession": "4DNFIJFSJMRQ", "file_size": 14987193, "upload_key": "f6c0f995-bbfb-4400-a713-1c40df638d6b/4DNFIJFSJMRQ.pairs.gz.px2", "file_format": {"@id": "/file-formats/pairs_px2/", "@type": ["FileFormat", "Item"], "display_title": "pairs_px2", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"@type": ["FileFormat", "Item"], "display_title": "pairs", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "@id": "/file-formats/pairs/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2020-01-24T02:01:39.811915+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-04-06T20:19:21.815941+00:00"}, "public_release": "2020-02-07", "quality_metric": {"@id": "/quality-metrics-pairsqc/630c48ea-0ac0-461e-80b5-6b69f092b740/", "Trans reads": 6004020, "uuid": "630c48ea-0ac0-461e-80b5-6b69f092b740", "Total reads": 30652291, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJFSJMRQ/pairsqc_report.html", "status": "released", "display_title": "QualityMetricPairsqc from 2020-01-24", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Short cis reads (<20kb)": 8194261, "Cis reads (>20kb)": 16454010, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "30652291", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "53.68", "tooltip": "Percent of filtered reads (=16.45m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "26.733", "tooltip": "Percent of filtered reads (=8.19m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "19.588", "tooltip": "Percent of filtered reads (=6.0m)", "numberType": "percent"}]}, "schema_version": "3", "genome_assembly": "GRCm38", "project_release": "2020-02-07", "source_experiments": ["98d0c5d3-7c2e-4125-96a7-9d5d21ca8539"], "file_classification": "processed file", "@id": "/files-processed/4DNFIJFSJMRQ/", "@type": ["FileProcessed", "File", "Item"], "uuid": "f6c0f995-bbfb-4400-a713-1c40df638d6b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIJFSJMRQ.pairs.gz", "external_references": [], "experiments": [{"status": "released", "display_title": "in situ Hi-C on embryo with MboI - 4DNEX9IOW37P", "@id": "/experiments-hi-c/4DNEX9IOW37P/", "uuid": "98d0c5d3-7c2e-4125-96a7-9d5d21ca8539", "accession": "4DNEX9IOW37P", "@type": ["ExperimentHiC", "Experiment", "Item"], "experiment_sets": [{"display_title": "4DNES7RYT7KA", "experimentset_type": "replicate", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "status": "released", "uuid": "33c55e29-e8d1-47c1-ae33-70c1e25eee26", "accession": "4DNES7RYT7KA", "@id": "/experiment-set-replicates/4DNES7RYT7KA/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosample": {"@id": "/biosamples/4DNBSU8A6PWM/", "display_title": "4DNBSU8A6PWM", "@type": ["Biosample", "Item"], "status": "released", "treatments_summary": "Alpha-amanitin treatment (100.0 \u03bcg/mL)", "modifications_summary": "None", "uuid": "a32e7088-3a66-4398-82c9-e768c1dce7c9", "biosource_summary": "embryo", "accession": "4DNBSU8A6PWM", "biosource": [{"@id": "/biosources/4DNSRSCRXOCG/", "biosource_type": "tissue", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "status": "released", "uuid": "d99e6d57-2418-4a01-9784-f102e72c579c", "display_title": "embryo - 4DNSRSCRXOCG", "individual": {"@id": "/individuals-mouse/4DNINNKVDPKM/", "display_title": "4DNINNKVDPKM", "@type": ["IndividualMouse", "Individual", "Item"], "uuid": "15556aef-771d-4338-9ed9-6cc0be87a0ea", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"term_name": "embryo", "term_id": "UBERON:0000922", "display_title": "embryo", "preferred_name": "embryo", "@id": "/ontology-terms/UBERON:0000922/", "status": "released", "uuid": "94a7d7e3-b38e-462a-91e6-55df4a2c120f", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"display_title": "M. musculus", "scientific_name": "Mus musculus", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "name": "mouse", "status": "released", "@id": "/organisms/10090/", "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_type": {"@id": "/experiment-types/in-situ-hi-c/", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "title": "in situ Hi-C", "status": "released", "@type": ["ExperimentType", "Item"], "display_title": "in situ Hi-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"name": "MboI", "display_title": "MboI", "@type": ["Enzyme", "Item"], "@id": "/enzymes/MboI/", "uuid": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-07-19T12:44:51.265125+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "file_type_detailed": "contact list-replicate (pairs)", "track_and_facet_info": {"experimental_lab": "Wei Xie, TSINGHUA", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "MboI", "dataset": "sisHi-C of early embryos in vitro", "condition": "In vitro for 45 h with alpha-amanitin (100 \u03bcg/ml)", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "embryo", "lab_name": "Wei Xie, TSINGHUA"}, "title": "4DNFIJFSJMRQ", "href": "/files-processed/4DNFIJFSJMRQ/@@download/4DNFIJFSJMRQ.pairs.gz", "upload_key": "f6c0f995-bbfb-4400-a713-1c40df638d6b/4DNFIJFSJMRQ.