{"lab": {"@id": "/labs/job-dekker-lab/", "title": "Job Dekker, UMMS", "display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "correspondence": [{"contact_email": "am9iLmRla2tlckB1bWFzc21lZC5lZHU=", "@id": "/users/83b5073a-069b-4162-9b30-6f42d5551e34/", "display_title": "Job Dekker"}], "status": "current", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "award": {"description": "Funding source is from outside 4DN.", "center": "External", "name": "external-award", "@id": "/awards/external-award/", "project": "External", "status": "current", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "center_title": "External", "@type": ["Award", "Item"], "display_title": "EXTERNAL AWARD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"display_title": "4DNFIPWGY2QZ.fastq.gz", "href": "/files-fastq/4DNFIPWGY2QZ/@@download/4DNFIPWGY2QZ.fastq.gz", "@type": ["FileFastq", "File", "Item"], "upload_key": "ba0ed2c6-7044-4fbd-8c08-d32129b11391/4DNFIPWGY2QZ.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "dbxrefs": ["SRA:SRR5939668"], "@id": "/files-fastq/4DNFIPWGY2QZ/", "accession": "4DNFIPWGY2QZ", "file_classification": "raw file", "uuid": "ba0ed2c6-7044-4fbd-8c08-d32129b11391", "paired_end": "1", "file_size": 3083033913, "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIPWGY2QZ/fastqc_report.html", "display_title": "QualityMetricFastqc from 2018-11-17", "uuid": "44082751-c026-4f87-b650-eeb434b86009", "overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/44082751-c026-4f87-b650-eeb434b86009/", "status": "released", "Total Sequences": 112184407, "Sequence length": "50", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "paired_end": "2", "accession": "4DNFIDSE8S1F", "uuid": "9a4aeb6a-84ee-47c6-9de0-ecf3f07c73e1", "@id": "/files-fastq/4DNFIDSE8S1F/", "status": "released", "display_title": "4DNFIDSE8S1F.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [{"ref": "SRA:SRR5939668", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5939668"}]}, {"display_title": "4DNFIDSE8S1F.fastq.gz", "href": "/files-fastq/4DNFIDSE8S1F/@@download/4DNFIDSE8S1F.fastq.gz", "@type": ["FileFastq", "File", "Item"], "upload_key": "9a4aeb6a-84ee-47c6-9de0-ecf3f07c73e1/4DNFIDSE8S1F.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "dbxrefs": ["SRA:SRR5939668"], "@id": "/files-fastq/4DNFIDSE8S1F/", "accession": "4DNFIDSE8S1F", "file_classification": "raw file", "uuid": "9a4aeb6a-84ee-47c6-9de0-ecf3f07c73e1", "paired_end": "2", "file_size": 3038491675, "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIDSE8S1F/fastqc_report.html", "display_title": "QualityMetricFastqc from 2018-11-17", "uuid": "e0923ce4-1011-4e3a-aae8-cda7298aaa27", "overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/e0923ce4-1011-4e3a-aae8-cda7298aaa27/", "status": "released", "Total Sequences": 112184407, "Sequence length": "50", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "paired_end": "1", "accession": "4DNFIPWGY2QZ", "uuid": "ba0ed2c6-7044-4fbd-8c08-d32129b11391", "@id": "/files-fastq/4DNFIPWGY2QZ/", "status": "released", "display_title": "4DNFIPWGY2QZ.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [{"ref": "SRA:SRR5939668", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5939668"}]}], "status": "released", "aliases": ["4dn-dcic-lab:GSM2745880"], "dbxrefs": ["GEO:GSM2745880"], "protocol": {"status": "released", "@type": ["Protocol", "Item"], "@id": "/protocols/e89ce7e7-92ba-4af4-b910-74b269c0e845/", "uuid": "e89ce7e7-92ba-4af4-b910-74b269c0e845", "display_title": "GSE102740_hic_protocol.pdf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEXBJKTWVH", "biosample": {"accession": "4DNBSAVIGK2P", "status": "released", "biosample_type": "immortalized cells", "treatments_summary": "1NM-PP1 treatment (2.0 \u03bcM, 13.0h) and Auxin treatment (125 \u03bcM)", "modifications_summary": "None", "@type": ["Biosample", "Item"], "biosource_summary": "DT40 with random integration of GFP and AID-tagged CAP-H2 gene, NCAPH2 disruption, random integration of X. laevis Cdk1, CDK1 disruption", "uuid": "72baf521-3862-4865-917f-92f4b05e5b13", "display_title": "4DNBSAVIGK2P", "@id": "/biosamples/4DNBSAVIGK2P/", "biosource": [{"lab": {"display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "award": {"uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@id": "/awards/external-award/", "status": "current", "display_title": "EXTERNAL AWARD", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"@type": ["OntologyTerm", "Item"], "uuid": "1bfd1088-3311-4711-8c41-83dbed3db972", "term_name": "bursa of Fabricius", "@id": "/ontology-terms/UBERON:0003903/", "display_title": "bursa of Fabricius", "slim_terms": [{"status": "released", "@id": "/ontology-terms/UBERON:0001007/", "display_title": "digestive