{"lab": {"uuid": "4dfac8f5-a868-4b29-9c11-a0932130e121", "@type": ["Lab", "Item"], "correspondence": [{"contact_email": "YmVub2l0LmJydW5lYXVAZ2xhZHN0b25lLnVjc2YuZWR1", "@id": "/users/c015dffd-4ca1-4070-905f-8a04b3754b2b/", "display_title": "Benoit Bruneau"}], "display_title": "Benoit Bruneau, UCSF", "title": "Benoit Bruneau, UCSF", "@id": "/labs/benoit-bruneau-lab/", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.4dfac8f5-a868-4b29-9c11-a0932130e121"]}}, "award": {"@id": "/awards/external-award/", "center": "External", "description": "Funding source is from outside 4DN.", "display_title": "EXTERNAL AWARD", "name": "external-award", "center_title": "External", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "status": "current", "@type": ["Award", "Item"], "project": "External", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["4dn-dcic-lab:GSM2609201-H3K27me3-ChIP-seq-CTCF-AID-auxin4days"], "accession": "4DNES6VO5VSG", "description": "ChIP-seq of CTCF-AID mouse embryonic stem cells treated with Auxin for 4 days targetting H3K27me3 gene", "date_created": "2018-11-07T21:13:01.456083+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-06-27T21:46:02.860211+00:00"}, "public_release": "2018-12-06", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"status": "released", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "a0a65621-d5a5-42b0-938d-12a338e7cac5", "@id": "/experiments-seq/4DNEXX785YMJ/", "display_title": "ChIP-seq against H3K27me3 on ES-E14TG2a with CTCF-AID - 4DNEXX785YMJ", "accession": "4DNEXX785YMJ", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"status": "released", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "bb12e3a0-9bc7-4f59-96ae-415b41a8fe8c", "@id": "/experiments-seq/4DNEXT9LL8UQ/", "display_title": "ChIP-seq against H3K27me3 on ES-E14TG2a with CTCF-AID - 4DNEXT9LL8UQ", "accession": "4DNEXT9LL8UQ", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"title": "4DNES6VO5VSG - Processed files", "@type": ["HiglassViewConfig", "UserContent", "Item"], "lab": {"@id": "/labs/benoit-bruneau-lab/", "uuid": "4dfac8f5-a868-4b29-9c11-a0932130e121", "status": "current", "@type": ["Lab", "Item"], "display_title": "Benoit Bruneau, UCSF", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.4dfac8f5-a868-4b29-9c11-a0932130e121"]}}, "uuid": "198fd1ae-52f6-47b2-b7dc-559c9078aa86", "description": "4DNES6VO5VSG (ChIP-seq of CTCF-AID mouse embryonic stem cells treated with Auxin for 4 days targetting H3K27me3 gene): 4DNFIURYD2M4, 4DNFICGKEUCN, 4DNFIIC6IUVD", "filetype": "HiglassViewConfig", "contributing_labs": [], "status": "released", "display_title": "4DNES6VO5VSG - Processed files", "@id": "/higlass-view-configs/198fd1ae-52f6-47b2-b7dc-559c9078aa86/", "name": "198fd1ae-52f6-47b2-b7dc-559c9078aa86", "award": {"status": "current", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "display_title": "EXTERNAL AWARD", "@type": ["Award", "Item"], "@id": "/awards/external-award/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}, "location": "tab:processed-files", "description": "auto_generated_higlass_view_config"}], "processed_files": [{"file_type": "peaks", "uuid": "e50124f1-9d43-4e3c-bbfc-4fa4cd0fde84", "file_type_detailed": "peaks (bigbed)", "@type": ["FileProcessed", "File", "Item"], "file_classification": "processed file", "display_title": "4DNFIURYD2M4.bb", "higlass_uid": "GWJVyiH3TMmXFKIaz-ZJTA", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e50124f1-9d43-4e3c-bbfc-4fa4cd0fde84/4DNFIURYD2M4.bb", "upload_key": "e50124f1-9d43-4e3c-bbfc-4fa4cd0fde84/4DNFIURYD2M4.bb", "md5sum": "93c3d49cd6cac7212c356928bba43203", "genome_assembly": "GRCm38", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "bigbed", "uuid": "bbafb7f8-98d5-48d7-8e75-dc40a5186e19", "@id": "/file-formats/bigbed/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFIURYD2M4", "href": "/files-processed/4DNFIURYD2M4/@@download/4DNFIURYD2M4.bb", "@id": "/files-processed/4DNFIURYD2M4/", "file_size": 2821143, "status": "released", "track_and_facet_info": {"experimental_lab": "Benoit