{"lab": {"uuid": "ce54a7f7-af8a-4505-8327-e430634f494b", "title": "Rafael Casellas, NIH", "@type": ["Lab", "Item"], "@id": "/labs/rafael-casellas-lab/", "correspondence": [{"contact_email": "Y2FzZWxsYXJAbWFpbC5uaWguZ292", "@id": "/users/68b09572-0c3e-48c7-90a9-7bad21d6bac1/", "display_title": "Rafael Casellas"}], "display_title": "Rafael Casellas, NIH", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.ce54a7f7-af8a-4505-8327-e430634f494b"]}}, "tags": ["stress_collection"], "award": {"center_title": "External", "@id": "/awards/external-award/", "status": "current", "@type": ["Award", "Item"], "project": "External", "center": "External", "display_title": "EXTERNAL AWARD", "description": "Funding source is from outside 4DN.", "name": "external-award", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["4dn-dcic-lab:B_cells_30h-act_ChIP-seq_CTCF"], "dbxrefs": ["GEO:GSE98119"], "accession": "4DNES64LTQ68", "condition": "anti-CTCF", "description": "ChIP-seq for CTCF on 30 hour activated B cells", "date_created": "2018-11-27T18:26:18.597198+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "ChIP-seq on activated B cells", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-07-08T16:46:23.549747+00:00"}, "public_release": "2019-12-02", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-seq/4DNEXRSHA3DA/", "status": "released", "accession": "4DNEXRSHA3DA", "@type": ["ExperimentSeq", "Experiment", "Item"], "display_title": "ChIP-seq against Ctcf mouse protein on B cell derived cell line - 4DNEXRSHA3DA", "uuid": "4922521d-6c6e-46e3-a9fe-dbc8b93a4611", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-seq/4DNEX2LXSAZK/", "status": "released", "accession": "4DNEX2LXSAZK", "@type": ["ExperimentSeq", "Experiment", "Item"], "display_title": "ChIP-seq against Ctcf mouse protein on B cell derived cell line - 4DNEX2LXSAZK", "uuid": "aa5ecd8d-096b-4859-9528-65873748f8d4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "b3e08a85-0ec4-4718-adb4-f056bff3fd9e", "name": "b3e08a85-0ec4-4718-adb4-f056bff3fd9e", "award": {"status": "current", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@id": "/awards/external-award/", "@type": ["Award", "Item"], "display_title": "EXTERNAL AWARD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "title": "4DNES64LTQ68 - Processed files", "description": "4DNES64LTQ68 (ChIP-seq for CTCF on 30 hour activated B cells): 4DNFII2SOIBG, 4DNFIPBD8GBC, 4DNFI7MWB1H7", "filetype": "HiglassViewConfig", "display_title": "4DNES64LTQ68 - Processed files", "@id": "/higlass-view-configs/b3e08a85-0ec4-4718-adb4-f056bff3fd9e/", "lab": {"display_title": "Rafael Casellas, NIH", "uuid": "ce54a7f7-af8a-4505-8327-e430634f494b", "@id": "/labs/rafael-casellas-lab/", "@type": ["Lab", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.ce54a7f7-af8a-4505-8327-e430634f494b"]}}, "contributing_labs": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}, "location": "tab:processed-files", "description": "auto_generated_higlass_view_config"}], "processed_files": [{"upload_key": "1d0b7c15-efb4-4362-b244-fd23538103d1/4DNFII2SOIBG.bb", "href": "/files-processed/4DNFII2SOIBG/@@download/4DNFII2SOIBG.bb", "genome_assembly": "GRCm38", "accession": "4DNFII2SOIBG", "file_size": 2892912, "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "peaks (bigbed)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/1d0b7c15-efb4-4362-b244-fd23538103d1/4DNFII2SOIBG.bb", "file_format": {"display_title": "bigbed", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bigbed/", "uuid": "bbafb7f8-98d5-48d7-8e75-dc40a5186e19", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_type": "peaks", "higlass_uid": "b65a7baa-7780-4994-ac03-c631cea8a3f2", "file_classification": "processed file", "status": "released", "display_title": "4DNFII2SOIBG.bb", "@id": "/files-processed/4DNFII2SOIBG/", "uuid": "1d0b7c15-efb4-4362-b244-fd23538103d1", "md5sum": "8e0a1538a2a254750b785a750b360dcc", "lab": {"status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "quality_metric": {"@id": "/quality-metrics-chipseq/91587be4-50d7-4217-9430-1bd29c3e98e1/", "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricChipseq", "QualityMetric", "Item"], "display_title": "QualityMetricChipseq from 