system", "@type": ["OntologyTerm", "Item"], "uuid": "111129bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/ontology-terms/UBERON:0000926/", "display_title": "mesoderm", "@type": ["OntologyTerm", "Item"], "uuid": "111120bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "preferred_name": "bursa of Fabricius", "term_id": "UBERON:0003903", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["4dn-dcic-lab:DT40-CAP-H2-AID-GFP-Cdk1as"], "accession": "4DNSRHKEBVUK", "cell_line": {"uuid": "fd057734-0765-4007-b7eb-d71ac7cbef65", "term_name": "DT40", "slim_terms": [{"status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "term_id": "EFO:0006274", "@id": "/ontology-terms/EFO:0006274/", "preferred_name": "DT40", "display_title": "DT40", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@type": ["IndividualChicken", "Individual", "Item"], "status": "released", "uuid": "836856fd-a0f7-4daf-afb2-4a098df8e8fc", "display_title": "4DNINYWTTO3D", "@id": "/individuals-chicken/4DNINYWTTO3D/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "CAPH2-AID expressing chicken cell line, expressing Cdk1as, a mutant sensitive to inhibition by 1NM-PP4", "date_created": "2018-10-30T15:04:16.841575+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-10-11T22:24:13.349426+00:00"}, "modifications": [{"uuid": "5384182d-cedf-45c8-a97b-35262bfc7615", "display_title": "random integration of GFP and AID-tagged CAP-H2 gene", "status": "released", "@id": "/modifications/5384182d-cedf-45c8-a97b-35262bfc7615/", "@type": ["Modification", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "0bd91d0a-3494-49e1-b444-5e1c5c03172b", "display_title": "Crispr disruption for NCAPH2 chicken gene", "status": "released", "@id": "/modifications/0bd91d0a-3494-49e1-b444-5e1c5c03172b/", "@type": ["Modification", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "4dca1ddb-ab74-44f5-ac84-738b0198886d", "display_title": "random integration of X. laevis Cdk1", "status": "released", "@id": "/modifications/4dca1ddb-ab74-44f5-ac84-738b0198886d/", "@type": ["Modification", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "fb27fdf6-4199-4179-8bb0-6101b1404aee", "display_title": "Crispr disruption for CDK1 chicken gene", "status": "released", "@id": "/modifications/fb27fdf6-4199-4179-8bb0-6101b1404aee/", "@type": ["Modification", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosource_type": "immortalized cell line", "cell_line_tier": "Unclassified", "public_release": "2019-10-11", "schema_version": "2", "project_release": "2019-10-11", "@id": "/biosources/4DNSRHKEBVUK/", "@type": ["Biosource", "Item"], "uuid": "0e212fbb-0895-4cbd-b29e-4baead329adc", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "DT40 with random integration of GFP and AID-tagged CAP-H2 gene, NCAPH2 disruption, random integration of X. laevis Cdk1, CDK1 disruption - 4DNSRHKEBVUK", "external_references": [], "biosource_name": "DT40 with random integration of GFP and AID-tagged CAP-H2 gene, NCAPH2 disruption, random integration of X. laevis Cdk1, CDK1 disruption", "biosource_category": ["Other"], "organism": {"@id": "/organisms/9031/", "@type": ["Organism", "Item"], "uuid": "fed8c206-762f-497f-821b-1c8ff7900bd2", "display_title": "G. gallus", "status": "released", "name": "chicken", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "treatments": [{"duration": 13.0, "treatment_type": "Chemical", "chemical": "1NM-PP1", "status": "released", "concentration": 2.0, "@type": ["TreatmentAgent", "Treatment", "Item"], "duration_units": "hour", "uuid": "697bc0a7-d8d3-4991-8e88-fa4953ad8abd", "@id": "/treatments-agent/697bc0a7-d8d3-4991-8e88-fa4953ad8abd/", "description": "Synchronization with 1NM-PP1 fo 13 hours", "concentration_units": "\u03bcM", "display_title": "1NM-PP1 treatment (2.0 \u03bcM, 13.0h)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"treatment_type": "Chemical", "chemical": "Auxin", "status": "released", "concentration": 125, "@type": ["TreatmentAgent", "Treatment", "Item"], "uuid": "75df7ccb-dd0e-4c45-bc39-2b094108fadd", "@id": "/treatments-agent/75df7ccb-dd0e-4c45-bc39-2b094108fadd/", "description": "Auxin treatment to induce degradation of auxin-inducible degron (AID) tagged protein", "concentration_units": "\u03bcM", "display_title": "Auxin treatment (125 \u03bcM)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing Cell Culture Details"], "badge": {"badge_icon": "/static/img/badges/biosample-icon.svg", "@type": ["Badge", "Item"], "display_title": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "badge_classification": "Warning", "warning": "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", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "20160714-15m-R1", "sop_mapping": {"has_sop": "No"}, "date_created": "2018-10-30T15:05:40.586760+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-10-11T20:54:42.902172+00:00"}, "ligation_time": 