Bruneau, UCSF", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "ChIP-seq", "assay_info": "H3K27me3", "biosource_name": "ES-E14TG2a with CTCF-AID", "lab_name": "4DN DCIC, HMS", "track_title": "peaks for ES-E14TG2a with CTCF-AID ChIP-seq H3K27me3"}, "external_references": [], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIIC6IUVDqc_report.html", "@id": "/quality-metrics-chipseq/1a785de7-50d3-47ef-970a-da4274bc7a13/", "overall_quality_status": "PASS", "display_title": "QualityMetricChipseq from 2019-01-31", "uuid": "1a785de7-50d3-47ef-970a-da4274bc7a13", "@type": ["QualityMetricChipseq", "QualityMetric", "Item"], "status": "released", "quality_metric_summary": [{"title": "Optimal Peaks", "value": "57339", "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": "1.04", "numberType": "float"}, {"title": "Self Consistency Ratio", "tooltip": "Ratio of number of peaks in two replicates [max(N1,N2) / min (N1,N2)]", "value": "1.24", "numberType": "float"}, {"title": "Fraction of Reads in Peaks", "value": "0.24", "numberType": "float"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"uuid": "4dfac8f5-a868-4b29-9c11-a0932130e121", "status": "current", "name": "benoit-bruneau-lab", "display_title": "Benoit Bruneau, UCSF", "@type": ["Lab", "Item"], "@id": "/labs/benoit-bruneau-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.4dfac8f5-a868-4b29-9c11-a0932130e121"]}}], "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"uuid": "8038a03f-bb68-4e96-a9db-ab5ef181178f", "@id": "/higlass-view-configs/8038a03f-bb68-4e96-a9db-ab5ef181178f/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIURYD2M4 - peaks for ES-E14TG2a with random integration of EGFP and AID-tagged CTCF, Tir1 insertion ChIP-seq H3K27me3", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "lab": {"display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "@type": ["Lab", "Item"], "status": "current", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2022-01-06T15:48:29.654981+00:00"}}, {"file_type": "conservative peaks", "uuid": "21cf0b55-fb5c-4ecb-acff-0a235280f6a0", "file_type_detailed": "conservative peaks (bigbed)", "@type": ["FileProcessed", "File", "Item"], "file_classification": "processed file", "display_title": "4DNFICGKEUCN.bb", "higlass_uid": "JWxkJ2jCQleZQMnn6h-ZBg", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/21cf0b55-fb5c-4ecb-acff-0a235280f6a0/4DNFICGKEUCN.bb", "upload_key": "21cf0b55-fb5c-4ecb-acff-0a235280f6a0/4DNFICGKEUCN.bb", "md5sum": "94f18dc1683ab38ffa4653175a8c6630", "genome_assembly": "GRCm38", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "bigbed", "uuid": "bbafb7f8-98d5-48d7-8e75-dc40a5186e19", "@id": "/file-formats/bigbed/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFICGKEUCN", "href": "/files-processed/4DNFICGKEUCN/@@download/4DNFICGKEUCN.bb", "@id": "/files-processed/4DNFICGKEUCN/", "file_size": 2727373, "status": "released", "track_and_facet_info": {"experimental_lab": "Benoit Bruneau, UCSF", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "ChIP-seq", "assay_info": "H3K27me3", "biosource_name": "ES-E14TG2a with CTCF-AID", "lab_name": "4DN DCIC, HMS", "track_title": "conservative peaks for ES-E14TG2a with CTCF-AID ChIP-seq H3K27me3"}, "external_references": [], "contributing_labs": [{"uuid": "4dfac8f5-a868-4b29-9c11-a0932130e121", "status": "current", "name": "benoit-bruneau-lab", "display_title": "Benoit Bruneau, UCSF", "@type": ["Lab", "Item"], "@id": "/labs/benoit-bruneau-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.4dfac8f5-a868-4b29-9c11-a0932130e121"]}}], "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"uuid": "c78e458f-7f29-4d23-ade7-1c49e4f564a5", "@id": "/higlass-view-configs/c78e458f-7f29-4d23-ade7-1c49e4f564a5/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFICGKEUCN - conservative peaks for ES-E14TG2a with random integration of EGFP and AID-tagged CTCF, Tir1 insertion ChIP-seq