{"lab": {"status": "current", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "display_title": "David Gilbert, SDBRI", "title": "David Gilbert, SDBRI", "@id": "/labs/david-gilbert-lab/", "@type": ["Lab", "Item"], "correspondence": [{"contact_email": "Z2lsYmVydEBzZGJyaS5vcmc=", "@id": "/users/1dbb8e49-38e4-4154-a97c-af8176a58c44/", "display_title": "David Gilbert"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "award": {"uuid": "91b694c3-f4d7-4ddd-8278-16f94e15c1c5", "center_title": "NOFIC - Belmont", "@type": ["Award", "Item"], "description": "NOFIC: Decades of microscopy have revealed that the nucleus is not a homogeneous organelle, but rather consists of distinct compartments such as nucleoli, nuclear speckles, the nuclear lamina, among other structures. Increasing evidence indicates that specific genomic regions each associate with these compartments. This genome compartmentalization has been linked to various functions, but these links are still poorly understood. Interestingly, Lamina Associated Domains (LADs) share specific heterochromatin marks, defining chromatin domains with distinct genetic and epigenetic properties. Genomic regions associating with other nuclear compartments may similarly define distinct classes of chromatin domains. One major bottleneck towards a deeper understanding of nuclear organization has been the inability to convert microscopy views of nuclear compartments into genome-wide maps that show which loci are associated with which compartment, and how the chromosomal fiber traverses between compartments. In addition, there is an urgent need for more efficient methods to dissect the mechanisms by which large genomic regions are targeted to specific nuclear compartments. Finally, there is an urgent need for high-throughput approaches that query the functional relevance of genome compartmentalization. For this Center grant, we propose to meet these needs through the following Aims: 1. Develop a strategy that connects microscopy views to genome-wide maps that, together with modeling, reveal the localization and dynamics of genomic regions relative to all major nuclear compartments. 2. Develop methods for efficient manipulation of the genome in order to elucidate mechanisms that target loci to specific compartments. 3. Develop methods to measure, model, and validate the functional relevance of nuclear compartments. The combined results of these approaches will reveal causal relationships now hidden among entangled genomic, epigenetic, and nuclear organization features. Deliverables of this proposal include a wide range of structural and functional maps of nuclear organization, reagents for visualizing endogenous chromosome loci, a powerful pipeline for synthesis of ~100kb DNA fragments, and cell lines facilitating repeated, high-fidelity insertio of these large fragments back into selected sites in the genome. These resources will provide a powerful complement to other 4D Nucleome Consortium efforts. A key strength of this Center proposal is the experience and complementary research capabilities of its five Investigators. Together they will pool their expertise for a concerted investigation into the biological functions of nuclear compartmentalization.", "project": "4DN", "display_title": "COMBINED CYTOLOGICAL, GENOMIC, AND FUNCTIONAL MAPPING OF NUCLEAR GENOME ORGANIZATION", "name": "1U54DK107965-01", "status": "current", "@id": "/awards/1U54DK107965-01/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["gilbert-lab:CTCF_KO_2_phase_repliseq"], "accession": "4DNESKVCLFGY", "condition": "CTCF knockdown", "description": "Early and Late 2 phase Repliseq on  CTCF knockdown EN52.9.1 mESCs", "date_created": "2019-11-15T18:56:28.874951+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "E/L repliseq on EN52.9 mESC with CTCF-AID", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-06-23T13:42:09.148087+00:00"}, "public_release": "2019-11-19", "schema_version": "2", "static_headers": [{"lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "\n**Data Use Guidelines:** This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) \nand the 4DN Data Portal paper \n([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).", "name": "item-page-headers.ExperimentSet.data-usage-guidelines", "award": {"uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "status": "current", "@type": ["Award", "Item"], "@id": "/awards/1U01CA200059-01/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Data Usage Guidelines", "status": "released", "aliases": [], "options": {"filetype": "md", "title_icon": "exclamation-circle", "collapsible": false, "default_open": true}, "date_created": "2018-08-06T03:09:55.543206+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-05-09T09:31:34.537494+00:00"}, "schema_version": "2", "@id": "/static-sections/621e8359-3885-40ce-965d-91894aa7b758/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "621e8359-3885-40ce-965d-91894aa7b758", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267228139"]}, "display_title": "Data Usage Guidelines", "external_references": [], "content": "\n**Data Use Guidelines:** This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) \nand the 4DN Data Portal paper \n([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p><strong>Data Use Guidelines:</strong> This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n(<a href=\"https://doi.org/10.1038/nature23884\" rel=\"noopener noreferrer\" target=\"_blank\">doi:10.1038/nature23884</a>) \nand the 4DN Data Portal paper \n(<a href=\"https://doi.org/10.1038/s41467-022-29697-4\" rel=\"noopener noreferrer\" target=\"_blank\">doi:10.1038/s41467-022-29697-4</a>), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the <a href=\"mailto:support@4dnucleome.org\">Data Coordination and Integration Center</a>.