240.0, "biotin_removed": "Yes", "digestion_time": 960.0, "public_release": "2019-10-11", "schema_version": "2", "tagging_method": "biotin-dCTP", "experiment_type": {"uuid": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "display_title": "Dilution Hi-C", "assay_subclass_short": "Hi-C", "@id": "/experiment-types/dilution-hi-c/", "@type": ["ExperimentType", "Item"], "experiment_category": "Sequencing", "title": "Dilution Hi-C", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/78cfbb04-5bed-44b2-8596-f40a4c1feb83/4DNFICUNNHKL.bam", "upload_key": "78cfbb04-5bed-44b2-8596-f40a4c1feb83/4DNFICUNNHKL.bam", "file_size": 6103590777, "uuid": "78cfbb04-5bed-44b2-8596-f40a4c1feb83", "file_format": {"status": "released", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "file_format": "bam", "@id": "/file-formats/bam/", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFICUNNHKL", "display_title": "4DNFICUNNHKL.bam", "file_classification": "processed file", "href": "/files-processed/4DNFICUNNHKL/@@download/4DNFICUNNHKL.bam", "@id": "/files-processed/4DNFICUNNHKL/", "status": "released", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "alignments (bam)", "file_type": "alignments", "quality_metric": {"display_title": "QualityMetricBamqc from 2020-01-16", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "status": "released", "@id": "/quality-metrics-bamqc/c4e14366-56c2-4dea-8d83-293ac0a7c340/", "uuid": "c4e14366-56c2-4dea-8d83-293ac0a7c340", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Reads", "value": "112184407", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "6.504", "tooltip": "Percent of total reads (=7.3m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "12.678", "tooltip": "Percent of total reads (=14.22m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "50.356", "tooltip": "Percent of total reads (=56.49m)", "numberType": "percent"}, {"title": "Walks", "value": "0.008", "tooltip": "Percent of total reads (=0.01m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.446", "tooltip": "Percent of total reads (=0.5m)", "numberType": "percent"}]}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Dilution Hi-C", "experiment_bucket": "processed file", "assay_info": "HindIII", "dataset": "HiC on sync. CAPH2-AID chicken cells", "condition": "prometaphase (15m), CAPH2-", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "DT40 with random integration of GFP and AID-tagged CAP-H2 gene, NCAPH2 disruption, random integration of X. laevis Cdk1, CDK1 disruption", "lab_name": "4DN DCIC, HMS"}, "external_references": []}, {"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/2ff576b8-cd51-49d9-a611-a3586ebd53f5/4DNFITSRGCJ7.pairs.gz", "upload_key": "2ff576b8-cd51-49d9-a611-a3586ebd53f5/4DNFITSRGCJ7.pairs.gz", "file_size": 404352906, "uuid": "2ff576b8-cd51-49d9-a611-a3586ebd53f5", "file_format": {"status": "released", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "@id": "/file-formats/pairs/", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFITSRGCJ7", "display_title": "4DNFITSRGCJ7.pairs.gz", "file_classification": "processed file", "href": "/files-processed/4DNFITSRGCJ7/@@download/4DNFITSRGCJ7.pairs.gz", "@id": "/files-processed/4DNFITSRGCJ7/", "status": "released", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "contact list-replicate (pairs)", "file_type": "contact list-replicate", "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFITSRGCJ7/pairsqc_report.html", "Total reads": 34164761, "display_title": "QualityMetricPairsqc from 2019-02-11", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "status": "released", "@id": "/quality-metrics-pairsqc/d9e7d521-e0de-4915-9431-08c107501756/", "uuid": "d9e7d521-e0de-4915-9431-08c107501756", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "34164761", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "4.568", "tooltip": "Percent of filtered reads (=1.56m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "92.52", "tooltip": "Percent of filtered reads (=31.61m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "2.912", "tooltip": "Percent of filtered reads (=0.99m)", "numberType": "percent"}]}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Dilution Hi-C", "experiment_bucket": "processed file", "assay_info": "HindIII", "dataset": "HiC on sync. CAPH2-AID chicken cells", "condition": "prometaphase (15m), CAPH2-", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "DT40 with random integration of GFP and AID-tagged CAP-H2 gene, NCAPH2 disruption, random integration of X. laevis Cdk1, CDK1 disruption", "lab_name": "4DN