{"lab": {"status": "current", "title": "Job Dekker, UMMS", "correspondence": [{"contact_email": "am9iLmRla2tlckB1bWFzc21lZC5lZHU=", "@id": "/users/83b5073a-069b-4162-9b30-6f42d5551e34/", "display_title": "Job Dekker"}], "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "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", "@type": ["Award", "Item"], "display_title": "EXTERNAL AWARD", "center_title": "External", "center": "External", "project": "External", "@id": "/awards/external-award/", "description": "Funding source is from outside 4DN.", "name": "external-award", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"file_type_detailed": "reads (fastq)", "dbxrefs": ["SRA:SRR5939677"], "file_size": 10812163894, "file_type": "reads", "status": "released", "@id": "/files-fastq/4DNFI7NKAVHB/", "file_classification": "raw file", "display_title": "4DNFI7NKAVHB.fastq.gz", "upload_key": "9a05e393-7e40-4d75-af01-9c92aa9b0e19/4DNFI7NKAVHB.fastq.gz", "@type": ["FileFastq", "File", "Item"], "uuid": "9a05e393-7e40-4d75-af01-9c92aa9b0e19", "href": "/files-fastq/4DNFI7NKAVHB/@@download/4DNFI7NKAVHB.fastq.gz", "paired_end": "1", "accession": "4DNFI7NKAVHB", "related_files": [{"relationship_type": "paired with", "file": {"status": "released", "file_type_detailed": "reads (fastq)", "uuid": "f67447b8-805a-4c05-80af-5664e4fd029f", "paired_end": "2", "file_type": "reads", "display_title": "4DNFIBUEUVOT.fastq.gz", "@id": "/files-fastq/4DNFIBUEUVOT/", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIBUEUVOT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2018-11-16", "uuid": "08546942-d25f-4388-971f-8b4dff8f817f", "overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/08546942-d25f-4388-971f-8b4dff8f817f/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI7NKAVHB/fastqc_report.html", "status": "released", "Sequence length": "50", "Total Sequences": 396028325, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR5939677", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5939677"}], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "reads (fastq)", "dbxrefs": ["SRA:SRR5939677"], "file_size": 11418159425, "file_type": "reads", "status": "released", "@id": "/files-fastq/4DNFIBUEUVOT/", "file_classification": "raw file", "display_title": "4DNFIBUEUVOT.fastq.gz", "upload_key": "f67447b8-805a-4c05-80af-5664e4fd029f/4DNFIBUEUVOT.fastq.gz", "@type": ["FileFastq", "File", "Item"], "uuid": "f67447b8-805a-4c05-80af-5664e4fd029f", "href": "/files-fastq/4DNFIBUEUVOT/@@download/4DNFIBUEUVOT.fastq.gz", "paired_end": "2", "accession": "4DNFIBUEUVOT", "related_files": [{"relationship_type": "paired with", "file": {"status": "released", "file_type_detailed": "reads (fastq)", "uuid": "9a05e393-7e40-4d75-af01-9c92aa9b0e19", "paired_end": "1", "file_type": "reads", "display_title": "4DNFI7NKAVHB.fastq.gz", "@id": "/files-fastq/4DNFI7NKAVHB/", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFI7NKAVHB", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2018-11-16", "uuid": "3f0cf84c-80bd-4c63-bc54-3d0d9f57f45a", "overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/3f0cf84c-80bd-4c63-bc54-3d0d9f57f45a/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIBUEUVOT/fastqc_report.html", "status": "released", "Sequence length": "50", "Total Sequences": 396028325, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR5939677", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5939677"}], "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "status": "released", "aliases": ["4dn-dcic-lab:GSM2745889"], "dbxrefs": ["GEO:GSM2745889"], "protocol": {"status": "released", "uuid": "e89ce7e7-92ba-4af4-b910-74b269c0e845", "@id": "/protocols/e89ce7e7-92ba-4af4-b910-74b269c0e845/", "display_title": "GSE102740_hic_protocol.pdf", "@type": ["Protocol", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEXLLAUZP9", "biosample": {"@id": "/biosamples/4DNBS73GICFV/", "status": "released", "accession": "4DNBS73GICFV", "modifications_summary": "None", "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", "display_title": "4DNBS73GICFV", "uuid": "1e459b11-444a-48bc-bc47-f325fb23618c", "treatments_summary": "1NM-PP1 treatment (2.0 \u03bcM, 13.0h) and Auxin treatment (125 \u03bcM) and nocodazole treatment (0.5 \u03bcg/mL)", "@type": ["Biosample", "Item"], "biosample_type": "immortalized cells", "treatments": [{"duration_units": "hour", "concentration_units": "\u03bcM", "chemical": "1NM-PP1", "duration": 13.0, "status": "released", "display_title": "1NM-PP1 treatment (2.0 \u03bcM, 13.0h)", "concentration": 2.0, "uuid": "697bc0a7-d8d3-4991-8e88-fa4953ad8abd", "@id": "/treatments-agent/697bc0a7-d8d3-4991-8e88-fa4953ad8abd/", "treatment_type": "Chemical", "@type": ["TreatmentAgent", "Treatment", "Item"], "description": "Synchronization with 1NM-PP1 fo 13 hours", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"concentration_units": "\u03bcM", "chemical": "Auxin", "status": "released", "display_title": "Auxin treatment (125 \u03bcM)", "concentration": 