2019-11-26", "uuid": "91587be4-50d7-4217-9430-1bd29c3e98e1", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFII2SOIBG/qc_report.html", "quality_metric_summary": [{"title": "Optimal Peaks", "value": "80475", "numberType": "integer"}, {"title": "Rescue Ratio", "tooltip": "Ratio of number of peaks (Nt) relative to peak calling based on psuedoreplicates (Np) [max(Np,Nt) / min (Np,Nt)]", "value": "1.13", "numberType": "float"}, {"title": "Self Consistency Ratio", "tooltip": "Ratio of number of peaks in two replicates [max(N1,N2) / min (N1,N2)]", "value": "1.45", "numberType": "float"}, {"title": "Fraction of Reads in Peaks", "value": "0.27", "numberType": "float"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"uuid": "ce54a7f7-af8a-4505-8327-e430634f494b", "display_title": "Rafael Casellas, NIH", "@type": ["Lab", "Item"], "name": "rafael-casellas-lab", "status": "current", "@id": "/labs/rafael-casellas-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.ce54a7f7-af8a-4505-8327-e430634f494b"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/085fc49c-1846-422f-b3b0-bc8b9892d25d/", "display_title": "4DNFII2SOIBG - peaks for B cell derived cell line ChIP-seq Ctcf mouse protein", "status": "released", "uuid": "085fc49c-1846-422f-b3b0-bc8b9892d25d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "track_and_facet_info": {"dataset": "ChIP-seq on activated B cells", "condition": "anti-CTCF", "experimental_lab": "Rafael Casellas, NIH", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "ChIP-seq", "assay_info": "Ctcf mouse protein", "biosource_name": "B cell derived cell line", "lab_name": "4DN DCIC, HMS", "track_title": "peaks for B cell derived cell line ChIP-seq Ctcf mouse protein"}, "last_modified": {"date_modified": "2022-01-05T09:50:49.828039+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"upload_key": "245e6685-c36f-49c9-9b2d-e7b3ded5844c/4DNFIPBD8GBC.bb", "href": "/files-processed/4DNFIPBD8GBC/@@download/4DNFIPBD8GBC.bb", "genome_assembly": "GRCm38", "accession": "4DNFIPBD8GBC", "file_size": 2024092, "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "conservative peaks (bigbed)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/245e6685-c36f-49c9-9b2d-e7b3ded5844c/4DNFIPBD8GBC.bb", "file_format": {"display_title": "bigbed", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bigbed/", "uuid": "bbafb7f8-98d5-48d7-8e75-dc40a5186e19", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_type": "conservative peaks", "higlass_uid": "ad6b7d1f-d4b6-445c-a99d-20b3d3285fad", "file_classification": "processed file", "status": "released", "display_title": "4DNFIPBD8GBC.bb", "@id": "/files-processed/4DNFIPBD8GBC/", "uuid": "245e6685-c36f-49c9-9b2d-e7b3ded5844c", "md5sum": "a208cdef159529eb2aebb2b0fa1455a6", "lab": {"status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"uuid": "ce54a7f7-af8a-4505-8327-e430634f494b", "display_title": "Rafael Casellas, NIH", "@type": ["Lab", "Item"], "name": "rafael-casellas-lab", "status": "current", "@id": "/labs/rafael-casellas-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.ce54a7f7-af8a-4505-8327-e430634f494b"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/3353eefb-17cb-456f-b0c6-635224f744af/", "display_title": "4DNFIPBD8GBC", "status": "released", "uuid": "3353eefb-17cb-456f-b0c6-635224f744af", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "track_and_facet_info": {"dataset": "ChIP-seq on activated B cells", "condition": "anti-CTCF", "experimental_lab": "Rafael Casellas, NIH", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "ChIP-seq", "assay_info": "Ctcf mouse protein", "biosource_name": "B cell derived cell line", "lab_name": "4DN DCIC, HMS", "track_title": "conservative peaks for B cell derived cell line ChIP-seq Ctcf mouse protein"}, "last_modified": {"date_modified": "2022-01-05T09:50:42.382646+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"upload_key": "26717881-b269-427b-9827-15cfea761b3f/4DNFI7MWB1H7.bw", "href": "/files-processed/4DNFI7MWB1H7/@@download/4DNFI7MWB1H7.bw", "genome_assembly": "GRCm38", "accession": "4DNFI7MWB1H7", "file_size": 991025363, "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "signal fold change (bw)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/26717881-b269-427b-9827-15cfea761b3f/4DNFI7MWB1H7.bw", "file_format": {"display_title": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_type": "signal