</p></div>"}], "project_release": "2019-11-19", "experiments_in_set": [{"files": [{"file_type_detailed": "reads (fastq)", "file_size": 508630679, "uuid": "6243eb05-5ddd-464b-8a0c-3851aeec8c5a", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/6243eb05-5ddd-464b-8a0c-3851aeec8c5a/4DNFIUHIP1TH.fastq.gz", "file_type": "reads", "upload_key": "6243eb05-5ddd-464b-8a0c-3851aeec8c5a/4DNFIUHIP1TH.fastq.gz", "@id": "/files-fastq/4DNFIUHIP1TH/", "display_title": "4DNFIUHIP1TH.fastq.gz", "accession": "4DNFIUHIP1TH", "file_classification": "raw file", "md5sum": "ccade995195bbfab7c2ab1c6a0f85467", "href": "/files-fastq/4DNFIUHIP1TH/@@download/4DNFIUHIP1TH.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "quality_metric": {"uuid": "29cca126-5eee-4b31-badc-4979b4e540f4", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIUHIP1TH/fastqc_report.html", "Total Sequences": 8910519, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "@id": "/quality-metrics-fastqc/29cca126-5eee-4b31-badc-4979b4e540f4/", "status": "released", "display_title": "QualityMetricFastqc from 2019-11-15", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "display_title": "David Gilbert, SDBRI", "@id": "/labs/david-gilbert-lab/", "name": "david-gilbert-lab", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "external_references": [], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "2-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "late of 2 fractions", "dataset": "E/L repliseq on EN52.9 mESC with CTCF-AID", "condition": "CTCF- depletion late fraction", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "ES-E14TG2a with CTCF-AID", "lab_name": "David Gilbert, SDBRI"}}], "display_title": "2-stage Repli-seq on ES-E14TG2a with CTCF-AID S-phase late - 4DNEX9RLOYU1", "@id": "/experiments-repliseq/4DNEX9RLOYU1/", "status": "released", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "uuid": "9daf16db-f91a-4f78-b1b7-069078238e2d", "accession": "4DNEX9RLOYU1", "biosample": {"treatments_summary": "Auxin treatment (0.5 mM, 48.0h)", "modifications_summary": "None", "@type": ["Biosample", "Item"], "uuid": "2866cd8f-3ea1-4799-98fa-3a96d23a539f", "biosample_category": ["Mouse stem cell"], "display_title": "4DNBS5KQENOI", "@id": "/biosamples/4DNBS5KQENOI/", "biosource_summary": "ES-E14TG2a with CTCF-AID", "biosample_type": "stem cells", "status": "released", "accession": "4DNBS5KQENOI", "biosource": [{"accession": "4DNSRLMKMT14", "display_title": "ES-E14TG2a with CTCF-AID - 4DNSRLMKMT14", "status": "released", "override_biosource_name": "ES-E14TG2a with CTCF-AID", "uuid": "9fd3c189-7169-4336-bfd1-545c3b53ca44", "biosource_type": "stem cell derived cell line", "@id": "/biosources/4DNSRLMKMT14/", "cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "tissue": {"preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "display_title": "stem cell", "synonyms": ["animal stem cell"], "@type": ["OntologyTerm", "Item"], "term_name": "stem cell", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "term_id": "CL:0000034", "status": "released", "slim_terms": [{"display_title": "cell", "status": "current", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "status": "released", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"uuid": "2262fd9b-3185-4c65-8ad5-bfe65e986954", "preferred_name": "ES-E14TG2a", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/EFO:0006275/", "term_id": "EFO:0006275", "display_title": "ES-E14TG2a", "status": "released", "term_name": "ES-E14TG2a", "slim_terms": [{"@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"display_title": "M. musculus", "@id": "/organisms/10090/", "@type": ["Organism", "Item"], "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "name": "mouse", "scientific_name": "Mus musculus", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing Cell Culture Details"], "badge": {"badge_classification": "Warning", "@type": ["Badge", "Item"], "title": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "warning": "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.", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "treatments": [{"@id": "/treatments-agent/17b3f532-060e-409c-85d2-0ddda423fcc4/", "treatment_type": "Chemical", "duration_units": "hour", "uuid": "17b3f532-060e-409c-85d2-0ddda423fcc4", "display_title": "Auxin treatment (0.5 mM, 48.0h)", "chemical": "Auxin", "concentration_units": "mM", "@type": ["TreatmentAgent", "Treatment", "Item"], "concentration": 0.5, "description": "Treatment of cells with Auxin for 48 hours to induce AID-dependent degradation of CTCF", "duration": 48.0, "status": "released", "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": [{"display_title": "4DNFI2D8BTI2.bam", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/6427920a-93eb-4463-9377-6969d98609f8/4DNFI2D8BTI2.bam", "file_type": "alignments", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "upload_key": "6427920a-93eb-4463-9377-6969d98609f8/4DNFI2D8BTI2.bam", "accession": "4DNFI2D8BTI2", "file_format": {"display_title": "bam", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 378711138, "@id": "/files-processed/4DNFI2D8BTI2/", "uuid": "6427920a-93eb-4463-9377-6969d98609f8", "file_type_detailed": "alignments (bam)", "file_classification": "processed file", "md5sum": "a1e1ac8be3a3b5512b38abdcf4d37548", "href": "/files-processed/4DNFI2D8BTI2/@@download/4DNFI2D8BTI2.bam", "last_modified": {"date_modified": "2021-03-28T14:42:47.153174+00:00"}, "quality_metric": {"@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2019-11-15", "status": "released", "uuid": "54bd6fce-1551-46a9-b24c-75b36bb48b6e", "@id": "/quality-metrics-dedupqc-repliseq/54bd6fce-1551-46a9-b24c-75b36bb48b6e/", "overall_quality_status": "PASS", "quality_metric_summary": [{"title": "Total Aligned", "value": "6336500", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "1.14", "tooltip": "Percent of total aligned reads (=0.07m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "david-gilbert-lab", "@id": "/labs/david-gilbert-lab/", "status": "current", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@type": ["Lab", "Item"], "display_title": "David Gilbert, SDBRI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"status": "current", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "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"]}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "2-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "late of 2 fractions", "dataset": "E/L repliseq on EN52.9 mESC with CTCF-AID", "condition": "CTCF- depletion late fraction", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "ES-E14TG2a with CTCF-AID", "lab_name": "4DN DCIC, HMS"}, "external_references": []}, {"display_title": "4DNFIEQJXDA7.bedGraph.gz", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/06e32cc6-c205-4135-950b-e1f5273fb679/4DNFIEQJXDA7.bedGraph.gz", "higlass_uid": "0459f49c-688c-4e90-b7bf-7bb08b30ba30", "file_type": "normalized counts", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "upload_key": "06e32cc6-c205-4135-950b-e1f5273fb679/4DNFIEQJXDA7.bedGraph.gz", "accession": "4DNFIEQJXDA7", "file_format": {"display_title": "bg", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bg/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 3139572, "@id": "/files-processed/4DNFIEQJXDA7/", "uuid": "06e32cc6-c205-4135-950b-e1f5273fb679", "file_type_detailed": "normalized counts (bg)", "file_classification": "processed file", "md5sum": "5b16d464c2181aa1c6433af6abb7940b", "href": "/files-processed/4DNFIEQJXDA7/@@download/4DNFIEQJXDA7.bedGraph.gz", "last_modified": {"date_modified": "2023-10-31T16:53:44.788842+00:00"}, "extra_files": [{"href": "/files-processed/4DNFIEQJXDA7/@@download/4DNFIEQJXDA7.bedGraph.gz.px2", "md5sum": "26a259773381f2962d0281ea0c0a838a", "file_size": 906450, "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/bg_px2/", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "display_title": "bg_px2", "file_format": "bg_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"href": "/files-processed/4DNFIEQJXDA7/@@download/4DNFIEQJXDA7.bw", "md5sum": "e6429e001922c0a2933b793005242f01", "file_size": 3677202, "use_for": "visualization", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/bw/", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "display_title": "bw", "file_format": "bw", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "contributing_labs": [{"name": "david-gilbert-lab", "@id": "/labs/david-gilbert-lab/", "status": "current", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@type": ["Lab", "Item"], "display_title": "David Gilbert, SDBRI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"status": "current", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFIEQJXDA7 - counts for ES-E14TG2a with random integration of EGFP and AID-tagged CTCF, Tir1 insertion 2-stage Repli-seq late of 2 fractions", "@id": "/higlass-view-configs/14669181-52ff-4576-874a-395f915724ce/", "uuid": "14669181-52ff-4576-874a-395f915724ce", "status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "2-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "late of 2 fractions", "dataset": "E/L repliseq on EN52.9 mESC with CTCF-AID", "condition": "CTCF- depletion late fraction", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "ES-E14TG2a with CTCF-AID", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for ES-E14TG2a with CTCF-AID 2-stage Repli-seq late of 2 fractions"}, "external_references": []}], "experiment_type": {"assay_classification": "Linear DNA Enrichment", "status": "released", "title": "2-stage Repli-seq", "assay_subclassification": "Replication Timing", "display_title": "2-stage Repli-seq", "other_tags": ["1D"], "uuid": "23e234e7-d59e-4c40-ae42-7a7d5339fa76", "assay_subclass_short": "Replication timing", "@id": "/experiment-types/2-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "experiment_category": "Sequencing", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"field": "Fraction", "value": "late of 2 fractions", "combined": "Fraction: late of 2 fractions"}, "last_modified": {"date_modified": "2019-11-19T17:19:58.005101+00:00"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"files": [{"file_type_detailed": "reads (fastq)", "file_size": 419525599, "uuid": "df48404b-29f6-45c2-8354-a58a1ac87545", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/df48404b-29f6-45c2-8354-a58a1ac87545/4DNFIA33NHHU.fastq.gz", "file_type": "reads", "upload_key": "df48404b-29f6-45c2-8354-a58a1ac87545/4DNFIA33NHHU.fastq.gz", "@id": "/files-fastq/4DNFIA33NHHU/", "display_title": "4DNFIA33NHHU.fastq.gz", "accession": "4DNFIA33NHHU", "file_classification": "raw file", "md5sum": "4d1be1f94d86b382270c0a8928effccf", "href": "/files-fastq/4DNFIA33NHHU/@@download/4DNFIA33NHHU.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "quality_metric": {"uuid": "313b54ef-db8e-4b25-8f49-be3b7c63fa4b", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIA33NHHU/fastqc_report.html", "Total Sequences": 7368022, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "@id": "/quality-metrics-fastqc/313b54ef-db8e-4b25-8f49-be3b7c63fa4b/", "status": "released", "display_title": "QualityMetricFastqc from 2019-11-15", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "display_title": "David Gilbert, SDBRI", "@id": "/labs/david-gilbert-lab/", "name": "david-gilbert-lab", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "external_references": [], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "2-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "late of 2 fractions", "dataset": "E/L repliseq on EN52.9 mESC with CTCF-AID", "condition": "CTCF- depletion late fraction", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "ES-E14TG2a with CTCF-AID", "lab_name": "David Gilbert, SDBRI"}}], "display_title": "2-stage