{"lab": {"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "title": "Job Dekker, UMMS", "status": "current", "correspondence": [{"contact_email": "am9iLmRla2tlckB1bWFzc21lZC5lZHU=", "@id": "/users/83b5073a-069b-4162-9b30-6f42d5551e34/", "display_title": "Job Dekker"}], "display_title": "Job Dekker, UMMS", "@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": {"@id": "/awards/external-award/", "display_title": "EXTERNAL AWARD", "status": "current", "center": "External", "center_title": "External", "project": "External", "description": "Funding source is from outside 4DN.", "name": "external-award", "@type": ["Award", "Item"], "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"display_title": "4DNFI5QXKXEY.fastq.gz", "accession": "4DNFI5QXKXEY", "file_size": 10797775444, "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI5QXKXEY/", "file_type_detailed": "reads (fastq)", "status": "released", "uuid": "7a282909-1e3d-4a12-aec4-6bac57401128", "href": "/files-fastq/4DNFI5QXKXEY/@@download/4DNFI5QXKXEY.fastq.gz", "file_type": "reads", "paired_end": "1", "upload_key": "7a282909-1e3d-4a12-aec4-6bac57401128/4DNFI5QXKXEY.fastq.gz", "dbxrefs": ["SRA:SRR5939671"], "file_classification": "raw file", "quality_metric": {"uuid": "8e5fabbc-e69c-4f30-9c24-df02939d19b9", "overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/8e5fabbc-e69c-4f30-9c24-df02939d19b9/", "Total Sequences": 395704573, "display_title": "QualityMetricFastqc from 2018-11-15", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI5QXKXEY/fastqc_report.html", "Sequence length": "50", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "uuid": "3088511e-e553-498c-a758-7f703c3525ad", "@id": "/files-fastq/4DNFI9ZUN5WD/", "file_type": "reads", "accession": "4DNFI9ZUN5WD", "status": "released", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFI9ZUN5WD.fastq.gz", "file_type_detailed": "reads (fastq)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5939671", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5939671"}]}, {"display_title": "4DNFI9ZUN5WD.fastq.gz", "accession": "4DNFI9ZUN5WD", "file_size": 11496108765, "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI9ZUN5WD/", "file_type_detailed": "reads (fastq)", "status": "released", "uuid": "3088511e-e553-498c-a758-7f703c3525ad", "href": "/files-fastq/4DNFI9ZUN5WD/@@download/4DNFI9ZUN5WD.fastq.gz", "file_type": "reads", "paired_end": "2", "upload_key": "3088511e-e553-498c-a758-7f703c3525ad/4DNFI9ZUN5WD.fastq.gz", "dbxrefs": ["SRA:SRR5939671"], "file_classification": "raw file", "quality_metric": {"uuid": "67b4f930-3db3-4910-ac69-44119f26e247", "overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/67b4f930-3db3-4910-ac69-44119f26e247/", "Total Sequences": 395704573, "display_title": "QualityMetricFastqc from 2018-11-15", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI9ZUN5WD/fastqc_report.html", "Sequence length": "50", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "uuid": "7a282909-1e3d-4a12-aec4-6bac57401128", "@id": "/files-fastq/4DNFI5QXKXEY/", "file_type": "reads", "accession": "4DNFI5QXKXEY", "status": "released", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFI5QXKXEY.fastq.gz", "file_type_detailed": "reads (fastq)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRR5939671", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5939671"}]}], "status": "released", "aliases": ["4dn-dcic-lab:GSM2745883"], "dbxrefs": ["GEO:GSM2745883"], "protocol": {"uuid": "e89ce7e7-92ba-4af4-b910-74b269c0e845", "status": "released", "display_title": "GSE102740_hic_protocol.pdf", "@id": "/protocols/e89ce7e7-92ba-4af4-b910-74b269c0e845/", "@type": ["Protocol", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEXRACVO74", "biosample": {"treatments_summary": "1NM-PP1 treatment (2.0 \u03bcM, 13.0h)", "display_title": "4DNBSEVPB2W1", "accession": "4DNBSEVPB2W1", "@id": "/biosamples/4DNBSEVPB2W1/", "uuid": "17949bb7-e461-4b82-87b7-37138e564de2", "biosource_summary": "DT40 with random integration of GFP and AID-tagged CAP-H gene, random integration of X. laevis Cdk1, CDK1 disruption, random integration of CAP-H gene, CAP-H gene