fold change", "higlass_uid": "c8395ca2-3e49-4c5b-92eb-ace3e3880cd6", "file_classification": "processed file", "status": "released", "display_title": "4DNFI7MWB1H7.bw", "@id": "/files-processed/4DNFI7MWB1H7/", "uuid": "26717881-b269-427b-9827-15cfea761b3f", "md5sum": "5a9f2da48fbd2711a5637f4540cbe0c6", "lab": {"status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"uuid": "ce54a7f7-af8a-4505-8327-e430634f494b", "display_title": "Rafael Casellas, NIH", "@type": ["Lab", "Item"], "name": "rafael-casellas-lab", "status": "current", "@id": "/labs/rafael-casellas-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.ce54a7f7-af8a-4505-8327-e430634f494b"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/9829c823-f010-4e66-a967-361018fdf621/", "display_title": "4DNFI7MWB1H7", "status": "released", "uuid": "9829c823-f010-4e66-a967-361018fdf621", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "track_and_facet_info": {"dataset": "ChIP-seq on activated B cells", "condition": "anti-CTCF", "experimental_lab": "Rafael Casellas, NIH", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "ChIP-seq", "assay_info": "Ctcf mouse protein", "biosource_name": "B cell derived cell line", "lab_name": "4DN DCIC, HMS", "track_title": "signal fold change for B cell derived cell line ChIP-seq Ctcf mouse protein"}, "last_modified": {"date_modified": "2022-01-05T09:50:34.527902+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}], "project_release": "2019-12-02", "experiments_in_set": [{"@id": "/experiments-seq/4DNEXRSHA3DA/", "status": "released", "accession": "4DNEXRSHA3DA", "dbxrefs": ["GEO:GSM3027983"], "files": [{"display_title": "4DNFIGCZOSLD.fastq.gz", "file_size": 1577383623, "uuid": "7431f96a-6dff-4881-ba2a-cc076b0bccf0", "href": "/files-fastq/4DNFIGCZOSLD/@@download/4DNFIGCZOSLD.fastq.gz", "upload_key": "7431f96a-6dff-4881-ba2a-cc076b0bccf0/4DNFIGCZOSLD.fastq.gz", "file_classification": "raw file", "dbxrefs": ["SRA:SRR6794594"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/7431f96a-6dff-4881-ba2a-cc076b0bccf0/4DNFIGCZOSLD.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIGCZOSLD", "md5sum": "d7121bfa6a50ea47fe3cc116a2ecf170", "@id": "/files-fastq/4DNFIGCZOSLD/", "file_type": "reads", "lab": {"@type": ["Lab", "Item"], "name": "rafael-casellas-lab", "uuid": "ce54a7f7-af8a-4505-8327-e430634f494b", "display_title": "Rafael Casellas, NIH", "@id": "/labs/rafael-casellas-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.ce54a7f7-af8a-4505-8327-e430634f494b"]}}, "file_format": {"display_title": "fastq", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"uuid": "14e467bf-de7a-4192-95db-a8f0cecf9bc6", "Total Sequences": 52871252, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIGCZOSLD/fastqc_report.html", "status": "released", "display_title": "QualityMetricFastqc from 2018-11-27", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "35-50", "@id": "/quality-metrics-fastqc/14e467bf-de7a-4192-95db-a8f0cecf9bc6/", "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR6794594", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR6794594"}], "track_and_facet_info": {"experimental_lab": "Rafael Casellas, NIH", "experiment_type": "ChIP-seq", "experiment_bucket": "raw file", "assay_info": "Ctcf mouse protein", "dataset": "ChIP-seq on activated B cells", "condition": "anti-CTCF", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "B cell derived cell line", "lab_name": "Rafael Casellas, NIH"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "4922521d-6c6e-46e3-a9fe-dbc8b93a4611", "display_title": "ChIP-seq against Ctcf mouse protein on B cell derived cell line - 4DNEXRSHA3DA", "biosample": {"modifications_summary": "None", "@id": "/biosamples/4DNBS5XJQVE8/", "biosample_type": "primary cells", "biosource_summary": "B cell derived cell line", "uuid": "41d48651-2337-45d5-8d21-341bd2f9d6ff", "accession": "4DNBS5XJQVE8", "display_title": "4DNBS5XJQVE8", "treatments_summary": "LPS (Sigma) treatment (50.0 \u03bcg/mL, 30.0h) and IL-4 (Sigma) treatment (2.5 ng/mL, 30.0h) and anti-CD180 (RP105) antibody, BD PharMingen treatment (0.5 \u03bcg/mL, 30.0h)", "@type": ["Biosample", "Item"], "status": "released", "biosample_category": ["Primary