Repli-seq on ES-E14TG2a with CTCF-AID S-phase late - 4DNEXKA5JCIZ", "@id": "/experiments-repliseq/4DNEXKA5JCIZ/", "status": "released", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "uuid": "e448011e-be4b-4d1d-9e21-d409275f2cb7", "accession": "4DNEXKA5JCIZ", "biosample": {"treatments_summary": "Auxin treatment (0.5 mM, 48.0h)", "modifications_summary": "None", "@type": ["Biosample", "Item"], "uuid": "f79588a2-419b-4377-bd50-59329e44ad6c", "biosample_category": ["Mouse stem cell"], "display_title": "4DNBSEAGAR1H", "@id": "/biosamples/4DNBSEAGAR1H/", "biosource_summary": "ES-E14TG2a with CTCF-AID", "biosample_type": "stem cells", "status": "released", "accession": "4DNBSEAGAR1H", "biosource": [{"accession": "4DNSRLMKMT14", "display_title": "ES-E14TG2a with CTCF-AID - 4DNSRLMKMT14", "status": "released", "override_biosource_name": "ES-E14TG2a with CTCF-AID", "uuid": "9fd3c189-7169-4336-bfd1-545c3b53ca44", "biosource_type": "stem cell derived cell line", "@id": "/biosources/4DNSRLMKMT14/", "cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "tissue": {"preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "display_title": "stem cell", "synonyms": ["animal stem cell"], "@type": ["OntologyTerm", "Item"], "term_name": "stem cell", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "term_id": "CL:0000034", "status": "released", "slim_terms": [{"display_title": "cell", "status": "current", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "status": "released", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"uuid": "2262fd9b-3185-4c65-8ad5-bfe65e986954", "preferred_name": "ES-E14TG2a", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/EFO:0006275/", "term_id": "EFO:0006275", "display_title": "ES-E14TG2a", "status": "released", "term_name": "ES-E14TG2a", "slim_terms": [{"@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"display_title": "M. musculus", "@id": "/organisms/10090/", "@type": ["Organism", "Item"], "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "name": "mouse", "scientific_name": "Mus musculus", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing Cell Culture Details"], "badge": {"badge_classification": "Warning", "@type": ["Badge", "Item"], "title": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "warning": "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.", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "treatments": [{"@id": "/treatments-agent/17b3f532-060e-409c-85d2-0ddda423fcc4/", "treatment_type": "Chemical", "duration_units": "hour", "uuid": "17b3f532-060e-409c-85d2-0ddda423fcc4", "display_title": "Auxin treatment (0.5 mM, 48.0h)", "chemical": "Auxin", "concentration_units": "mM", "@type": ["TreatmentAgent", "Treatment", "Item"], "concentration": 0.5, "description": "Treatment of cells with Auxin for 48 hours to induce AID-dependent degradation of CTCF", "duration": 48.0, "status": "released", "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": [{"display_title": "4DNFI1NOVNJL.bam", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ec308886-92fc-45a2-a6b9-3e530723ce12/4DNFI1NOVNJL.bam", "file_type": "alignments", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "upload_key": "ec308886-92fc-45a2-a6b9-3e530723ce12/4DNFI1NOVNJL.bam", "accession": "4DNFI1NOVNJL", "file_format": {"display_title": "bam", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 310661307, "@id": "/files-processed/4DNFI1NOVNJL/", "uuid": "ec308886-92fc-45a2-a6b9-3e530723ce12", "file_type_detailed": "alignments (bam)", "file_classification": "processed file", "md5sum": "06a072971b2698e93f71452f7b1a57ea", "href": "/files-processed/4DNFI1NOVNJL/@@download/4DNFI1NOVNJL.bam", "last_modified": {"date_modified": "2021-03-28T14:42:28.486529+00:00"}, "quality_metric": {"@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2019-11-18", "status": "released", "uuid": "a04e72c7-2ddb-41ff-804d-6717e5308c0c", "@id": "/quality-metrics-dedupqc-repliseq/a04e72c7-2ddb-41ff-804d-6717e5308c0c/", "overall_quality_status": "PASS", "quality_metric_summary": [{"title": "Total Aligned", "value": "5203545", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "1.178", "tooltip": "Percent of total aligned reads (=0.06m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "david-gilbert-lab", "@id": "/labs/david-gilbert-lab/", "status": "current", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@type": ["Lab", "Item"], "display_title": "David Gilbert, SDBRI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"status": "current", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "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"]}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "2-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "late of 2 fractions", "dataset": "E/L repliseq on EN52.9 mESC with CTCF-AID", "condition": "CTCF- depletion late fraction", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "ES-E14TG2a with CTCF-AID", "lab_name": "4DN DCIC, HMS"}, "external_references": []}, {"display_title": "4DNFI5AMLA4S.bedGraph.gz", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/7b054b14-fc69-4712-bd3a-9757bc7cd992/4DNFI5AMLA4S.bedGraph.gz", "higlass_uid": "4fbf167f-6816-44ad-8d65-fdd067277f9e", "file_type": "normalized counts", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "upload_key": "7b054b14-fc69-4712-bd3a-9757bc7cd992/4DNFI5AMLA4S.bedGraph.gz", "accession": "4DNFI5AMLA4S", "file_format": {"display_title": "bg", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bg/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 3094927, "@id": "/files-processed/4DNFI5AMLA4S/", "uuid": "7b054b14-fc69-4712-bd3a-9757bc7cd992", "file_type_detailed": "normalized counts (bg)", "file_classification": "processed