{"lab": {"title": "Job Dekker, UMMS", "status": "current", "@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@id": "/labs/job-dekker-lab/", "correspondence": [{"contact_email": "am9iLmRla2tlckB1bWFzc21lZC5lZHU=", "@id": "/users/83b5073a-069b-4162-9b30-6f42d5551e34/", "display_title": "Job Dekker"}], "pi": {"error": "no view permissions"}, "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", "project": "External", "center": "External", "description": "Funding source is from outside 4DN.", "status": "current", "@type": ["Award", "Item"], "center_title": "External", "name": "external-award", "@id": "/awards/external-award/", "display_title": "EXTERNAL AWARD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"uuid": "eff954fa-fea8-4afc-8100-091de53825ab", "file_size": 9223441412, "href": "/files-fastq/4DNFI7Q5Y9HY/@@download/4DNFI7Q5Y9HY.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "file_classification": "raw file", "accession": "4DNFI7Q5Y9HY", "paired_end": "1", "@id": "/files-fastq/4DNFI7Q5Y9HY/", "dbxrefs": ["SRA:SRR5939665"], "upload_key": "eff954fa-fea8-4afc-8100-091de53825ab/4DNFI7Q5Y9HY.fastq.gz", "display_title": "4DNFI7Q5Y9HY.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_format": {"file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "display_title": "4DNFIK3QZECU.fastq.gz", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "uuid": "e0e1a018-7771-4f48-936b-3f9c49d27a49", "file_type": "reads", "@id": "/files-fastq/4DNFIK3QZECU/", "accession": "4DNFIK3QZECU", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI7Q5Y9HY/fastqc_report.html", "Sequence length": "50", "status": "released", "uuid": "ebcb80fb-0ba2-4080-b970-dced8c393100", "Total Sequences": 338067225, "display_title": "QualityMetricFastqc from 2018-11-17", "@id": "/quality-metrics-fastqc/ebcb80fb-0ba2-4080-b970-dced8c393100/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR5939665", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5939665"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "e0e1a018-7771-4f48-936b-3f9c49d27a49", "file_size": 9758141514, "href": "/files-fastq/4DNFIK3QZECU/@@download/4DNFIK3QZECU.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "file_classification": "raw file", "accession": "4DNFIK3QZECU", "paired_end": "2", "@id": "/files-fastq/4DNFIK3QZECU/", "dbxrefs": ["SRA:SRR5939665"], "upload_key": "e0e1a018-7771-4f48-936b-3f9c49d27a49/4DNFIK3QZECU.fastq.gz", "display_title": "4DNFIK3QZECU.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_format": {"file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "display_title": "4DNFI7Q5Y9HY.fastq.gz", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "uuid": "eff954fa-fea8-4afc-8100-091de53825ab", "file_type": "reads", "@id": "/files-fastq/4DNFI7Q5Y9HY/", "accession": "4DNFI7Q5Y9HY", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIK3QZECU/fastqc_report.html", "Sequence length": "50", "status": "released", "uuid": "b9cd78bf-5667-4c20-b3b1-b796b0ee26e3", "Total Sequences": 338067225, "display_title": "QualityMetricFastqc from 2018-11-17", "@id": "/quality-metrics-fastqc/b9cd78bf-5667-4c20-b3b1-b796b0ee26e3/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR5939665", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5939665"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "status": "released", "aliases": ["4dn-dcic-lab:GSM2745877"], "dbxrefs": ["GEO:GSM2745877"], "protocol": {"@id": "/protocols/e89ce7e7-92ba-4af4-b910-74b269c0e845/", "status": "released", "display_title": "GSE102740_hic_protocol.pdf", "uuid": "e89ce7e7-92ba-4af4-b910-74b269c0e845", "@type": ["Protocol", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEXMOSRYT5", "biosample": {"status": "released", "@id": "/biosamples/4DNBS4CW53T4/", "display_title": "4DNBS4CW53T4", "accession": "4DNBS4CW53T4", "@type": ["Biosample", "Item"], "biosample_type": "immortalized cells", "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": "310a6fcf-3f62-4506-9c8c-a63069c7da73", "treatments_summary": "1NM-PP1 treatment (2.0 \u03bcM, 13.0h)", "modifications_summary": "None", "biosource": [{"lab": {"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@type": ["Lab", "Item"], "display_title": "Job Dekker, UMMS", "status": "current", "@id": "/labs/job-dekker-lab/", "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", "@type": ["Award", "Item"], "status": "current", "@id": "/awards/external-award/", "display_title": "EXTERNAL AWARD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"term_id": "UBERON:0003903", "uuid": "1bfd1088-3311-4711-8c41-83dbed3db972", "status": "released", "term_name": "bursa of Fabricius", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0003903/", "display_title": "bursa of