deletion", "@type": ["Biosample", "Item"], "status": "released", "biosample_type": "immortalized cells", "modifications_summary": "None", "biosource": [{"lab": {"status": "current", "display_title": "Job Dekker, UMMS", "@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "award": {"status": "current", "display_title": "EXTERNAL AWARD", "@type": ["Award", "Item"], "@id": "/awards/external-award/", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"display_title": "bursa of Fabricius", "preferred_name": "bursa of Fabricius", "uuid": "1bfd1088-3311-4711-8c41-83dbed3db972", "@type": ["OntologyTerm", "Item"], "term_id": "UBERON:0003903", "status": "released", "slim_terms": [{"status": "released", "display_title": "digestive system", "@type": ["OntologyTerm", "Item"], "uuid": "111129bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0001007/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "mesoderm", "@type": ["OntologyTerm", "Item"], "uuid": "111120bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0000926/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "term_name": "bursa of Fabricius", "@id": "/ontology-terms/UBERON:0003903/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["4dn-dcic-lab:DT40-CAP-H-AID-GFP-Cdk1as"], "accession": "4DNSRYL63MO8", "cell_line": {"status": "released", "display_title": "DT40", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["OntologyTerm", "Item"], "preferred_name": "DT40", "@id": "/ontology-terms/EFO:0006274/", "term_id": "EFO:0006274", "term_name": "DT40", "uuid": "fd057734-0765-4007-b7eb-d71ac7cbef65", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"status": "released", "uuid": "836856fd-a0f7-4daf-afb2-4a098df8e8fc", "@type": ["IndividualChicken", "Individual", "Item"], "@id": "/individuals-chicken/4DNINYWTTO3D/", "display_title": "4DNINYWTTO3D", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "CAPH-AID expressing chicken cell line, expressing Cdk1as, a mutant sensitive to inhibition by 1NM-PP3", "date_created": "2018-10-30T15:04:15.001224+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-10-11T22:24:13.056344+00:00"}, "modifications": [{"status": "released", "display_title": "random integration of GFP and AID-tagged CAP-H gene", "@type": ["Modification", "Item"], "uuid": "0cfd60d9-8ebc-4d33-aee5-0e8510f511a4", "@id": "/modifications/0cfd60d9-8ebc-4d33-aee5-0e8510f511a4/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "random integration of X. laevis Cdk1", "@type": ["Modification", "Item"], "uuid": "4dca1ddb-ab74-44f5-ac84-738b0198886d", "@id": "/modifications/4dca1ddb-ab74-44f5-ac84-738b0198886d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "Crispr disruption for CDK1 chicken gene", "@type": ["Modification", "Item"], "uuid": "fb27fdf6-4199-4179-8bb0-6101b1404aee", "@id": "/modifications/fb27fdf6-4199-4179-8bb0-6101b1404aee/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "random integration of CAP-H gene", "@type": ["Modification", "Item"], "uuid": "cc47db95-4fd6-4868-a606-8c5f50826812", "@id": "/modifications/cc47db95-4fd6-4868-a606-8c5f50826812/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "CAP-H gene deletion", "@type": ["Modification", "Item"], "uuid": "430cd51c-d2b1-4ea6-b057-6f8d55b40c7f", "@id": "/modifications/430cd51c-d2b1-4ea6-b057-6f8d55b40c7f/", "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/4DNSRYL63MO8/", "@type": ["Biosource", "Item"], "uuid": "fa5fef67-fd18-4aa1-a92b-1d8a87cd2d9b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "DT40 with random integration of GFP and AID-tagged CAP-H gene, random integration of X. laevis Cdk1, CDK1 disruption, random integration of CAP-H gene, CAP-H gene deletion - 4DNSRYL63MO8", "external_references": [], "biosource_name": "DT40 with random integration of GFP and AID-tagged CAP-H gene, random integration of X. laevis Cdk1, CDK1 disruption, random integration of CAP-H gene, CAP-H gene deletion", "biosource_category": ["Other"], "organism": {"display_title": "G. gallus", "@type": ["Organism", "Item"], "name": "chicken", "@id": "/organisms/9031/", "status": "released", "uuid": "fed8c206-762f-497f-821b-1c8ff7900bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "treatments": [{"duration": 