125, "uuid": "75df7ccb-dd0e-4c45-bc39-2b094108fadd", "@id": "/treatments-agent/75df7ccb-dd0e-4c45-bc39-2b094108fadd/", "treatment_type": "Chemical", "@type": ["TreatmentAgent", "Treatment", "Item"], "description": "Auxin treatment to induce degradation of auxin-inducible degron (AID) tagged protein", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"concentration_units": "\u03bcg/mL", "chemical": "nocodazole", "status": "released", "display_title": "nocodazole treatment (0.5 \u03bcg/mL)", "concentration": 0.5, "uuid": "cfce7629-46e6-4edd-8496-bd727b51e98f", "@id": "/treatments-agent/cfce7629-46e6-4edd-8496-bd727b51e98f/", "treatment_type": "Chemical", "@type": ["TreatmentAgent", "Treatment", "Item"], "description": "Nocodazole treatment for prometaphase block", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosource": [{"lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "award": {"@type": ["Award", "Item"], "@id": "/awards/external-award/", "status": "current", "display_title": "EXTERNAL AWARD", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"term_id": "UBERON:0003903", "uuid": "1bfd1088-3311-4711-8c41-83dbed3db972", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "display_title": "digestive system", "uuid": "111129bc-8535-4448-903e-854af460a233", "status": "released", "@id": "/ontology-terms/UBERON:0001007/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "display_title": "mesoderm", "uuid": "111120bc-8535-4448-903e-854af460a233", "status": "released", "@id": "/ontology-terms/UBERON:0000926/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "status": "released", "preferred_name": "bursa of Fabricius", "@id": "/ontology-terms/UBERON:0003903/", "term_name": "bursa of Fabricius", "display_title": "bursa of Fabricius", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["4dn-dcic-lab:DT40-CAP-H-AID-GFP-Cdk1as"], "accession": "4DNSRYL63MO8", "cell_line": {"slim_terms": [{"status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "term_name": "DT40", "@id": "/ontology-terms/EFO:0006274/", "status": "released", "term_id": "EFO:0006274", "preferred_name": "DT40", "uuid": "fd057734-0765-4007-b7eb-d71ac7cbef65", "@type": ["OntologyTerm", "Item"], "display_title": "DT40", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@type": ["IndividualChicken", "Individual", "Item"], "display_title": "4DNINYWTTO3D", "status": "released", "uuid": "836856fd-a0f7-4daf-afb2-4a098df8e8fc", "@id": "/individuals-chicken/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": [{"@id": "/modifications/0cfd60d9-8ebc-4d33-aee5-0e8510f511a4/", "uuid": "0cfd60d9-8ebc-4d33-aee5-0e8510f511a4", "status": "released", "@type": ["Modification", "Item"], "display_title": "random integration of GFP and AID-tagged CAP-H gene", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/modifications/4dca1ddb-ab74-44f5-ac84-738b0198886d/", "uuid": "4dca1ddb-ab74-44f5-ac84-738b0198886d", "status": "released", "@type": ["Modification", "Item"], "display_title": "random integration of X. laevis Cdk1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/modifications/fb27fdf6-4199-4179-8bb0-6101b1404aee/", "uuid": "fb27fdf6-4199-4179-8bb0-6101b1404aee", "status": "released", "@type": ["Modification", "Item"], "display_title": "Crispr disruption for CDK1 chicken gene", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/modifications/cc47db95-4fd6-4868-a606-8c5f50826812/", "uuid": "cc47db95-4fd6-4868-a606-8c5f50826812", "status": "released", "@type": ["Modification", "Item"], "display_title": "random integration of CAP-H gene", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/modifications/430cd51c-d2b1-4ea6-b057-6f8d55b40c7f/", "uuid": "430cd51c-d2b1-4ea6-b057-6f8d55b40c7f", "status": "released", "@type": ["Modification", "Item"], "display_title": "CAP-H gene deletion", "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": {"@id": "/organisms/9031/", "display_title": "G. gallus", "@type": ["Organism", "Item"], "name": "chicken", "status": "released", "uuid": "fed8c206-762f-497f-821b-1c8ff7900bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "badges": [{"messages": ["Biosample missing Cell Culture Details"], "badge": {"warning": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "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.", "@type": ["Badge", "Item"], "display_title": "Biosample Metadata Incomplete", "status": "released", "badge_classification": "Warning", "title": "Biosample Metadata Incomplete", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "20160919-60m-R2", "sop_mapping": {"has_sop": "No"}, "date_created": "2018-10-30T15:05:48.647222+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-10-11T20:54:51.755923+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": {"status": "released", "assay_subclass_short": "Hi-C", "@type": ["ExperimentType", "Item"], "display_title": "Dilution Hi-C", "@id": "/experiment-types/dilution-hi-c/", "title": "Dilution