Fabricius", "slim_terms": [{"uuid": "111129bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0001007/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "digestive system", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111120bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0000926/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "mesoderm", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "preferred_name": "bursa of Fabricius", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["4dn-dcic-lab:DT40-CAP-H2-AID-GFP-Cdk1as"], "accession": "4DNSRHKEBVUK", "cell_line": {"slim_terms": [{"display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/ontology-terms/EFO:0006274/", "uuid": "fd057734-0765-4007-b7eb-d71ac7cbef65", "term_name": "DT40", "term_id": "EFO:0006274", "@type": ["OntologyTerm", "Item"], "display_title": "DT40", "preferred_name": "DT40", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"status": "released", "uuid": "836856fd-a0f7-4daf-afb2-4a098df8e8fc", "@id": "/individuals-chicken/4DNINYWTTO3D/", "display_title": "4DNINYWTTO3D", "@type": ["IndividualChicken", "Individual", "Item"], "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": [{"@id": "/modifications/5384182d-cedf-45c8-a97b-35262bfc7615/", "@type": ["Modification", "Item"], "status": "released", "display_title": "random integration of GFP and AID-tagged CAP-H2 gene", "uuid": "5384182d-cedf-45c8-a97b-35262bfc7615", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/modifications/0bd91d0a-3494-49e1-b444-5e1c5c03172b/", "@type": ["Modification", "Item"], "status": "released", "display_title": "Crispr disruption for NCAPH2 chicken gene", "uuid": "0bd91d0a-3494-49e1-b444-5e1c5c03172b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/modifications/4dca1ddb-ab74-44f5-ac84-738b0198886d/", "@type": ["Modification", "Item"], "status": "released", "display_title": "random integration of X. laevis Cdk1", "uuid": "4dca1ddb-ab74-44f5-ac84-738b0198886d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/modifications/fb27fdf6-4199-4179-8bb0-6101b1404aee/", "@type": ["Modification", "Item"], "status": "released", "display_title": "Crispr disruption for CDK1 chicken gene", "uuid": "fb27fdf6-4199-4179-8bb0-6101b1404aee", "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": {"display_title": "G. gallus", "name": "chicken", "@id": "/organisms/9031/", "@type": ["Organism", "Item"], "status": "released", "uuid": "fed8c206-762f-497f-821b-1c8ff7900bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "badges": [{"messages": ["Biosample missing Cell Culture Details"], "badge": {"@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", "display_title": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-icon.svg", "title": "Biosample Metadata Incomplete", "warning": "Biosample Metadata Incomplete", "badge_classification": "Warning", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "treatments": [{"@type": ["TreatmentAgent", "Treatment", "Item"], "description": "Synchronization with 1NM-PP1 fo 13 hours", "concentration": 2.0, "chemical": "1NM-PP1", "concentration_units": "\u03bcM", "treatment_type": "Chemical", "duration": 13.0, "display_title": "1NM-PP1 treatment (2.0 \u03bcM, 13.0h)", "status": "released", "@id": "/treatments-agent/697bc0a7-d8d3-4991-8e88-fa4953ad8abd/", "uuid": "697bc0a7-d8d3-4991-8e88-fa4953ad8abd", "duration_units": "hour", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "20160714-G2n-R1", "sop_mapping": {"has_sop": "No"}, "date_created": "2018-10-30T15:05:37.882885+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-10-11T20:55:40.555644+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": {"display_title": "Dilution Hi-C", "title": "Dilution Hi-C", "@type": ["ExperimentType", "Item"], "uuid": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "experiment_category": "Sequencing", "status": "released", "assay_subclass_short": "Hi-C", "@id": "/experiment-types/dilution-hi-c/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"@id": "/files-processed/4DNFINMA6UXS/", "file_size": 19644506894, "display_title": "4DNFINMA6UXS.bam", "status": "released", "href": "/files-processed/4DNFINMA6UXS/@@download/4DNFINMA6UXS.bam", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/648bcc18-8e6f-47a9-8133-f4fca0f9b747/4DNFINMA6UXS.bam", "@type": ["FileProcessed", "File", "Item"], "uuid": "648bcc18-8e6f-47a9-8133-f4fca0f9b747", "accession": "4DNFINMA6UXS", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "bam", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_type": "alignments", "file_classification": "processed file", "file_type_detailed": "alignments (bam)", "upload_key": "648bcc18-8e6f-47a9-8133-f4fca0f9b747/4DNFINMA6UXS.bam", "quality_metric": {"@id": "/quality-metrics-bamqc/13532d58-3cb4-45c5-bb52-a362c41f0687/", "status": "released", "display_title": "QualityMetricBamqc from 