13.0, "uuid": "697bc0a7-d8d3-4991-8e88-fa4953ad8abd", "duration_units": "hour", "chemical": "1NM-PP1", "concentration_units": "\u03bcM", "treatment_type": "Chemical", "@id": "/treatments-agent/697bc0a7-d8d3-4991-8e88-fa4953ad8abd/", "description": "Synchronization with 1NM-PP1 fo 13 hours", "@type": ["TreatmentAgent", "Treatment", "Item"], "display_title": "1NM-PP1 treatment (2.0 \u03bcM, 13.0h)", "status": "released", "concentration": 2.0, "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"], "status": "released", "title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "display_title": "Biosample Metadata Incomplete", "badge_classification": "Warning", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "warning": "Biosample Metadata Incomplete", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "20160919-G2p-R2", "sop_mapping": {"has_sop": "No"}, "date_created": "2018-10-30T15:05:43.180815+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-10-11T20:55:37.595571+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": {"experiment_category": "Sequencing", "status": "released", "@id": "/experiment-types/dilution-hi-c/", "uuid": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "assay_subclass_short": "Hi-C", "display_title": "Dilution Hi-C", "title": "Dilution Hi-C", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_size": 28592557633, "accession": "4DNFIU8UPVNI", "display_title": "4DNFIU8UPVNI.bam", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/11fea547-2fe8-4beb-af6d-219c1f376a4a/4DNFIU8UPVNI.bam", "file_type": "alignments", "upload_key": "11fea547-2fe8-4beb-af6d-219c1f376a4a/4DNFIU8UPVNI.bam", "file_format": {"file_format": "bam", "status": "released", "display_title": "bam", "@id": "/file-formats/bam/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/files-processed/4DNFIU8UPVNI/", "status": "released", "href": "/files-processed/4DNFIU8UPVNI/@@download/4DNFIU8UPVNI.bam", "uuid": "11fea547-2fe8-4beb-af6d-219c1f376a4a", "file_type_detailed": "alignments (bam)", "file_classification": "processed file", "@type": ["FileProcessed", "File", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "uuid": "a5d2c347-3d97-4646-adbc-44f40ea973b9", "status": "released", "display_title": "QualityMetricBamqc from 2020-01-16", "overall_quality_status": "PASS", "@id": "/quality-metrics-bamqc/a5d2c347-3d97-4646-adbc-44f40ea973b9/", "quality_metric_summary": [{"title": "Total Reads", "value": "395704573", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "16.308", "tooltip": "Percent of total reads (=64.53m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "10.704", "tooltip": "Percent of total reads (=42.36m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "20.958", "tooltip": "Percent of total reads (=82.93m)", "numberType": "percent"}, {"title": "Walks", "value": "0.003", "tooltip": "Percent of total reads (=0.01m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.353", "tooltip": "Percent of total reads (=1.4m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "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. CAPH-AID chicken cells", "condition": "G2 block (0m), CAPH+", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "DT40 with random integration of GFP and AID-tagged CAP-H gene, random integration of X. laevis Cdk1, CDK1 disruption, random integration of CAP-H gene, CAP-H gene deletion", "lab_name": "4DN DCIC, HMS"}}, {"file_size": 2816783479, "accession": "4DNFIWFUK3WX", "display_title": "4DNFIWFUK3WX.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a1d3853c-6db9-45cc-88ba-ee515b5df246/4DNFIWFUK3WX.pairs.gz", "file_type": "contact list-replicate", "upload_key": "a1d3853c-6db9-45cc-88ba-ee515b5df246/4DNFIWFUK3WX.pairs.gz", "file_format": {"file_format": "pairs", "status": "released", "display_title": "pairs", "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/files-processed/4DNFIWFUK3WX/", "status": "released", "href": "/files-processed/4DNFIWFUK3WX/@@download/4DNFIWFUK3WX.pairs.gz", "uuid": "a1d3853c-6db9-45cc-88ba-ee515b5df246", "file_type_detailed": "contact list-replicate (pairs)", "file_classification": "processed