DCIC, HMS"}, "external_references": []}], "project_release": "2019-10-11", "digestion_enzyme": {"name": "HindIII", "display_title": "HindIII", "@type": ["Enzyme", "Item"], "@id": "/enzymes/HindIII/", "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "crosslinking_time": 10.0, "crosslinking_method": "1% Formaldehyde", "fragment_size_range": "150-350", "fragmentation_method": "sonication", "ligation_temperature": 16.0, "digestion_temperature": 37.0, "crosslinking_temperature": 23.0, "library_preparation_date": "2016-06-24", "fragment_size_selection_method": "SPRI beads", "@id": "/experiments-hi-c/4DNEXBJKTWVH/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "ebef21ae-73f5-4f72-ad45-848d46af25b0", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "Dilution Hi-C on DT40 with random integration of GFP and AID-tagged CAP-H2 gene, NCAPH2 disruption, random integration of X. laevis Cdk1, CDK1 disruption with HindIII - 4DNEXBJKTWVH", "external_references": [{"ref": "GEO:GSM2745880", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2745880"}], "experiment_sets": [{"status": "released", "accession": "4DNES6FARLK8", "@id": "/experiment-set-replicates/4DNES6FARLK8/", "uuid": "6f414a9d-baf7-44ae-99d0-e04c0fcd376d", "display_title": "4DNES6FARLK8", "experimentset_type": "replicate", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"status": "current", "short_attribution": "Gibcus JH et al. (2018)", "display_title": "Gibcus JH et al. (2018) PMID:29348367", "@type": ["Publication", "Item"], "authors": ["Gibcus JH", "Samejima K", "Goloborodko A", "Samejima I", "Naumova N", "Nuebler J", "Kanemaki MT", "Xie L", "Paulson JR", "Earnshaw WC", "Mirny LA", "Dekker J"], "@id": "/publications/84fa5633-aac7-4cb3-b53b-0f0234ea06dd/", "uuid": "84fa5633-aac7-4cb3-b53b-0f0234ea06dd", "date_published": "2018-02-09", "title": "A pathway for mitotic chromosome formation.", "journal": "Science (New York, N.Y.)", "abstract": "Mitotic chromosomes fold as compact arrays of chromatin loops. To identify the pathway of mitotic chromosome formation, we combined imaging and Hi-C analysis of synchronous DT40 cell cultures with polymer simulations. Here we show that in prophase, the interphase organization is rapidly lost in a condensin-dependent manner, and arrays of consecutive 60-kilobase (kb) loops are formed. During prometaphase, ~80-kb inner loops are nested within ~400-kb outer loops. The loop  array acquires a helical arrangement with consecutive loops emanating from a central \"spiral staircase\" condensin scaffold. The size of helical turns progressively increases to ~12 megabases during prometaphase. Acute depletion of  condensin I or II shows that nested loops form by differential action of the two  condensins, whereas condensin II is required for helical winding.", "ID": "PMID:29348367", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"date_published": "2018-02-09", "@type": ["Publication", "Item"], "uuid": "84fa5633-aac7-4cb3-b53b-0f0234ea06dd", "ID": "PMID:29348367", "authors": ["Gibcus JH", "Samejima K", "Goloborodko A", "Samejima I", "Naumova N", "Nuebler J", "Kanemaki MT", "Xie L", "Paulson JR", "Earnshaw WC", "Mirny LA", "Dekker J"], "abstract": "Mitotic chromosomes fold as compact arrays of chromatin loops. To identify the pathway of mitotic chromosome formation, we combined imaging and Hi-C analysis of synchronous DT40 cell cultures with polymer simulations. Here we show that in prophase, the interphase organization is rapidly lost in a condensin-dependent manner, and arrays of consecutive 60-kilobase (kb) loops are formed. During prometaphase, ~80-kb inner loops are nested within ~400-kb outer loops. The loop  array acquires a helical arrangement with consecutive loops emanating from a central \"spiral staircase\" condensin scaffold. The size of helical turns progressively increases to ~12 megabases during prometaphase. Acute depletion of  condensin I or II shows that nested loops form by differential action of the two  condensins, whereas condensin II is required for helical winding.", "short_attribution": "Gibcus JH et al. (2018)", "@id": "/publications/84fa5633-aac7-4cb3-b53b-0f0234ea06dd/", "display_title": "Gibcus JH et al. (2018) PMID:29348367", "title": "A pathway for mitotic chromosome formation.", "status": "current", "journal": "Science (New York, N.Y.)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Enzyme", "value": "HindIII", "combined": "Enzyme: HindIII"}, "experiment_summary": "Dilution Hi-C on DT40 with random integration of GFP and AID-tagged CAP-H2 gene, NCAPH2 disruption, random integration of X. laevis Cdk1, CDK1 disruption with HindIII", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSAVIGK2P/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample missing Cell Culture Details"], "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": []}