Cells"], "biosource": [{"cell_line_tier": "Unclassified", "uuid": "469a5e58-d40f-4536-8df9-5c603111ba1f", "accession": "4DNSRA3JY5KY", "@id": "/biosources/4DNSRA3JY5KY/", "biosource_type": "primary cell", "display_title": "B cell derived cell line - 4DNSRA3JY5KY", "status": "released", "@type": ["Biosource", "Item"], "cell_line": {"@type": ["OntologyTerm", "Item"], "term_id": "EFO:0001640", "preferred_name": "B cell derived cell line", "uuid": "a35ee804-9776-45b2-8b66-d29b00558c8d", "display_title": "B cell derived cell line", "term_name": "B cell derived cell line", "@id": "/ontology-terms/EFO:0001640/", "status": "released", "slim_terms": [{"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000000/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "status": "current", "@id": "/ontology-terms/GO:0005623/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/10090/", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "status": "released", "name": "mouse", "scientific_name": "Mus musculus", "@type": ["Organism", "Item"], "display_title": "M. musculus", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"status": "released", "display_title": "splenocyte", "uuid": "94bbfc93-633a-450a-92d9-261c13d3548a", "@id": "/ontology-terms/CL:2000074/", "@type": ["OntologyTerm", "Item"], "preferred_name": "splenocyte", "term_name": "splenocyte", "term_id": "CL:2000074", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"display_title": "spleen", "uuid": "111177bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0002106/", "status": "released", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "immune system", "uuid": "111133bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0002405/", "status": "released", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "mesoderm", "uuid": "111120bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0000926/", "status": "released", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "digestive system", "uuid": "111129bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0001007/", "status": "released", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"organ_system": ["spleen", "immune system", "mesoderm", "digestive system"], "tissue_source": "splenocyte"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "treatments": [{"@type": ["TreatmentAgent", "Treatment", "Item"], "uuid": "b1084704-6134-4e10-81d6-57022eaf9607", "concentration": 50.0, "status": "released", "description": "part of B-cell activation", "duration": 30.0, "treatment_type": "Chemical", "chemical": "LPS (Sigma)", "concentration_units": "\u03bcg/mL", "duration_units": "hour", "@id": "/treatments-agent/b1084704-6134-4e10-81d6-57022eaf9607/", "display_title": "LPS (Sigma) treatment (50.0 \u03bcg/mL, 30.0h)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["TreatmentAgent", "Treatment", "Item"], "uuid": "88ac225f-14c8-4aa0-b826-72f2cc8c3a92", "concentration": 2.5, "status": "released", "description": "part of B-cell activation", "duration": 30.0, "treatment_type": "Chemical", "chemical": "IL-4 (Sigma)", "concentration_units": "ng/mL", "duration_units": "hour", "@id": "/treatments-agent/88ac225f-14c8-4aa0-b826-72f2cc8c3a92/", "display_title": "IL-4 (Sigma) treatment (2.5 ng/mL, 30.0h)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["TreatmentAgent", "Treatment", "Item"], "uuid": "664f44e3-d5d2-4f15-ad43-09b6f341e5f4", "concentration": 0.5, "status": "released", "description": "part of B-cell activation", "duration": 30.0, "treatment_type": "Chemical", "chemical": "anti-CD180 (RP105) antibody, BD PharMingen", "concentration_units": "\u03bcg/mL", "duration_units": "hour", "@id": "/treatments-agent/664f44e3-d5d2-4f15-ad43-09b6f341e5f4/", "display_title": "anti-CD180 (RP105) antibody, BD PharMingen treatment (0.5 \u03bcg/mL, 30.0h)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "processed_files": [{"file_format": {"@type": ["FileFormat", "Item"], "status": "released", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "@id": "/file-formats/bed/", "display_title": "bed", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_classification": "processed file", "file_type_detailed": "read positions (bed)", "href": "/files-processed/4DNFI9295QE8/@@download/4DNFI9295QE8.bed.gz", "status": "released", "@id": "/files-processed/4DNFI9295QE8/", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFI9295QE8", "uuid": "debd9ca1-9863-4533-9161-969267ce242a", "genome_assembly": "GRCm38", "md5sum": "b14eb6f489752ab054254f1077e9c28d", "file_type": "read positions", "file_size": 203024754, "display_title": "4DNFI9295QE8.bed.