file", "@type": ["FileProcessed", "File", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "uuid": "e6b894d3-aa78-4db2-8628-7cba5f18c902", "status": "released", "Total reads": 205869421, "display_title": "QualityMetricPairsqc from 2019-02-11", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIWFUK3WX/pairsqc_report.html", "@id": "/quality-metrics-pairsqc/e6b894d3-aa78-4db2-8628-7cba5f18c902/", "quality_metric_summary": [{"title": "Filtered Reads", "value": "205869421", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "55.111", "tooltip": "Percent of filtered reads (=113.46m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "19.176", "tooltip": "Percent of filtered reads (=39.48m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "25.713", "tooltip": "Percent of filtered reads (=52.94m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "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. CAPH-AID chicken cells", "condition": "G2 block (0m), CAPH+", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "DT40 with random integration of GFP and AID-tagged CAP-H gene, random integration of X. laevis Cdk1, CDK1 disruption, random integration of CAP-H gene, CAP-H gene deletion", "lab_name": "4DN DCIC, HMS"}}], "project_release": "2019-10-11", "digestion_enzyme": {"@id": "/enzymes/HindIII/", "name": "HindIII", "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "status": "released", "display_title": "HindIII", "@type": ["Enzyme", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "crosslinking_time": 10.0, "biosample_quantity": 27000000.0, "crosslinking_method": "1% Formaldehyde", "fragment_size_range": "150-350", "fragmentation_method": "sonication", "ligation_temperature": 16.0, "digestion_temperature": 37.0, "biosample_quantity_units": "cells", "crosslinking_temperature": 23.0, "library_preparation_date": "2016-08-10", "fragment_size_selection_method": "SPRI beads", "@id": "/experiments-hi-c/4DNEXRACVO74/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "819485d3-1f14-4fe6-965d-17cc88b080fe", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "Dilution Hi-C on DT40 with random integration of GFP and AID-tagged CAP-H gene, random integration of X. laevis Cdk1, CDK1 disruption, random integration of CAP-H gene, CAP-H gene deletion with HindIII - 4DNEXRACVO74", "external_references": [{"ref": "GEO:GSM2745883", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2745883"}], "experiment_sets": [{"uuid": "11063cb9-dc9d-4d6d-9503-728726585bdf", "display_title": "4DNESEC33NM7", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "accession": "4DNESEC33NM7", "status": "released", "experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESEC33NM7/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"journal": "Science (New York, N.Y.)", "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"], "@type": ["Publication", "Item"], "short_attribution": "Gibcus JH et al. (2018)", "date_published": "2018-02-09", "uuid": "84fa5633-aac7-4cb3-b53b-0f0234ea06dd", "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.", "status": "current", "@id": "/publications/84fa5633-aac7-4cb3-b53b-0f0234ea06dd/", "title": "A pathway for mitotic chromosome formation.", "display_title": "Gibcus JH et al. (2018) PMID:29348367", "ID": "PMID:29348367", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"ID": "PMID:29348367", "@type": ["Publication", "Item"], "status": "current", "@id": "/publications/84fa5633-aac7-4cb3-b53b-0f0234ea06dd/", "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.", "date_published": "2018-02-09", "title": "A pathway for mitotic chromosome formation.", "short_attribution": "Gibcus JH et al. (2018)", "display_title": "Gibcus JH et al. (2018) PMID:29348367", "uuid": "84fa5633-aac7-4cb3-b53b-0f0234ea06dd", "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"], "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-H gene, random integration of X. laevis Cdk1, CDK1 disruption, random integration of CAP-H gene, CAP-H gene deletion with HindIII", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSEVPB2W1/", "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": []}