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f6c0f995-bbfb-4400-a713-1c40df638d6b/4DNFIJFSJMRQ.pairs.gz", "tsv_notes": "", "workflow_run_inputs": [{"uuid": "aa38e013-e02d-4eb4-bca0-c3f11246d212", "display_title": "pairsqc-single 0.2.6 run 2020-01-24 08:01:10.819925", "@id": "/workflow-runs-awsem/aa38e013-e02d-4eb4-bca0-c3f11246d212/", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "status": "released", "output_files": [{"workflow_argument_name": "report", "value_qc": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJFSJMRQ/pairsqc_report.html", "overall_quality_status": "PASS", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "display_title": "QualityMetricPairsqc from 2020-01-24", "uuid": "630c48ea-0ac0-461e-80b5-6b69f092b740", "status": "released", "@id": "/quality-metrics-pairsqc/630c48ea-0ac0-461e-80b5-6b69f092b740/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "chromsizes", "value": {"uuid": "bd0784a5-2a3d-42f0-ba9c-d9b3dc0539c6", "@id": "/files-reference/4DNFI3UBJ3HZ/", "filename": "mm10.mainonly.chrom.sizes", "@type": ["FileReference", "File", "Item"], "display_title": "4DNFI3UBJ3HZ.chrom.sizes", "accession": "4DNFI3UBJ3HZ", "status": "released", "file_format": {"@id": "/file-formats/chromsizes/", "status": "released", "file_format": "chromsizes", "display_title": "chromsizes", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "@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": {"uuid": "f6c0f995-bbfb-4400-a713-1c40df638d6b", "@id": "/files-processed/4DNFIJFSJMRQ/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIJFSJMRQ.pairs.gz", "accession": "4DNFIJFSJMRQ", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"title": "PairsQC 0.2.6", "uuid": "b8c533e0-f8c0-4510-b4a1-ac35158e27c3", "@id": "/workflows/4DNWFHB26CID/", "@type": ["Workflow", "Item"], "display_title": "PairsQC 0.2.6 - 4DNWFHB26CID", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "d5caff18-3407-4785-92aa-d84a2175104c", "display_title": "hi-c-processing-pairs 0.2.7 run 2020-01-24 09:01:24.463108", "@id": "/workflow-runs-awsem/d5caff18-3407-4785-92aa-d84a2175104c/", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "status": "released", "output_files": [{"workflow_argument_name": "merged_pairs", "value": {"@id": "/files-processed/4DNFIHQVAYDM/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "display_title": "4DNFIHQVAYDM.pairs.gz", "uuid": "d0b771c5-1e0e-4d88-9942-4f042293700b", "accession": "4DNFIHQVAYDM", "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/", "status": "released", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "hic", "value": {"@id": "/files-processed/4DNFIMOCN1YS/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "display_title": "4DNFIMOCN1YS.hic", "uuid": "3e80ca41-b3e0-4f4f-a05e-8f95fe96d938", "accession": "4DNFIMOCN1YS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "hic", "@type": ["FileFormat", "Item"], "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "@id": "/file-formats/hic/", "status": "released", "display_title": "hic", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "mcool", "value": {"@id": "/files-processed/4DNFIDIZMP9E/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "display_title": "4DNFIDIZMP9E.mcool", "uuid": "8bd5b180-2c88-4b72-a830-5137647ccbbb", "accession": "4DNFIDIZMP9E", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "mcool", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "@id": "/file-formats/mcool/", "status": "released", "display_title": "mcool", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "input_files": [{"workflow_argument_name": "chromsizes", "value": {"uuid": "bd0784a5-2a3d-42f0-ba9c-d9b3dc0539c6", "@id": "/files-reference/4DNFI3UBJ3HZ/", "filename": "mm10.mainonly.chrom.sizes", "@type": ["FileReference", "File", "Item"], "display_title": "4DNFI3UBJ3HZ.chrom.sizes", "accession": "4DNFI3UBJ3HZ", "status": "released", "file_format": {"@id": "/file-formats/chromsizes/", "status": "released", "file_format": "chromsizes", "display_title": "chromsizes", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "@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": {"uuid": "11dc1ace-001a-411f-bedc-b337cd667568", "@id": "/files-processed/4DNFIK5JY283/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIK5JY283.pairs.gz", "accession": "4DNFIK5JY283", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@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": {"uuid": "f6c0f995-bbfb-4400-a713-1c40df638d6b", "@id": "/files-processed/4DNFIJFSJMRQ/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIJFSJMRQ.pairs.gz", "accession": "4DNFIJFSJMRQ", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@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": {"uuid": "cb3c293b-b5fe-4f47-9373-a29399ea1edc", "@id": "/files-reference/4DNFIONK4G14/", "filename": "mm10_MboI.txt", "@type": ["FileReference", "File", "Item"], "display_title": "4DNFIONK4G14.txt", "accession": "4DNFIONK4G14", "status": "released", "file_format": {"@id": "/file-formats/juicer_format_restriction_site_file/", "status": "released", "file_format": "juicer_format_restriction_site_file", "display_title": "juicer_format_restriction_site_file", "uuid": "d13d06cf-218e-4f61-55f0-94f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"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/", "@type": ["Workflow", "Item"], "display_title": "Generation of multiresolution Hi-C contact matrices from a set of contact lists 0.2.7 - 4DNWF2YBHXQM", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [{"display_title": "hi-c-processing-bam 0.2.6 run 2020-01-24 02:01:41.794220", "@id": "/workflow-runs-awsem/2130ba47-02ad-4c56-aba7-40b89d049a90/", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "2130ba47-02ad-4c56-aba7-40b89d049a90", "input_files": [{"workflow_argument_name": "chromsize", "value": {"@id": "/files-reference/4DNFI3UBJ3HZ/", "accession": "4DNFI3UBJ3HZ", "display_title": "4DNFI3UBJ3HZ.chrom.sizes", "uuid": "bd0784a5-2a3d-42f0-ba9c-d9b3dc0539c6", "@type": ["FileReference", "File", "Item"], "filename": "mm10.mainonly.chrom.sizes", "status": "released", "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/chromsizes/", "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_bams", "value": {"@id": "/files-processed/4DNFIOVHV38Z/", "accession": "4DNFIOVHV38Z", "display_title": "4DNFIOVHV38Z.bam", "uuid": "02d05e3d-7561-4f1d-8390-c0d630117ebd", "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "file_format": "bam", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "output_files": [{"workflow_argument_name": "annotated_bam", "value": {"accession": "4DNFIQIDEBXC", "@type": ["FileProcessed", "File", "Item"], "status": "released", "uuid": "5bfd016d-0e91-42f0-916d-d003f5c74932", "display_title": "4DNFIQIDEBXC.bam", "@id": "/files-processed/4DNFIQIDEBXC/", "file_format": {"file_format": "bam", "status": "released", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "filtered_pairs", "value": {"accession": "4DNFIJFSJMRQ", "@type": ["FileProcessed", "File", "Item"], "status": "released", "uuid": "f6c0f995-bbfb-4400-a713-1c40df638d6b", "display_title": "4DNFIJFSJMRQ.pairs.gz", "@id": "/files-processed/4DNFIJFSJMRQ/", "file_format": {"file_format": "pairs", "status": "released", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"status": "released", "@type": ["Workflow", "Item"], "uuid": "023bfb3e-9a8b-42b9-a9d4-216079526f68", "display_title": "Hi-C Post-alignment Processing 0.2.6 - 4DNWFT69RBY4", "@id": "/workflows/4DNWFT69RBY4/", "title": "Hi-C Post-alignment Processing 0.2.6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_sets": [], "pairsqc_table": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJFSJMRQ/4DNFIJFSJMRQ.plot_table.out", "source_experiment_sets": [{"display_title": "4DNES7RYT7KA", "status": "released", "uuid": "33c55e29-e8d1-47c1-ae33-70c1e25eee26", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNES7RYT7KA/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-hi-c/4DNEX9IOW37P/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2024-07-19T12:44:51.265125+00:00"}}, {"parent": "/files-processed/4DNFIJFSJMRQ/", "embedded_path": "last_modified", "item": {"date_modified": "2021-04-06T20:19:21.815941+00:00"}}]}, "validation-errors": []}