H3K27me3", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "lab": {"display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "@type": ["Lab", "Item"], "status": "current", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2022-01-06T09:47:07.811189+00:00"}}, {"file_type": "signal fold change", "uuid": "aa5d0c30-3b23-4379-ab62-97ea4a494199", "file_type_detailed": "signal fold change (bw)", "@type": ["FileProcessed", "File", "Item"], "file_classification": "processed file", "display_title": "4DNFIIC6IUVD.bw", "higlass_uid": "T4E-i5bsQWaRuZiOJxYAfg", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/aa5d0c30-3b23-4379-ab62-97ea4a494199/4DNFIIC6IUVD.bw", "upload_key": "aa5d0c30-3b23-4379-ab62-97ea4a494199/4DNFIIC6IUVD.bw", "md5sum": "eeb01cc6e5bbdfd33f5373ed94ed603c", "genome_assembly": "GRCm38", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFIIC6IUVD", "href": "/files-processed/4DNFIIC6IUVD/@@download/4DNFIIC6IUVD.bw", "@id": "/files-processed/4DNFIIC6IUVD/", "file_size": 1220384410, "status": "released", "track_and_facet_info": {"experimental_lab": "Benoit Bruneau, UCSF", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "ChIP-seq", "assay_info": "H3K27me3", "biosource_name": "ES-E14TG2a with CTCF-AID", "lab_name": "4DN DCIC, HMS", "track_title": "signal fold change for ES-E14TG2a with CTCF-AID ChIP-seq H3K27me3"}, "external_references": [], "contributing_labs": [{"uuid": "4dfac8f5-a868-4b29-9c11-a0932130e121", "status": "current", "name": "benoit-bruneau-lab", "display_title": "Benoit Bruneau, UCSF", "@type": ["Lab", "Item"], "@id": "/labs/benoit-bruneau-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.4dfac8f5-a868-4b29-9c11-a0932130e121"]}}], "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"uuid": "46fd7a63-0723-480f-a14d-6155deb9cddf", "@id": "/higlass-view-configs/46fd7a63-0723-480f-a14d-6155deb9cddf/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIIC6IUVD - signal fold change for ES-E14TG2a with random integration of EGFP and AID-tagged CTCF, Tir1 insertion ChIP-seq H3K27me3", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "lab": {"display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "@type": ["Lab", "Item"], "status": "current", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2022-01-06T09:47:06.258142+00:00"}}], "project_release": "2018-12-06", "experiments_in_set": [{"display_title": "ChIP-seq against H3K27me3 on ES-E14TG2a with CTCF-AID - 4DNEXX785YMJ", "@type": ["ExperimentSeq", "Experiment", "Item"], "dbxrefs": ["GEO:GSM2609201"], "status": "released", "uuid": "a0a65621-d5a5-42b0-938d-12a338e7cac5", "accession": "4DNEXX785YMJ", "files": [{"uuid": "3710532e-eddb-4e57-958f-71410dee8c46", "accession": "4DNFIOJHUQPJ", "file_classification": "raw file", "display_title": "4DNFIOJHUQPJ.fastq.gz", "file_size": 1895130579, "href": "/files-fastq/4DNFIOJHUQPJ/@@download/4DNFIOJHUQPJ.fastq.gz", "dbxrefs": ["SRA:SRR5517492"], "md5sum": "773b0f017f57a18bfa7968c068c7cf67", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/3710532e-eddb-4e57-958f-71410dee8c46/4DNFIOJHUQPJ.fastq.gz", "@id": "/files-fastq/4DNFIOJHUQPJ/", "upload_key": "3710532e-eddb-4e57-958f-71410dee8c46/4DNFIOJHUQPJ.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "benoit-bruneau-lab", "display_title": "Benoit Bruneau, UCSF", "uuid": "4dfac8f5-a868-4b29-9c11-a0932130e121", "@id": "/labs/benoit-bruneau-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.4dfac8f5-a868-4b29-9c11-a0932130e121"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIOJHUQPJ/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 44070124, "uuid": "832f57e5-5b99-464b-b60e-527e84a7fd0d", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-11-19", "status": "released", "Sequence length": "76", "@id": "/quality-metrics-fastqc/832f57e5-5b99-464b-b60e-527e84a7fd0d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Benoit Bruneau, UCSF", "experiment_type": "ChIP-seq", "experiment_bucket": "raw file", "assay_info": "H3K27me3", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "ES-E14TG2a with CTCF-AID", "lab_name": "Benoit