{"lab": {"status": "current", "display_title": "Wei Xie, TSINGHUA", "@id": "/labs/wei-xie-lab/", "@type": ["Lab", "Item"], "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": {"uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "center_title": "External", "name": "external-award", "@id": "/awards/external-award/", "status": "current", "center": "External", "@type": ["Award", "Item"], "project": "External", "description": "Funding source is from outside 4DN.", "display_title": "EXTERNAL AWARD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "b384910136776f15325afcd6b60dbebd", "status": "released", "accession": "4DNFISBS6K1G", "file_size": 72186348478, "file_type": "alignments", "description": "This is an output file of the Hi-C processing pipeline", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "status": "released", "@id": "/file-formats/bam/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2020-01-24T05:01:32.825117+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-02-16T13:43:13.226608+00:00"}, "public_release": "2020-02-07", "quality_metric": {"status": "released", "@id": "/quality-metrics-bamqc/7d12649c-d90c-490d-9ce1-344c292bf432/", "display_title": "QualityMetricBamqc from 2020-01-24", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "uuid": "7d12649c-d90c-490d-9ce1-344c292bf432", "quality_metric_summary": [{"title": "Total Reads", "value": "277845449", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "10.911", "tooltip": "Percent of total reads (=30.32m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "8.875", "tooltip": "Percent of total reads (=24.66m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "30.318", "tooltip": "Percent of total reads (=84.24m)", "numberType": "percent"}, {"title": "Walks", "value": "24.315", "tooltip": "Percent of total reads (=67.56m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.098", "tooltip": "Percent of total reads (=0.27m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "3", "genome_assembly": "GRCm38", "project_release": "2020-02-07", "source_experiments": ["77f1fc7a-2447-475c-982a-6361d72393ae"], "file_classification": "processed file", "percent_clipped_sites_with_re_motif": 79.4, "@id": "/files-processed/4DNFISBS6K1G/", "@type": ["FileProcessed", "File", "Item"], "uuid": "8fc2570b-462d-43f6-931d-74173d85ada3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFISBS6K1G.bam", "external_references": [], "experiments": [{"uuid": "77f1fc7a-2447-475c-982a-6361d72393ae", "status": "released", "@id": "/experiments-hi-c/4DNEXUMDIVVM/", "@type": ["ExperimentHiC", "Experiment", "Item"], "display_title": "in situ Hi-C on inner cell mass with MboI - 4DNEXUMDIVVM", "accession": "4DNEXUMDIVVM", "experiment_type": {"title": "in situ Hi-C", "@type": ["ExperimentType", "Item"], "status": "released", "display_title": "in situ Hi-C", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "@id": "/experiment-types/in-situ-hi-c/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "biosample": {"uuid": "de915e85-fcab-44a7-9430-e46e211f3d01", "status": "released", "display_title": "4DNBS26PRJMB", "treatments_summary": "None", "accession": "4DNBS26PRJMB", "@type": ["Biosample", "Item"], "biosource_summary": "inner cell mass", "@id": "/biosamples/4DNBS26PRJMB/", "modifications_summary": "None", "biosource": [{"biosource_type": "tissue", "@id": "/biosources/4DNSR6EL5DE2/", "display_title": "inner cell mass - 4DNSR6EL5DE2", "uuid": "07b93f25-1a9b-4e0f-82de-de79e85ce37c", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "status": "released", "tissue": {"term_id": "UBERON:0000087", "@type": ["OntologyTerm", "Item"], "term_name": "inner cell mass", "@id": "/ontology-terms/UBERON:0000087/", "display_title": "inner cell mass", "status": "released", "preferred_name": "inner cell mass", "uuid": "c9a533f1-f116-4af8-8a54-783e89b06448", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@type": ["Organism", "Item"], "status": "released", "name": "mouse", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "scientific_name": "Mus musculus", "@id": "/organisms/10090/", "display_title": "M. musculus", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"uuid": "15556aef-771d-4338-9ed9-6cc0be87a0ea", "display_title": "4DNINNKVDPKM", "@id": "/individuals-mouse/4DNINNKVDPKM/", "status": "released", "@type": ["IndividualMouse", "Individual", "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": [{"@id": "/experiment-set-replicates/4DNESSL62JQK/", "status": "released", "uuid": "b2e52b63-4fdc-4ff6-99e9-239828da5e05", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "accession": "4DNESSL62JQK", "display_title": "4DNESSL62JQK", "experimentset_type": "replicate", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "digestion_enzyme": {"@id": "/enzymes/MboI/", "display_title": "MboI", "@type": ["Enzyme", "Item"], "name": "MboI", "status": "released", "uuid": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2024-07-19T12:45:05.942096+00:00"}}], "file_type_detailed": "alignments (bam)", "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 during early embryonic development", "condition": "ICM", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "inner cell mass", "lab_name": "Wei Xie, TSINGHUA"}, "title": "4DNFISBS6K1G", "href": "/files-processed/4DNFISBS6K1G/@@download/4DNFISBS6K1G.bam", "upload_key": "8fc2570b-462d-43f6-931d-74173d85ada3/4DNFISBS6K1G.bam", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8fc2570b-462d-43f6-931d-74173d85ada3/4DNFISBS6K1G.bam", "tsv_notes": "", "workflow_run_inputs": [{"display_title": "bamqc v3 run 2020-01-24 