2020-01-16", "overall_quality_status": "PASS", "uuid": "13532d58-3cb4-45c5-bb52-a362c41f0687", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Reads", "value": "338067225", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "9.52", "tooltip": "Percent of total reads (=32.18m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "9.924", "tooltip": "Percent of total reads (=33.55m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "43.203", "tooltip": "Percent of total reads (=146.05m)", "numberType": "percent"}, {"title": "Walks", "value": "0.006", "tooltip": "Percent of total reads (=0.02m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.317", "tooltip": "Percent of total reads (=1.07m)", "numberType": "percent"}]}, "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. CAPH2-AID chicken cells", "condition": "G2 block (0m), 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"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/files-processed/4DNFIWNT3P3U/", "file_size": 1510280253, "display_title": "4DNFIWNT3P3U.pairs.gz", "status": "released", "href": "/files-processed/4DNFIWNT3P3U/@@download/4DNFIWNT3P3U.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e9effc58-3cba-4cef-a788-7acdbfb97282/4DNFIWNT3P3U.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "e9effc58-3cba-4cef-a788-7acdbfb97282", "accession": "4DNFIWNT3P3U", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "pairs", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_type": "contact list-replicate", "file_classification": "processed file", "file_type_detailed": "contact list-replicate (pairs)", "upload_key": "e9effc58-3cba-4cef-a788-7acdbfb97282/4DNFIWNT3P3U.pairs.gz", "quality_metric": {"@id": "/quality-metrics-pairsqc/080ff5d7-0329-4e72-97ca-4839f4a9e8ef/", "status": "released", "display_title": "QualityMetricPairsqc from 2019-02-11", "overall_quality_status": "PASS", "uuid": "080ff5d7-0329-4e72-97ca-4839f4a9e8ef", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIWNT3P3U/pairsqc_report.html", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Total reads": 126257445, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "126257445", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "11.379", "tooltip": "Percent of filtered reads (=14.37m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "83.169", "tooltip": "Percent of filtered reads (=105.01m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "5.452", "tooltip": "Percent of filtered reads (=6.88m)", "numberType": "percent"}]}, "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. CAPH2-AID chicken cells", "condition": "G2 block (0m), 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"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "project_release": "2019-10-11", "digestion_enzyme": {"display_title": "HindIII", "@type": ["Enzyme", "Item"], "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "@id": "/enzymes/HindIII/", "status": "released", "name": "HindIII", "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/4DNEXMOSRYT5/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "46e306f1-438c-4cc6-9c91-8cb1c9539611", "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 - 4DNEXMOSRYT5", "external_references": [{"ref": "GEO:GSM2745877", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2745877"}], "experiment_sets": [{"experimentset_type": "replicate", "status": "released", "@id": "/experiment-set-replicates/4DNESYIMR82X/", "accession": "4DNESYIMR82X", "uuid": "c929c149-4052-41d5-b11c-1caa69004082", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNESYIMR82X", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"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"], "short_attribution": "Gibcus JH et al. (2018)", "status": "current", "uuid": "84fa5633-aac7-4cb3-b53b-0f0234ea06dd", "@type": ["Publication", "Item"], "ID": "PMID:29348367", "display_title": "Gibcus JH et al. (2018) PMID:29348367", "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.", "title": "A pathway for mitotic chromosome formation.", "journal": "Science (New York, N.Y.)", "@id": "/publications/84fa5633-aac7-4cb3-b53b-0f0234ea06dd/", "date_published": "2018-02-09", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"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.", "@type": ["Publication", "Item"], "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"], "@id": "/publications/84fa5633-aac7-4cb3-b53b-0f0234ea06dd/", "short_attribution": "Gibcus JH et al. (2018)", "display_title": "Gibcus JH et al. (2018) PMID:29348367", "title": "A pathway for mitotic chromosome formation.", "status": "current", "uuid": "84fa5633-aac7-4cb3-b53b-0f0234ea06dd", "date_published": "2018-02-09", "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/4DNBS4CW53T4/", "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": []}