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/debd9ca1-9863-4533-9161-969267ce242a/4DNFI9295QE8.bed.gz", "upload_key": "debd9ca1-9863-4533-9161-969267ce242a/4DNFI9295QE8.bed.gz", "quality_metric": {"@type": ["QualityMetricChipseq", "QualityMetric", "Item"], "display_title": "QualityMetricChipseq from 2019-06-18", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI9295QE8qc_report.html", "overall_quality_status": "PASS", "@id": "/quality-metrics-chipseq/0c1feddf-dd16-4d89-87ca-674c3f3d0e94/", "uuid": "0c1feddf-dd16-4d89-87ca-674c3f3d0e94", "status": "released", "quality_metric_summary": [{"title": "Nonredundant Read Fraction (NRF)", "value": "0.77", "tooltip": "distinct non-mito read pairs / total non-mito read pairs", "numberType": "float"}, {"title": "PCR Bottleneck Coefficient (PBC)", "value": "0.79", "tooltip": "one-read non-mito read pairs / distinct non-mito read pairs", "numberType": "float"}, {"title": "Filtered & Deduped Reads", "value": "31927572", "numberType": "integer"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "contributing_labs": [{"display_title": "Rafael Casellas, NIH", "@id": "/labs/rafael-casellas-lab/", "status": "current", "name": "rafael-casellas-lab", "uuid": "ce54a7f7-af8a-4505-8327-e430634f494b", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.ce54a7f7-af8a-4505-8327-e430634f494b"]}}], "last_modified": {"date_modified": "2022-01-06T08:45:59.413705+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Rafael Casellas, NIH", "experiment_type": "ChIP-seq", "experiment_bucket": "processed file", "assay_info": "Ctcf mouse protein", "dataset": "ChIP-seq on activated B cells", "condition": "anti-CTCF", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "B cell derived cell line", "lab_name": "4DN DCIC, HMS"}}], "experiment_type": {"assay_classification": "Linear DNA Enrichment", "title": "ChIP-seq", "@type": ["ExperimentType", "Item"], "display_title": "ChIP-seq", "experiment_category": "Sequencing", "uuid": "47a593da-c458-422a-a974-82b3302e89cb", "other_tags": ["1D"], "assay_subclassification": "DNA Binding", "assay_subclass_short": "DNA binding", "status": "released", "@id": "/experiment-types/chip-seq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2019-12-02T01:08:47.607208+00:00"}, "experiment_categorizer": {"field": "Target", "combined": "Target: Ctcf mouse protein", "value": "Ctcf mouse protein"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "GEO:GSM3027983", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3027983"}]}, {"@id": "/experiments-seq/4DNEX2LXSAZK/", "status": "released", "accession": "4DNEX2LXSAZK", "dbxrefs": ["GEO:GSM3027984"], "files": [{"display_title": "4DNFID1DZTGT.fastq.gz", "file_size": 1068544581, "uuid": "e14b6c83-c583-4af8-bb1a-018e62fc630e", "href": "/files-fastq/4DNFID1DZTGT/@@download/4DNFID1DZTGT.fastq.gz", "upload_key": "e14b6c83-c583-4af8-bb1a-018e62fc630e/4DNFID1DZTGT.fastq.gz", "file_classification": "raw file", "dbxrefs": ["SRA:SRR6794595"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/e14b6c83-c583-4af8-bb1a-018e62fc630e/4DNFID1DZTGT.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFID1DZTGT", "md5sum": "2430314bb6a9c3b782db201b5ae86625", "@id": "/files-fastq/4DNFID1DZTGT/", "file_type": "reads", "lab": {"@type": ["Lab", "Item"], "name": "rafael-casellas-lab", "uuid": "ce54a7f7-af8a-4505-8327-e430634f494b", "display_title": "Rafael Casellas, NIH", "@id": "/labs/rafael-casellas-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.ce54a7f7-af8a-4505-8327-e430634f494b"]}}, "file_format": {"display_title": "fastq", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"uuid": "06354080-d541-4318-98f1-b935429ad55a", "Total Sequences": 36130589, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFID1DZTGT/fastqc_report.html", "status": "released", "display_title": "QualityMetricFastqc from 2018-11-27", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "35-50", "@id": "/quality-metrics-fastqc/06354080-d541-4318-98f1-b935429ad55a/", "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR6794595", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR6794595"}], "track_and_facet_info": {"experimental_lab": "Rafael