Bruneau, UCSF"}, "external_references": [{"ref": "SRA:SRR5517492", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5517492"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-seq/4DNEXX785YMJ/", "biosample": {"display_title": "4DNBSHMW15NW", "biosample_category": ["Mouse stem cell"], "uuid": "0b5e182a-9604-4187-bda9-98d5784e85c2", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBSHMW15NW", "@id": "/biosamples/4DNBSHMW15NW/", "treatments_summary": "indole-3-acetic acid treatment (500.0 \u03bcM, 4.0d at 4.0\u00b0C)", "status": "released", "biosource_summary": "ES-E14TG2a with CTCF-AID", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "9fd3c189-7169-4336-bfd1-545c3b53ca44", "@id": "/biosources/4DNSRLMKMT14/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Unclassified", "override_biosource_name": "ES-E14TG2a with CTCF-AID", "@type": ["Biosource", "Item"], "display_title": "ES-E14TG2a with CTCF-AID - 4DNSRLMKMT14", "accession": "4DNSRLMKMT14", "status": "released", "cell_line": {"term_id": "EFO:0006275", "@id": "/ontology-terms/EFO:0006275/", "term_name": "ES-E14TG2a", "preferred_name": "ES-E14TG2a", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "ES-E14TG2a", "uuid": "2262fd9b-3185-4c65-8ad5-bfe65e986954", "slim_terms": [{"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/10090/", "status": "released", "display_title": "M. musculus", "name": "mouse", "@type": ["Organism", "Item"], "scientific_name": "Mus musculus", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "treatments": [{"treatment_type": "Chemical", "temperature": 4.0, "concentration_units": "\u03bcM", "description": "Addition of indole-3-acetic acid (analog of Auxin) in the culture medium for 4 days", "status": "released", "@id": "/treatments-agent/09f18e7a-33f1-4868-b93b-f5645fe6236b/", "duration": 4.0, "concentration": 500.0, "@type": ["TreatmentAgent", "Treatment", "Item"], "display_title": "indole-3-acetic acid treatment (500.0 \u03bcM, 4.0d at 4.0\u00b0C)", "duration_units": "day", "chemical": "indole-3-acetic acid", "uuid": "09f18e7a-33f1-4868-b93b-f5645fe6236b", "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/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-icon.svg", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "title": "Biosample Metadata Incomplete", "badge_classification": "Warning", "status": "released", "display_title": "Biosample Metadata Incomplete", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "read positions", "genome_assembly": "GRCm38", "display_title": "4DNFIUV4Z68T.bed.gz", "upload_key": "8bdedaab-fc00-469c-a676-99a09544badd/4DNFIUV4Z68T.bed.gz", "href": "/files-processed/4DNFIUV4Z68T/@@download/4DNFIUV4Z68T.bed.gz", "accession": "4DNFIUV4Z68T", "md5sum": "9dae91b05445a588a53ea9960a2bc5a0", "file_format": {"display_title": "bed", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bed/", "status": "released", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIUV4Z68T/", "file_size": 197828175, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8bdedaab-fc00-469c-a676-99a09544badd/4DNFIUV4Z68T.bed.gz", "file_type_detailed": "read positions (bed)", "uuid": "8bdedaab-fc00-469c-a676-99a09544badd", "status": "released", "quality_metric": {"status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIUV4Z68Tqc_report.html", "uuid": "5c9c749d-ccf8-4643-9ed1-19b2d3de2c0d", "@type": ["QualityMetricChipseq", "QualityMetric", "Item"], "display_title": "QualityMetricChipseq from 2019-01-30", "overall_quality_status": "PASS", "@id": "/quality-metrics-chipseq/5c9c749d-ccf8-4643-9ed1-19b2d3de2c0d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Nonredundant Read Fraction (NRF)", "value": "0.84", "tooltip": "distinct non-mito read pairs / total non-mito read pairs", "numberType": "float"}, {"title": "PCR Bottleneck Coefficient (PBC)", "value": "0.84", "tooltip": "one-read non-mito read pairs / distinct non-mito read pairs", "numberType": "float"}, {"title": "Filtered & Deduped Reads", "value": "29461471", "numberType": "integer"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/benoit-bruneau-lab/", "display_title": "Benoit