file", "md5sum": "56702415b9857f2b5c7dbabfe39deffb", "href": "/files-processed/4DNFI5AMLA4S/@@download/4DNFI5AMLA4S.bedGraph.gz", "last_modified": {"date_modified": "2023-10-31T16:53:32.440974+00:00"}, "extra_files": [{"href": "/files-processed/4DNFI5AMLA4S/@@download/4DNFI5AMLA4S.bedGraph.gz.px2", "md5sum": "a338332a9ea922a953451720e048fbb5", "file_size": 905807, "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/bg_px2/", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "display_title": "bg_px2", "file_format": "bg_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"href": "/files-processed/4DNFI5AMLA4S/@@download/4DNFI5AMLA4S.bw", "md5sum": "0917b6546e95e3847440f2da7a51e7d8", "file_size": 3632269, "use_for": "visualization", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/bw/", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "display_title": "bw", "file_format": "bw", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "contributing_labs": [{"name": "david-gilbert-lab", "@id": "/labs/david-gilbert-lab/", "status": "current", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@type": ["Lab", "Item"], "display_title": "David Gilbert, SDBRI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"status": "current", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFI5AMLA4S - counts for ES-E14TG2a with random integration of EGFP and AID-tagged CTCF, Tir1 insertion 2-stage Repli-seq late of 2 fractions", "@id": "/higlass-view-configs/9a253eff-bfe3-416d-88eb-42f24344f6fb/", "uuid": "9a253eff-bfe3-416d-88eb-42f24344f6fb", "status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "2-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "late of 2 fractions", "dataset": "E/L repliseq on EN52.9 mESC with CTCF-AID", "condition": "CTCF- depletion late fraction", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "ES-E14TG2a with CTCF-AID", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for ES-E14TG2a with CTCF-AID 2-stage Repli-seq late of 2 fractions"}, "external_references": []}], "experiment_type": {"assay_classification": "Linear DNA Enrichment", "status": "released", "title": "2-stage Repli-seq", "assay_subclassification": "Replication Timing", "display_title": "2-stage Repli-seq", "other_tags": ["1D"], "uuid": "23e234e7-d59e-4c40-ae42-7a7d5339fa76", "assay_subclass_short": "Replication timing", "@id": "/experiment-types/2-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "experiment_category": "Sequencing", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"field": "Fraction", "value": "late of 2 fractions", "combined": "Fraction: late of 2 fractions"}, "last_modified": {"date_modified": "2019-11-19T17:19:56.229746+00:00"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"files": [{"file_type_detailed": "reads (fastq)", "file_size": 569037082, "uuid": "e3036a52-1ed4-4b7f-a679-5ea6106cb936", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/e3036a52-1ed4-4b7f-a679-5ea6106cb936/4DNFIL1FZDVU.fastq.gz", "file_type": "reads", "upload_key": "e3036a52-1ed4-4b7f-a679-5ea6106cb936/4DNFIL1FZDVU.fastq.gz", "@id": "/files-fastq/4DNFIL1FZDVU/", "display_title": "4DNFIL1FZDVU.fastq.gz", "accession": "4DNFIL1FZDVU", "file_classification": "raw file", "md5sum": "456055a5e6669d442247a76ea62831fe", "href": "/files-fastq/4DNFIL1FZDVU/@@download/4DNFIL1FZDVU.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "quality_metric": {"uuid": "7ae07a2f-da78-48cf-887d-dd9e2db591b0", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIL1FZDVU/fastqc_report.html", "Total Sequences": 9799900, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "@id": "/quality-metrics-fastqc/7ae07a2f-da78-48cf-887d-dd9e2db591b0/", "status": "released", "display_title": "QualityMetricFastqc from 2019-11-15", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "display_title": "David Gilbert, SDBRI", "@id": "/labs/david-gilbert-lab/", "name": "david-gilbert-lab", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "external_references": [], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "2-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "late of 2 fractions", "dataset": "E/L repliseq on EN52.9 mESC with CTCF-AID", "condition": "CTCF- depletion early fraction", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "ES-E14TG2a with CTCF-AID", "lab_name": "David Gilbert, SDBRI"}}], "display_title": "2-stage Repli-seq on ES-E14TG2a with CTCF-AID S-phase late - 4DNEXH38RSQJ", "@id": "/experiments-repliseq/4DNEXH38RSQJ/", "status": "released", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "uuid": "97d5943d-28ae-4f2e-a46c-f30f2d283b43", "accession": "4DNEXH38RSQJ", "biosample": {"treatments_summary": "Auxin treatment (0.5 mM, 48.0h)", "modifications_summary": "None", "@type": ["Biosample", "Item"], "uuid": "9b87edd6-5d98-4814-b9a3-21910d94b5ce", "biosample_category": ["Mouse stem cell"], "display_title": "4DNBSOLF2INS", "@id": "/biosamples/4DNBSOLF2INS/", "biosource_summary": "ES-E14TG2a with CTCF-AID", "biosample_type": "stem cells", "status": "released", "accession": "4DNBSOLF2INS", "biosource": [{"accession": "4DNSRLMKMT14", "display_title": "ES-E14TG2a with CTCF-AID - 4DNSRLMKMT14", "status": "released", "override_biosource_name": "ES-E14TG2a with CTCF-AID", "uuid": "9fd3c189-7169-4336-bfd1-545c3b53ca44", "biosource_type": "stem cell derived cell line", "@id": "/biosources/4DNSRLMKMT14/", "cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "tissue": {"preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "display_title": "stem cell", "synonyms": ["animal stem cell"], "@type": ["OntologyTerm", "Item"], "term_name": "stem