Hi-C", "experiment_category": "Sequencing", "uuid": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"uuid": "a6ddd22a-ca07-4639-ada2-1fce7f81cf5b", "status": "released", "file_size": 28622281887, "display_title": "4DNFIHLEU96J.bam", "accession": "4DNFIHLEU96J", "file_type": "alignments", "@id": "/files-processed/4DNFIHLEU96J/", "upload_key": "a6ddd22a-ca07-4639-ada2-1fce7f81cf5b/4DNFIHLEU96J.bam", "href": "/files-processed/4DNFIHLEU96J/@@download/4DNFIHLEU96J.bam", "file_type_detailed": "alignments (bam)", "file_classification": "processed file", "file_format": {"status": "released", "file_format": "bam", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a6ddd22a-ca07-4639-ada2-1fce7f81cf5b/4DNFIHLEU96J.bam", "quality_metric": {"@id": "/quality-metrics-bamqc/cf70e370-a840-4431-a84d-0afc8f5f053c/", "uuid": "cf70e370-a840-4431-a84d-0afc8f5f053c", "display_title": "QualityMetricBamqc from 2020-01-17", "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Reads", "value": "396028325", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "15.937", "tooltip": "Percent of total reads (=63.11m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "11.265", "tooltip": "Percent of total reads (=44.61m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "20.38", "tooltip": "Percent of total reads (=80.71m)", "numberType": "percent"}, {"title": "Walks", "value": "0.004", "tooltip": "Percent of total reads (=0.02m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.439", "tooltip": "Percent of total reads (=1.74m)", "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": "prometaphase block (60m), 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"}}, {"uuid": "aa932f4e-f9ae-47f6-bda9-14e16e175aa4", "status": "released", "file_size": 2914419446, "display_title": "4DNFI2Q5RHQX.pairs.gz", "accession": "4DNFI2Q5RHQX", "file_type": "contact list-replicate", "@id": "/files-processed/4DNFI2Q5RHQX/", "upload_key": "aa932f4e-f9ae-47f6-bda9-14e16e175aa4/4DNFI2Q5RHQX.pairs.gz", "href": "/files-processed/4DNFI2Q5RHQX/@@download/4DNFI2Q5RHQX.pairs.gz", "file_type_detailed": "contact list-replicate (pairs)", "file_classification": "processed file", "file_format": {"status": "released", "file_format": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/aa932f4e-f9ae-47f6-bda9-14e16e175aa4/4DNFI2Q5RHQX.pairs.gz", "quality_metric": {"@id": "/quality-metrics-pairsqc/ae5aea6e-b522-41e9-98aa-abcea7dc5cf1/", "uuid": "ae5aea6e-b522-41e9-98aa-abcea7dc5cf1", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI2Q5RHQX/pairsqc_report.html", "display_title": "QualityMetricPairsqc from 2019-02-11", "Total reads": 207574713, "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "207574713", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "36.316", "tooltip": "Percent of filtered reads (=75.38m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "23.305", "tooltip": "Percent of filtered reads (=48.37m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "40.379", "tooltip": "Percent of filtered reads (=83.82m)", "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": "prometaphase block (60m), 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": {"status": "released", "display_title": "HindIII", "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "name": "HindIII", "@id": "/enzymes/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/4DNEXLLAUZP9/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "adabf0b8-4311-426c-93ea-7c1eb590100b", "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 - 4DNEXLLAUZP9", "external_references": [{"ref": "GEO:GSM2745889", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2745889"}], "experiment_sets": [{"@id": "/experiment-set-replicates/4DNESSU8NFVC/", "accession": "4DNESSU8NFVC", "display_title": "4DNESSU8NFVC", "status": "released", "experimentset_type": "replicate", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "8d86b5b6-b0a9-47c2-8371-e31e4c506017", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"short_attribution": "Gibcus JH et al. (2018)", "status": "current", "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/", "title": "A pathway for mitotic chromosome formation.", "uuid": "84fa5633-aac7-4cb3-b53b-0f0234ea06dd", "display_title": "Gibcus JH et al. (2018) PMID:29348367", "journal": "Science (New York, N.Y.)", "@type": ["Publication", "Item"], "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", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"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.", "ID": "PMID:29348367", "short_attribution": "Gibcus JH et al. (2018)", "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.)", "date_published": "2018-02-09", "status": "current", "@id": "/publications/84fa5633-aac7-4cb3-b53b-0f0234ea06dd/", "display_title": "Gibcus JH et al. (2018) PMID:29348367", "title": "A pathway for mitotic chromosome formation.", "@type": ["Publication", "Item"], "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/4DNBS73GICFV/", "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": []}