18:00:55.536934", "uuid": "69304793-55ad-4dd7-84ca-d904d2a0a40c", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/69304793-55ad-4dd7-84ca-d904d2a0a40c/", "input_files": [{"workflow_argument_name": "bamfile", "value": {"@type": ["FileProcessed", "File", "Item"], "accession": "4DNFISBS6K1G", "display_title": "4DNFISBS6K1G.bam", "uuid": "8fc2570b-462d-43f6-931d-74173d85ada3", "@id": "/files-processed/4DNFISBS6K1G/", "status": "released", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "file_format": "bam", "status": "released", "@id": "/file-formats/bam/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chromsizes", "value": {"@type": ["FileReference", "File", "Item"], "accession": "4DNFI3UBJ3HZ", "display_title": "4DNFI3UBJ3HZ.chrom.sizes", "uuid": "bd0784a5-2a3d-42f0-ba9c-d9b3dc0539c6", "filename": "mm10.mainonly.chrom.sizes", "@id": "/files-reference/4DNFI3UBJ3HZ/", "status": "released", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "chromsizes", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "file_format": "chromsizes", "status": "released", "@id": "/file-formats/chromsizes/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "output_files": [{"workflow_argument_name": "bam_qc", "value_qc": {"@id": "/quality-metrics-bamqc/7d12649c-d90c-490d-9ce1-344c292bf432/", "overall_quality_status": "PASS", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "status": "released", "display_title": "QualityMetricBamqc from 2020-01-24", "uuid": "7d12649c-d90c-490d-9ce1-344c292bf432", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"title": "Quality metrics for annotated bam files", "@id": "/workflows/4DNWFBAMQCV3/", "uuid": "42683ab1-59bf-4ec5-a973-030053a134f1", "display_title": "Quality metrics for annotated bam files - 4DNWFBAMQCV3", "@type": ["Workflow", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "re_checker_workflow v1.1 run 2020-04-23 04:32:38.340035", "uuid": "d6cc7b4c-8c22-4fc1-abcf-708e35fff710", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/d6cc7b4c-8c22-4fc1-abcf-708e35fff710/", "input_files": [{"workflow_argument_name": "bamfile", "value": {"@type": ["FileProcessed", "File", "Item"], "accession": "4DNFISBS6K1G", "display_title": "4DNFISBS6K1G.bam", "uuid": "8fc2570b-462d-43f6-931d-74173d85ada3", "@id": "/files-processed/4DNFISBS6K1G/", "status": "released", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "file_format": "bam", "status": "released", "@id": "/file-formats/bam/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "output_files": [{"workflow_argument_name": "motif_percent"}], "workflow": {"title": "Restriction Enzyme Check, 1.1", "@id": "/workflows/4DNWFA4YPAGI/", "uuid": "e9eefa69-39b1-4e61-8889-5cb1cea401c0", "display_title": "Restriction Enzyme Check, 1.1 - 4DNWFA4YPAGI", "@type": ["Workflow", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [{"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "display_title": "hi-c-processing-bam 0.2.6 run 2020-01-24 05:01:34.393924", "@id": "/workflow-runs-awsem/66c628c5-9816-4b7a-b01c-1b872e21c362/", "uuid": "66c628c5-9816-4b7a-b01c-1b872e21c362", "status": "released", "output_files": [{"workflow_argument_name": "annotated_bam", "value": {"status": "released", "uuid": "8fc2570b-462d-43f6-931d-74173d85ada3", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFISBS6K1G.bam", "accession": "4DNFISBS6K1G", "@id": "/files-processed/4DNFISBS6K1G/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "filtered_pairs", "value": {"status": "released", "uuid": "77502185-df5e-41bc-b12b-7fb894797c25", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIS6Q1NMW.pairs.gz", "accession": "4DNFIS6Q1NMW", "@id": "/files-processed/4DNFIS6Q1NMW/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "input_files": [{"workflow_argument_name": "chromsize", "value": {"@type": ["FileReference", "File", "Item"], "accession": "4DNFI3UBJ3HZ", "filename": "mm10.mainonly.chrom.sizes", "@id": "/files-reference/4DNFI3UBJ3HZ/", "uuid": "bd0784a5-2a3d-42f0-ba9c-d9b3dc0539c6", "display_title": "4DNFI3UBJ3HZ.chrom.sizes", "status": "released", "file_format": {"@id": "/file-formats/chromsizes/", "status": "released", "display_title": "chromsizes", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "@type": ["FileFormat", "Item"], "file_format": "chromsizes", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_bams", "value": {"@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIQNWLZFT", "@id": "/files-processed/4DNFIQNWLZFT/", "uuid": "c5f03b56-e253-406b-8927-c9ece87c90e1", "display_title": "4DNFIQNWLZFT.bam", "status": "released", "file_format": {"@id": "/file-formats/bam/", "status": "released", "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@type": ["FileFormat", "Item"], "file_format": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@id": "/workflows/4DNWFT69RBY4/", "status": "released", "@type": ["Workflow", "Item"], "display_title": "Hi-C Post-alignment Processing 0.2.6 - 4DNWFT69RBY4", "title": "Hi-C Post-alignment Processing 0.2.6", "uuid": "023bfb3e-9a8b-42b9-a9d4-216079526f68", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_sets": [], "source_experiment_sets": [{"@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNESSL62JQK", "@id": "/experiment-set-replicates/4DNESSL62JQK/", "status": "released", "uuid": "b2e52b63-4fdc-4ff6-99e9-239828da5e05", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-hi-c/4DNEXUMDIVVM/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2024-07-19T12:45:05.942096+00:00"}}, {"parent": "/files-processed/4DNFISBS6K1G/", "embedded_path": "last_modified", "item": {"date_modified": "2021-02-16T13:43:13.226608+00:00"}}]}, "validation-errors": []}