Bruneau, UCSF", "uuid": "4dfac8f5-a868-4b29-9c11-a0932130e121", "name": "benoit-bruneau-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.4dfac8f5-a868-4b29-9c11-a0932130e121"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2022-01-06T15:07:50.113384+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Benoit Bruneau, UCSF", "experiment_type": "ChIP-seq", "experiment_bucket": "processed file", "assay_info": "H3K27me3", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "ES-E14TG2a with CTCF-AID", "lab_name": "4DN DCIC, HMS"}}], "experiment_type": {"uuid": "47a593da-c458-422a-a974-82b3302e89cb", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "ChIP-seq", "assay_subclassification": "DNA Binding", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "DNA binding", "display_title": "ChIP-seq", "@id": "/experiment-types/chip-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "GEO:GSM2609201", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2609201"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Target", "combined": "Target: H3K27me3", "value": "H3K27me3"}, "last_modified": {"date_modified": "2019-06-20T19:38:46.229944+00:00"}}, {"display_title": "ChIP-seq against H3K27me3 on ES-E14TG2a with CTCF-AID - 4DNEXT9LL8UQ", "@type": ["ExperimentSeq", "Experiment", "Item"], "dbxrefs": ["GEO:GSM2609205"], "status": "released", "uuid": "bb12e3a0-9bc7-4f59-96ae-415b41a8fe8c", "accession": "4DNEXT9LL8UQ", "files": [{"uuid": "7f0a0ef8-28c1-48de-88a3-451314ba9edd", "accession": "4DNFI7Y8JLIH", "file_classification": "raw file", "display_title": "4DNFI7Y8JLIH.fastq.gz", "file_size": 2341961359, "href": "/files-fastq/4DNFI7Y8JLIH/@@download/4DNFI7Y8JLIH.fastq.gz", "dbxrefs": ["SRA:SRR5517496"], "md5sum": "5980341f7db0b9522d6a4fba35acaedb", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/7f0a0ef8-28c1-48de-88a3-451314ba9edd/4DNFI7Y8JLIH.fastq.gz", "@id": "/files-fastq/4DNFI7Y8JLIH/", "upload_key": "7f0a0ef8-28c1-48de-88a3-451314ba9edd/4DNFI7Y8JLIH.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "benoit-bruneau-lab", "display_title": "Benoit Bruneau, UCSF", "uuid": "4dfac8f5-a868-4b29-9c11-a0932130e121", "@id": "/labs/benoit-bruneau-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.4dfac8f5-a868-4b29-9c11-a0932130e121"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI7Y8JLIH/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 55496250, "uuid": "19c55ed4-5022-412c-8520-7e76222a2d97", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-11-19", "status": "released", "Sequence length": "76", "@id": "/quality-metrics-fastqc/19c55ed4-5022-412c-8520-7e76222a2d97/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Benoit Bruneau, UCSF", "experiment_type": "ChIP-seq", "experiment_bucket": "raw file", "assay_info": "H3K27me3", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "ES-E14TG2a with CTCF-AID", "lab_name": "Benoit Bruneau, UCSF"}, "external_references": [{"ref": "SRA:SRR5517496", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5517496"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-seq/4DNEXT9LL8UQ/", "biosample": {"display_title": "4DNBS2OFA5FQ", "biosample_category": ["Mouse stem cell"], "uuid": "8e7ff596-2278-4b26-87e7-13426e259a26", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS2OFA5FQ", "@id": "/biosamples/4DNBS2OFA5FQ/", "treatments_summary": "indole-3-acetic acid treatment (500.0 \u03bcM, 4.0d at 4.0\u00b0C)", "status": "released", "biosource_summary": "ES-E14TG2a with CTCF-AID", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "9fd3c189-7169-4336-bfd1-545c3b53ca44", "@id": "/biosources/4DNSRLMKMT14/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Unclassified", "override_biosource_name": "ES-E14TG2a with CTCF-AID", "@type": ["Biosource", "Item"], "display_title": "ES-E14TG2a with CTCF-AID - 