cell", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "term_id": "CL:0000034", "status": "released", "slim_terms": [{"display_title": "cell", "status": "current", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "status": "released", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"uuid": "2262fd9b-3185-4c65-8ad5-bfe65e986954", "preferred_name": "ES-E14TG2a", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/EFO:0006275/", "term_id": "EFO:0006275", "display_title": "ES-E14TG2a", "status": "released", "term_name": "ES-E14TG2a", "slim_terms": [{"@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"display_title": "M. musculus", "@id": "/organisms/10090/", "@type": ["Organism", "Item"], "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "name": "mouse", "scientific_name": "Mus musculus", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing Cell Culture Details"], "badge": {"badge_classification": "Warning", "@type": ["Badge", "Item"], "title": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "warning": "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.", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "treatments": [{"@id": "/treatments-agent/17b3f532-060e-409c-85d2-0ddda423fcc4/", "treatment_type": "Chemical", "duration_units": "hour", "uuid": "17b3f532-060e-409c-85d2-0ddda423fcc4", "display_title": "Auxin treatment (0.5 mM, 48.0h)", "chemical": "Auxin", "concentration_units": "mM", "@type": ["TreatmentAgent", "Treatment", "Item"], "concentration": 0.5, "description": "Treatment of cells with Auxin for 48 hours to induce AID-dependent degradation of CTCF", "duration": 48.0, "status": "released", "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": [{"display_title": "4DNFI6OBQAIK.bam", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e7528a9a-c224-4a42-bb05-09d4d909f943/4DNFI6OBQAIK.bam", "file_type": "alignments", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "upload_key": "e7528a9a-c224-4a42-bb05-09d4d909f943/4DNFI6OBQAIK.bam", "accession": "4DNFI6OBQAIK", "file_format": {"display_title": "bam", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 476362976, "@id": "/files-processed/4DNFI6OBQAIK/", "uuid": "e7528a9a-c224-4a42-bb05-09d4d909f943", "file_type_detailed": "alignments (bam)", "file_classification": "processed file", "md5sum": "670f4560026eba97f665035988be6628", "href": "/files-processed/4DNFI6OBQAIK/@@download/4DNFI6OBQAIK.bam", "last_modified": {"date_modified": "2021-03-28T14:42:26.875908+00:00"}, "quality_metric": {"@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2019-11-18", "status": "released", "uuid": "bb418d53-7a11-4d6c-816a-09406ee705d7", "@id": "/quality-metrics-dedupqc-repliseq/bb418d53-7a11-4d6c-816a-09406ee705d7/", "overall_quality_status": "PASS", "quality_metric_summary": [{"title": "Total Aligned", "value": "7996479", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "0.806", "tooltip": "Percent of total aligned reads (=0.06m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "david-gilbert-lab", "@id": "/labs/david-gilbert-lab/", "status": "current", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@type": ["Lab", "Item"], "display_title": "David Gilbert, SDBRI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"status": "current", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "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"]}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "2-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "late of 2 fractions", "dataset": "E/L repliseq on EN52.9 mESC with CTCF-AID", "condition": "CTCF- depletion early fraction", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "ES-E14TG2a with CTCF-AID", "lab_name": "4DN DCIC, HMS"}, "external_references": []}, {"display_title": "4DNFIC9B6KAJ.bedGraph.gz", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/621ef73b-ce1e-454c-86b0-51ddcb13d80d/4DNFIC9B6KAJ.bedGraph.gz", "higlass_uid": "43f3ab73-2d52-4bae-98d3-4b1d6bf683ff", "file_type": "normalized counts", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "upload_key": "621ef73b-ce1e-454c-86b0-51ddcb13d80d/4DNFIC9B6KAJ.bedGraph.gz", "accession": "4DNFIC9B6KAJ", "file_format": {"display_title": "bg", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bg/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 3169836, "@id": "/files-processed/4DNFIC9B6KAJ/", "uuid": "621ef73b-ce1e-454c-86b0-51ddcb13d80d", "file_type_detailed": "normalized counts (bg)", "file_classification": "processed file", "md5sum": "c8e4d1afa32a490c7567172851c01883", "href": "/files-processed/4DNFIC9B6KAJ/@@download/4DNFIC9B6KAJ.bedGraph.gz", "last_modified": {"date_modified": "2023-10-31T16:53:31.087794+00:00"}, "extra_files": [{"href": "/files-processed/4DNFIC9B6KAJ/@@download/4DNFIC9B6KAJ.bedGraph.gz.px2", "md5sum": "4d6a4bbac48f54d4a9a468b21c03b678", "file_size": 905583, "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/bg_px2/", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "display_title": "bg_px2", "file_format": "bg_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"href": "/files-processed/4DNFIC9B6KAJ/@@download/4DNFIC9B6KAJ.bw", "md5sum": "e8a23bd2a4c8a79e0e39b2409dcd3649", "file_size": 3635804, "use_for": "visualization", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/bw/", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "display_title": "bw", "file_format": "bw", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "contributing_labs": [{"name": "david-gilbert-lab", "@id": "/labs/david-gilbert-lab/", "status": "current", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@type": ["Lab", "Item"], "display_title": "David Gilbert, SDBRI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"status": "current", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFIC9B6KAJ - counts for ES-E14TG2a with random integration of EGFP and AID-tagged CTCF, Tir1 insertion 2-stage Repli-seq late of 2 fractions", "@id": "/higlass-view-configs/923fecdd-de95-48b1-ae96-4036d2db7fa9/", "uuid": "923fecdd-de95-48b1-ae96-4036d2db7fa9", "status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "2-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "late of 2 fractions", "dataset": "E/L repliseq on EN52.9 mESC with CTCF-AID", "condition": "CTCF- depletion