Casellas, NIH", "experiment_type": "ChIP-seq", "experiment_bucket": "raw file", "assay_info": "Ctcf mouse protein", "dataset": "ChIP-seq on activated B cells", "condition": "anti-CTCF", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "B cell derived cell line", "lab_name": "Rafael Casellas, NIH"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "aa5ecd8d-096b-4859-9528-65873748f8d4", "display_title": "ChIP-seq against Ctcf mouse protein on B cell derived cell line - 4DNEX2LXSAZK", "biosample": {"modifications_summary": "None", "@id": "/biosamples/4DNBSFQKSSDU/", "biosample_type": "primary cells", "biosource_summary": "B cell derived cell line", "uuid": "9183ba71-2252-4c34-a1b3-58d46037abad", "accession": "4DNBSFQKSSDU", "display_title": "4DNBSFQKSSDU", "treatments_summary": "LPS (Sigma) treatment (50.0 \u03bcg/mL, 30.0h) and IL-4 (Sigma) treatment (2.5 ng/mL, 30.0h) and anti-CD180 (RP105) antibody, BD PharMingen treatment (0.5 \u03bcg/mL, 30.0h)", "@type": ["Biosample", "Item"], "status": "released", "biosample_category": ["Primary Cells"], "biosource": [{"cell_line_tier": "Unclassified", "uuid": "469a5e58-d40f-4536-8df9-5c603111ba1f", "accession": "4DNSRA3JY5KY", "@id": "/biosources/4DNSRA3JY5KY/", "biosource_type": "primary cell", "display_title": "B cell derived cell line - 4DNSRA3JY5KY", "status": "released", "@type": ["Biosource", "Item"], "cell_line": {"@type": ["OntologyTerm", "Item"], "term_id": "EFO:0001640", "preferred_name": "B cell derived cell line", "uuid": "a35ee804-9776-45b2-8b66-d29b00558c8d", "display_title": "B cell derived cell line", "term_name": "B cell derived cell line", "@id": "/ontology-terms/EFO:0001640/", "status": "released", "slim_terms": [{"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000000/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "status": "current", "@id": "/ontology-terms/GO:0005623/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/10090/", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "status": "released", "name": "mouse", "scientific_name": "Mus musculus", "@type": ["Organism", "Item"], "display_title": "M. musculus", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"status": "released", "display_title": "splenocyte", "uuid": "94bbfc93-633a-450a-92d9-261c13d3548a", "@id": "/ontology-terms/CL:2000074/", "@type": ["OntologyTerm", "Item"], "preferred_name": "splenocyte", "term_name": "splenocyte", "term_id": "CL:2000074", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"display_title": "spleen", "uuid": "111177bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0002106/", "status": "released", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "immune system", "uuid": "111133bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0002405/", "status": "released", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "mesoderm", "uuid": "111120bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0000926/", "status": "released", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "digestive system", "uuid": "111129bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0001007/", "status": "released", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"organ_system": ["spleen", "immune system", "mesoderm", "digestive system"], "tissue_source": "splenocyte"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "treatments": [{"@type": ["TreatmentAgent", "Treatment", "Item"], "uuid": "b1084704-6134-4e10-81d6-57022eaf9607", "concentration": 50.0, "status": "released", "description": "part of B-cell activation", "duration": 30.0, "treatment_type": "Chemical", "chemical": "LPS (Sigma)", "concentration_units": "\u03bcg/mL", "duration_units": "hour", "@id": "/treatments-agent/b1084704-6134-4e10-81d6-57022eaf9607/", "display_title": "LPS (Sigma) treatment (50.0 \u03bcg/mL, 30.0h)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["TreatmentAgent", "Treatment", "Item"], "uuid": "88ac225f-14c8-4aa0-b826-72f2cc8c3a92", "concentration": 2.5, "status": "released", "description": "part of B-cell activation", "duration": 30.0, "treatment_type": "Chemical", "chemical": "IL-4 (Sigma)", "concentration_units": "ng/mL", "duration_units": "hour", "@id": "/treatments-agent/88ac225f-14c8-4aa0-b826-72f2cc8c3a92/", "display_title": "IL-4 (Sigma) treatment (2.5 ng/mL, 30.0h)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["TreatmentAgent", "Treatment", "Item"], "uuid": "664f44e3-d5d2-4f15-ad43-09b6f341e5f4", "concentration": 0.5, "status": "released", "description": "part of B-cell activation", "duration": 30.0, "treatment_type": "Chemical", "chemical": "anti-CD180 (RP105) antibody, BD PharMingen", "concentration_units": "\u03bcg/mL", "duration_units": "hour", "@id": "/treatments-agent/664f44e3-d5d2-4f15-ad43-09b6f341e5f4/", "display_title": "anti-CD180 (RP105) antibody, BD PharMingen treatment (0.5 \u03bcg/mL, 30.0h)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "processed_files": [{"file_format": {"@type": ["FileFormat", "Item"], "status": "released", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "@id": "/file-formats/bed/", "display_title": "bed", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_classification": "processed file", "file_type_detailed": "read positions (bed)", "href": "/files-processed/4DNFIUJYJ8IP/@@download/4DNFIUJYJ8IP.bed.gz", "status": "released", "@id": "/files-processed/4DNFIUJYJ8IP/", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIUJYJ8IP", "uuid": "eb5fdec5-7ee7-4328-afaa-73d1f81b373e", "genome_assembly": "GRCm38", "md5sum": "054621cce4620a3c2047572bc2086b3d", "file_type": "read positions", "file_size": 160396113, "display_title": "4DNFIUJYJ8IP.bed.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/eb5fdec5-7ee7-4328-afaa-73d1f81b373e/4DNFIUJYJ8IP.bed.gz", "upload_key": "eb5fdec5-7ee7-4328-afaa-73d1f81b373e/4DNFIUJYJ8IP.bed.gz", "quality_metric": {"@type": ["QualityMetricChipseq", "QualityMetric", "Item"], "display_title": "QualityMetricChipseq from 2019-06-18", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIUJYJ8IPqc_report.html", "overall_quality_status": "PASS", "@id": "/quality-metrics-chipseq/56d3f403-47cf-43c2-b4e7-14e596cb6a7e/", "uuid": "56d3f403-47cf-43c2-b4e7-14e596cb6a7e", "status": "released", "quality_metric_summary": [{"title": "Nonredundant Read Fraction (NRF)", "value": "0.88", "tooltip": "distinct non-mito read pairs / total non-mito read pairs", "numberType": "float"}, {"title": "PCR Bottleneck Coefficient (PBC)", "value": "0.88", "tooltip": "one-read non-mito read pairs / distinct non-mito read pairs", "numberType": "float"}, {"title": "Filtered & Deduped Reads", "value": "24091640", "numberType": "integer"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "contributing_labs": [{"display_title": "Rafael Casellas, NIH", "@id": "/labs/rafael-casellas-lab/", "status": "current", "name": "rafael-casellas-lab", "uuid": "ce54a7f7-af8a-4505-8327-e430634f494b", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.ce54a7f7-af8a-4505-8327-e430634f494b"]}}], "last_modified": {"date_modified": "2022-01-06T08:42:11.473111+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Rafael Casellas, NIH", "experiment_type": "ChIP-seq", "experiment_bucket": "processed file", "assay_info": "Ctcf mouse protein", "dataset": "ChIP-seq on activated B cells", "condition": "anti-CTCF", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "B cell derived cell line", "lab_name": "4DN DCIC, HMS"}}], "experiment_type": {"assay_classification": "Linear DNA Enrichment", "title": "ChIP-seq", "@type": ["ExperimentType", "Item"], "display_title": "ChIP-seq", "experiment_category": "Sequencing", "uuid": "47a593da-c458-422a-a974-82b3302e89cb", "other_tags": ["1D"], "assay_subclassification": "DNA Binding", "assay_subclass_short": "DNA binding", "status": "released", "@id": "/experiment-types/chip-seq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2019-12-02T01:08:51.892726+00:00"}, "experiment_categorizer": {"field": "Target", "combined": "Target: Ctcf mouse protein", "value": "Ctcf mouse protein"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "GEO:GSM3027984", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3027984"}]}], "experimentset_type": "replicate", "completed_processes": ["ENCODE_ChIP_Pipeline_1.1.1"], "@id": "/experiment-set-replicates/4DNES64LTQ68/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "be73f370-01a3-4f7c-965f-73805f84d81d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNES64LTQ68", "external_references": [{"ref": "GEO:GSE98119", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98119"}], "produced_in_pub": {"@type": ["Publication", "Item"], "uuid": "89ec268b-d05c-4841-8806-a49fb0d99e78", "title": "The