4DNSRLMKMT14", "accession": "4DNSRLMKMT14", "status": "released", "cell_line": {"term_id": "EFO:0006275", "@id": "/ontology-terms/EFO:0006275/", "term_name": "ES-E14TG2a", "preferred_name": "ES-E14TG2a", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "ES-E14TG2a", "uuid": "2262fd9b-3185-4c65-8ad5-bfe65e986954", "slim_terms": [{"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/10090/", "status": "released", "display_title": "M. musculus", "name": "mouse", "@type": ["Organism", "Item"], "scientific_name": "Mus musculus", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "treatments": [{"treatment_type": "Chemical", "temperature": 4.0, "concentration_units": "\u03bcM", "description": "Addition of indole-3-acetic acid (analog of Auxin) in the culture medium for 4 days", "status": "released", "@id": "/treatments-agent/09f18e7a-33f1-4868-b93b-f5645fe6236b/", "duration": 4.0, "concentration": 500.0, "@type": ["TreatmentAgent", "Treatment", "Item"], "display_title": "indole-3-acetic acid treatment (500.0 \u03bcM, 4.0d at 4.0\u00b0C)", "duration_units": "day", "chemical": "indole-3-acetic acid", "uuid": "09f18e7a-33f1-4868-b93b-f5645fe6236b", "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/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-icon.svg", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "title": "Biosample Metadata Incomplete", "badge_classification": "Warning", "status": "released", "display_title": "Biosample Metadata Incomplete", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "read positions", "genome_assembly": "GRCm38", "display_title": "4DNFIJDB9SVU.bed.gz", "upload_key": "ab380cde-2b2f-4fbd-9162-6389580ce18f/4DNFIJDB9SVU.bed.gz", "href": "/files-processed/4DNFIJDB9SVU/@@download/4DNFIJDB9SVU.bed.gz", "accession": "4DNFIJDB9SVU", "md5sum": "226326587e7a5470e15f5dd6857f5ea9", "file_format": {"display_title": "bed", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bed/", "status": "released", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIJDB9SVU/", "file_size": 231342054, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ab380cde-2b2f-4fbd-9162-6389580ce18f/4DNFIJDB9SVU.bed.gz", "file_type_detailed": "read positions (bed)", "uuid": "ab380cde-2b2f-4fbd-9162-6389580ce18f", "status": "released", "quality_metric": {"status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJDB9SVUqc_report.html", "uuid": "d7791c1a-a19f-4a15-a930-bc1507133dc3", "@type": ["QualityMetricChipseq", "QualityMetric", "Item"], "display_title": "QualityMetricChipseq from 2019-01-30", "overall_quality_status": "PASS", "@id": "/quality-metrics-chipseq/d7791c1a-a19f-4a15-a930-bc1507133dc3/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Nonredundant Read Fraction (NRF)", "value": "0.79", "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": "34841596", "numberType": "integer"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/benoit-bruneau-lab/", "display_title": "Benoit Bruneau, UCSF", "uuid": "4dfac8f5-a868-4b29-9c11-a0932130e121", "name": "benoit-bruneau-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.4dfac8f5-a868-4b29-9c11-a0932130e121"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2022-01-06T15:07:41.572935+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Benoit Bruneau, UCSF", "experiment_type": "ChIP-seq", "experiment_bucket": "processed file", "assay_info": "H3K27me3", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "ES-E14TG2a with CTCF-AID", "lab_name": "4DN DCIC, HMS"}}], "experiment_type": {"uuid": "47a593da-c458-422a-a974-82b3302e89cb", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "ChIP-seq", "assay_subclassification": "DNA Binding", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "DNA binding", "display_title": "ChIP-seq", "@id": "/experiment-types/chip-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "GEO:GSM2609205", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2609205"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Target", "combined": "Target: H3K27me3", "value": "H3K27me3"}, "last_modified": {"date_modified": "2019-06-20T19:38:49.205198+00:00"}}], "experimentset_type": "replicate", "completed_processes": ["ENCODE_ChIP_Pipeline_1.1.1"], "@id": "/experiment-set-replicates/4DNES6VO5VSG/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "3b150f92-2a8a-4d40-b74b-5ce964c4dafe", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNES6VO5VSG", "external_references": [], "produced_in_pub": {"url": "https://www.ncbi.nlm.nih.gov/pubmed/28525758", "@id": "/publications/1ec54a03-0aaa-4d17-91d5-7a6ae3b12157/", "short_attribution": "Nora EP et al. (2017)", "ID": "PMID:28525758", "journal": "Cell", "uuid": "1ec54a03-0aaa-4d17-91d5-7a6ae3b12157", "abstract": "The molecular mechanisms underlying folding of mammalian chromosomes remain poorly understood. The transcription factor CTCF is a candidate regulator of chromosomal structure. Using the auxin-inducible degron system in mouse embryonic stem cells, we show that CTCF is absolutely and dose-dependently required for looping between CTCF target sites and insulation of topologically associating domains (TADs). Restoring CTCF reinstates proper architecture on altered chromosomes, indicating a powerful instructive function for CTCF in chromatin folding. CTCF remains essential for TAD organization in non-dividing cells. Surprisingly, active and inactive genome compartments remain properly segregated  upon CTCF depletion, revealing that compartmentalization of mammalian chromosomes emerges independently of proper insulation of TADs. Furthermore, our data support that CTCF mediates transcriptional insulator function through enhancer blocking but not as a direct barrier to heterochromatin spreading. Beyond defining the functions of CTCF in chromosome folding, these results provide new fundamental insights into the rules governing mammalian genome organization.", "authors": ["Nora EP", "Goloborodko A", "Valton AL", "Gibcus JH", "Uebersohn A", "Abdennur N", "Dekker J", "Mirny LA", "Bruneau BG"], "date_published": "2017-05-18", "@type": ["Publication", "Item"], "display_title": "Nora EP et al. (2017) PMID:28525758", "status": "current", "title": "Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"date_published": "2017-05-18", "ID": "PMID:28525758", "status": "current", "authors": ["Nora EP", "Goloborodko A", "Valton AL", "Gibcus JH", "Uebersohn A", "Abdennur N", "Dekker J", "Mirny LA", "Bruneau BG"], "@id": "/publications/1ec54a03-0aaa-4d17-91d5-7a6ae3b12157/", "abstract": "The molecular mechanisms underlying folding of mammalian chromosomes remain poorly understood. The transcription factor CTCF is a candidate regulator of chromosomal structure. Using the auxin-inducible degron system in mouse embryonic stem cells, we show that CTCF is absolutely and dose-dependently required for looping between CTCF target sites and insulation of topologically associating domains (TADs). Restoring CTCF reinstates proper architecture on altered chromosomes, indicating a powerful instructive function for CTCF in chromatin folding. CTCF remains essential for TAD organization in non-dividing cells. Surprisingly, active and inactive genome compartments remain properly segregated  upon CTCF depletion, revealing that compartmentalization of mammalian chromosomes emerges independently of proper insulation of TADs. Furthermore, our data support that CTCF mediates transcriptional insulator function through enhancer blocking but not as a direct barrier to heterochromatin spreading. Beyond defining the functions of CTCF in chromosome folding, these results provide new fundamental insights into the rules governing mammalian genome organization.", "@type": ["Publication", "Item"], "title": "Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.", "journal": "Cell", "display_title": "Nora EP et al. (2017) PMID:28525758", "uuid": "1ec54a03-0aaa-4d17-91d5-7a6ae3b12157", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 2, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSHMW15NW/", "embedded_path": "experiments_in_set.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."}}}, {"parent": "/biosamples/4DNBS2OFA5FQ/", "embedded_path": "experiments_in_set.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": []}