early fraction", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "ES-E14TG2a with CTCF-AID", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for ES-E14TG2a with CTCF-AID 2-stage Repli-seq late of 2 fractions"}, "external_references": []}], "experiment_type": {"assay_classification": "Linear DNA Enrichment", "status": "released", "title": "2-stage Repli-seq", "assay_subclassification": "Replication Timing", "display_title": "2-stage Repli-seq", "other_tags": ["1D"], "uuid": "23e234e7-d59e-4c40-ae42-7a7d5339fa76", "assay_subclass_short": "Replication timing", "@id": "/experiment-types/2-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "experiment_category": "Sequencing", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"field": "Fraction", "value": "late of 2 fractions", "combined": "Fraction: late of 2 fractions"}, "last_modified": {"date_modified": "2019-11-19T17:19:58.740935+00:00"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"files": [{"file_type_detailed": "reads (fastq)", "file_size": 436445453, "uuid": "de70665f-786e-4d31-90c5-02f71928fb24", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/de70665f-786e-4d31-90c5-02f71928fb24/4DNFI4KDNUJE.fastq.gz", "file_type": "reads", "upload_key": "de70665f-786e-4d31-90c5-02f71928fb24/4DNFI4KDNUJE.fastq.gz", "@id": "/files-fastq/4DNFI4KDNUJE/", "display_title": "4DNFI4KDNUJE.fastq.gz", "accession": "4DNFI4KDNUJE", "file_classification": "raw file", "md5sum": "625afe2f2fb1958a762b0d539828c715", "href": "/files-fastq/4DNFI4KDNUJE/@@download/4DNFI4KDNUJE.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "quality_metric": {"uuid": "a363783a-dc84-4c95-8f29-28dc1dc07159", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI4KDNUJE/fastqc_report.html", "Total Sequences": 7553150, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "@id": "/quality-metrics-fastqc/a363783a-dc84-4c95-8f29-28dc1dc07159/", "status": "released", "display_title": "QualityMetricFastqc from 2019-11-15", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "display_title": "David Gilbert, SDBRI", "@id": "/labs/david-gilbert-lab/", "name": "david-gilbert-lab", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "external_references": [], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "2-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "late of 2 fractions", "dataset": "E/L repliseq on EN52.9 mESC with CTCF-AID", "condition": "CTCF- depletion early fraction", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "ES-E14TG2a with CTCF-AID", "lab_name": "David Gilbert, SDBRI"}}], "display_title": "2-stage Repli-seq on ES-E14TG2a with CTCF-AID S-phase late - 4DNEXJ57TKZK", "@id": "/experiments-repliseq/4DNEXJ57TKZK/", "status": "released", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "uuid": "bedc62ed-7e7e-42ac-abcb-3625a43f5993", "accession": "4DNEXJ57TKZK", "biosample": {"treatments_summary": "Auxin treatment (0.5 mM, 48.0h)", "modifications_summary": "None", "@type": ["Biosample", "Item"], "uuid": "e52c0b0c-b145-4c9b-aa92-94d5f6ab52bd", "biosample_category": ["Mouse stem cell"], "display_title": "4DNBSDR9PO96", "@id": "/biosamples/4DNBSDR9PO96/", "biosource_summary": "ES-E14TG2a with CTCF-AID", "biosample_type": "stem cells", "status": "released", "accession": "4DNBSDR9PO96", "biosource": [{"accession": "4DNSRLMKMT14", "display_title": "ES-E14TG2a with CTCF-AID - 4DNSRLMKMT14", "status": "released", "override_biosource_name": "ES-E14TG2a with CTCF-AID", "uuid": "9fd3c189-7169-4336-bfd1-545c3b53ca44", "biosource_type": "stem cell derived cell line", "@id": "/biosources/4DNSRLMKMT14/", "cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "tissue": {"preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "display_title": "stem cell", "synonyms": ["animal stem cell"], "@type": ["OntologyTerm", "Item"], "term_name": "stem cell", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "term_id": "CL:0000034", "status": "released", "slim_terms": [{"display_title": "cell", "status": "current", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "status": "released", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"uuid": "2262fd9b-3185-4c65-8ad5-bfe65e986954", "preferred_name": "ES-E14TG2a", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/EFO:0006275/", "term_id": "EFO:0006275", "display_title": "ES-E14TG2a", "status": "released", "term_name": "ES-E14TG2a", "slim_terms": [{"@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"display_title": "M. musculus", "@id": "/organisms/10090/", "@type": ["Organism", "Item"], "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "name": "mouse", "scientific_name": "Mus musculus", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing Cell Culture Details"], "badge": {"badge_classification": "Warning", "@type": ["Badge", "Item"], "title": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "warning": "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.", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "treatments": [{"@id": "/treatments-agent/17b3f532-060e-409c-85d2-0ddda423fcc4/", "treatment_type": "Chemical", "duration_units": "hour", "uuid": "17b3f532-060e-409c-85d2-0ddda423fcc4", "display_title": "Auxin treatment (0.5 mM, 48.0h)", "chemical": "Auxin", "concentration_units": "mM", "@type": ["TreatmentAgent", "Treatment", "Item"], "concentration": 0.5, "description": "Treatment of cells with Auxin for 48 hours to induce AID-dependent degradation of CTCF", "duration": 48.0, "status": "released", "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": [{"display_title": "4DNFI2ZBVW65.bam", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/2bf69ed3-f86e-4fc2-8aeb-b9db7f5e50aa/4DNFI2ZBVW65.bam", "file_type": "alignments", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "upload_key": "2bf69ed3-f86e-4fc2-8aeb-b9db7f5e50aa/4DNFI2ZBVW65.bam", "accession": "4DNFI2ZBVW65", "file_format": {"display_title": "bam", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 