Energetics and Physiological Impact of Cohesin Extrusion.", "journal": "Cell", "status": "current", "abstract": "Cohesin extrusion is thought to play a central role in establishing the architecture of mammalian genomes. However, extrusion has not been visualized in  vivo, and thus, its functional impact and energetics are unknown. Using ultra-deep Hi-C, we show that loop domains form by a process that requires cohesin ATPases. Once formed, however, loops and compartments are maintained for  hours without energy input. Strikingly, without ATP, we observe the emergence of  hundreds of CTCF-independent loops that link regulatory DNA. We also identify architectural \"stripes,\" where a loop anchor interacts with entire domains at high frequency. Stripes often tether super-enhancers to cognate promoters, and in B cells, they facilitate Igh transcription and recombination. Stripe anchors represent major hotspots for topoisomerase-mediated lesions, which promote chromosomal translocations and cancer. In plasmacytomas, stripes can deregulate Igh-translocated oncogenes. We propose that higher organisms have coopted cohesin extrusion to enhance transcription and recombination, with implications for tumor development.", "@id": "/publications/89ec268b-d05c-4841-8806-a49fb0d99e78/", "ID": "PMID:29706548", "date_published": "2018-04-26", "display_title": "Vian L et al. (2018) PMID:29706548", "authors": ["Vian L", "Pekowska A", "Rao SSP", "Kieffer-Kwon KR", "Jung S", "Baranello L", "Huang SC", "El Khattabi L", "Dose M", "Pruett N", "Sanborn AL", "Canela A", "Maman Y", "Oksanen A", "Resch W", "Li X", "Lee B", "Kovalchuk AL", "Tang Z", "Nelson S", "Di Pierro M", "Cheng RR", "Machol I", "St Hilaire BG", "Durand NC", "Shamim MS", "Stamenova EK", "Onuchic JN", "Ruan Y", "Nussenzweig A", "Levens D", "Aiden EL", "Casellas R"], "url": "https://www.ncbi.nlm.nih.gov/pubmed/29706548", "short_attribution": "Vian L et al. (2018)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"@type": ["Publication", "Item"], "@id": "/publications/89ec268b-d05c-4841-8806-a49fb0d99e78/", "title": "The Energetics and Physiological Impact of Cohesin Extrusion.", "date_published": "2018-04-26", "status": "current", "ID": "PMID:29706548", "journal": "Cell", "display_title": "Vian L et al. (2018) PMID:29706548", "authors": ["Vian L", "Pekowska A", "Rao SSP", "Kieffer-Kwon KR", "Jung S", "Baranello L", "Huang SC", "El Khattabi L", "Dose M", "Pruett N", "Sanborn AL", "Canela A", "Maman Y", "Oksanen A", "Resch W", "Li X", "Lee B", "Kovalchuk AL", "Tang Z", "Nelson S", "Di Pierro M", "Cheng RR", "Machol I", "St Hilaire BG", "Durand NC", "Shamim MS", "Stamenova EK", "Onuchic JN", "Ruan Y", "Nussenzweig A", "Levens D", "Aiden EL", "Casellas R"], "uuid": "89ec268b-d05c-4841-8806-a49fb0d99e78", "abstract": "Cohesin extrusion is thought to play a central role in establishing the architecture of mammalian genomes. However, extrusion has not been visualized in  vivo, and thus, its functional impact and energetics are unknown. Using ultra-deep Hi-C, we show that loop domains form by a process that requires cohesin ATPases. Once formed, however, loops and compartments are maintained for  hours without energy input. Strikingly, without ATP, we observe the emergence of  hundreds of CTCF-independent loops that link regulatory DNA. We also identify architectural \"stripes,\" where a loop anchor interacts with entire domains at high frequency. Stripes often tether super-enhancers to cognate promoters, and in B cells, they facilitate Igh transcription and recombination. Stripe anchors represent major hotspots for topoisomerase-mediated lesions, which promote chromosomal translocations and cancer. In plasmacytomas, stripes can deregulate Igh-translocated oncogenes. We propose that higher organisms have coopted cohesin extrusion to enhance transcription and recombination, with implications for tumor development.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 2, "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}