373809774, "@id": "/files-processed/4DNFI2ZBVW65/", "uuid": "2bf69ed3-f86e-4fc2-8aeb-b9db7f5e50aa", "file_type_detailed": "alignments (bam)", "file_classification": "processed file", "md5sum": "420fd827c03004c24b2de49269fc69da", "href": "/files-processed/4DNFI2ZBVW65/@@download/4DNFI2ZBVW65.bam", "last_modified": {"date_modified": "2021-03-28T14:42:25.181477+00:00"}, "quality_metric": {"@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2019-11-18", "status": "released", "uuid": "b0967a7b-5b06-43f7-9c65-60f9ac8a22c0", "@id": "/quality-metrics-dedupqc-repliseq/b0967a7b-5b06-43f7-9c65-60f9ac8a22c0/", "overall_quality_status": "PASS", "quality_metric_summary": [{"title": "Total Aligned", "value": "6266667", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "0.692", "tooltip": "Percent of total aligned reads (=0.04m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "david-gilbert-lab", "@id": "/labs/david-gilbert-lab/", "status": "current", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@type": ["Lab", "Item"], "display_title": "David Gilbert, SDBRI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"status": "current", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "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"]}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "2-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "late of 2 fractions", "dataset": "E/L repliseq on EN52.9 mESC with CTCF-AID", "condition": "CTCF- depletion early fraction", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "ES-E14TG2a with CTCF-AID", "lab_name": "4DN DCIC, HMS"}, "external_references": []}, {"display_title": "4DNFIVSG4LVV.bedGraph.gz", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/bf991e0b-5f1c-4fdb-9567-59039b8ff105/4DNFIVSG4LVV.bedGraph.gz", "higlass_uid": "9ec90870-7913-4099-8133-f9da6b1c1d23", "file_type": "normalized counts", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "upload_key": "bf991e0b-5f1c-4fdb-9567-59039b8ff105/4DNFIVSG4LVV.bedGraph.gz", "accession": "4DNFIVSG4LVV", "file_format": {"display_title": "bg", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bg/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 3110644, "@id": "/files-processed/4DNFIVSG4LVV/", "uuid": "bf991e0b-5f1c-4fdb-9567-59039b8ff105", "file_type_detailed": "normalized counts (bg)", "file_classification": "processed file", "md5sum": "13437732d7d1083c4d53210f0016dcb6", "href": "/files-processed/4DNFIVSG4LVV/@@download/4DNFIVSG4LVV.bedGraph.gz", "last_modified": {"date_modified": "2023-10-31T16:53:29.989560+00:00"}, "extra_files": [{"href": "/files-processed/4DNFIVSG4LVV/@@download/4DNFIVSG4LVV.bedGraph.gz.px2", "md5sum": "e4949c5a1ade9d78fc8298db5c638776", "file_size": 903144, "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/bg_px2/", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "display_title": "bg_px2", "file_format": "bg_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"href": "/files-processed/4DNFIVSG4LVV/@@download/4DNFIVSG4LVV.bw", "md5sum": "52a9aa838e7d36a0defc36ac03dd2d4d", "file_size": 3555835, "use_for": "visualization", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/bw/", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "display_title": "bw", "file_format": "bw", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "contributing_labs": [{"name": "david-gilbert-lab", "@id": "/labs/david-gilbert-lab/", "status": "current", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@type": ["Lab", "Item"], "display_title": "David Gilbert, SDBRI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"status": "current", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFIVSG4LVV - counts for ES-E14TG2a with random integration of EGFP and AID-tagged CTCF, Tir1 insertion 2-stage Repli-seq late of 2 fractions", "@id": "/higlass-view-configs/72fa36bd-50c2-407d-a963-8d5735c15ec2/", "uuid": "72fa36bd-50c2-407d-a963-8d5735c15ec2", "status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "2-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "late of 2 fractions", "dataset": "E/L repliseq on EN52.9 mESC with CTCF-AID", "condition": "CTCF- depletion early fraction", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "ES-E14TG2a with CTCF-AID", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for ES-E14TG2a with CTCF-AID 2-stage Repli-seq late of 2 fractions"}, "external_references": []}], "experiment_type": {"assay_classification": "Linear DNA Enrichment", "status": "released", "title": "2-stage Repli-seq", "assay_subclassification": "Replication Timing", "display_title": "2-stage Repli-seq", "other_tags": ["1D"], "uuid": "23e234e7-d59e-4c40-ae42-7a7d5339fa76", "assay_subclass_short": "Replication timing", "@id": "/experiment-types/2-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "experiment_category": "Sequencing", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"field": "Fraction", "value": "late of 2 fractions", "combined": "Fraction: late of 2 fractions"}, "last_modified": {"date_modified": "2019-11-19T17:19:57.471699+00:00"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experimentset_type": "custom", "@id": "/experiment-sets/4DNESKVCLFGY/", "@type": ["ExperimentSet", "Item"], "uuid": "e96f8eeb-d91a-48b4-9929-564c2d60247b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESKVCLFGY", "external_references": [], "pubs_using": [], "publications_of_set": [], "number_of_experiments": 4, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBS5KQENOI/", "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/4DNBSEAGAR1H/", "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/4DNBSOLF2INS/", "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/4DNBSDR9PO96/", "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": []}