{"lab": {"uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "display_title": "David Gilbert, SDBRI", "@type": ["Lab", "Item"], "title": "David Gilbert, SDBRI", "status": "current", "correspondence": [{"contact_email": "Z2lsYmVydEBzZGJyaS5vcmc=", "@id": "/users/1dbb8e49-38e4-4154-a97c-af8176a58c44/", "display_title": "David Gilbert"}], "@id": "/labs/david-gilbert-lab/", "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": "9f6d9e4a-9542-49c7-8a54-c6c9a1862d90", "center_title": "CDIMV - Ma", "project": "4DN", "description": "CDIMV: The cell nucleus is a heterogeneous organelle that consists of nuclear bodies such as nuclear lamina, speckles, nucleoli and PML bodies. These structures continuously tether and tug chromatin at the small and large scales to synergistically orchestrate dynamic functions in distinct spatio-temporal compartments. A major obstacle to the production of navigable 4D reference maps and relating structure to function in the nucleus remains understanding how these different scales of organization influence each other. In particular, we have a poor understanding of the large-scale genome organization. Growing evidence suggests that such nuclear compartmentalization is causally connected with vital genome functions in human health and disease. However, the principles of this nuclear compartmentalization, its dynamics during changes in cell conditions, and its functional relevance are poorly understood. One lesson from Phase 1 4DN was the huge gap in throughput between imaging methods, that directly measure large-scale multi-landmark relationships, and genomic methods, that aim for whole genome high-resolution maps but are indirect measurements and provide limited information about large-scale compartments. For this 4DN UM1 Center application, we propose to meet these needs through the following Aims: (1) Generate multi-modal imaging and genomic datasets to reveal the structure, dynamics, and function of nuclear compartmentalization; (2) Develop and apply computational tools for data-driven genome structure modeling and integrative analysis of nuclear compartmentalization; (3) Develop an integrative analysis and visualization platform with navigable 4D reference maps of nuclear organization. The combined datasets and results of our proposed approaches will advance our understanding of nuclear compartmentalization, the interwoven connections among different nuclear components, and their functional significance. Our new integrative analysis tools and data-driven predictive models will produce more complete nuclear organization reference maps that integrate large-scale chromosome structure data from live and super-resolution microscopy with multi-modal genomic data including smaller scale chromatin interaction maps and predict functional relationships and dynamic responses. Our navigable reference maps will be publicly accessible through an analysis platform that provides interactive visualization of multiple data types, thus enabling investigators with diverse expertise to simultaneously explore their own data and related datasets/tools and promoting collaborations that will open new horizons into the role of the 4D nucleome in human health and disease.", "@id": "/awards/1UM1HG011593-01/", "@type": ["Award", "Item"], "display_title": "MULTISCALE ANALYSES OF 4D NUCLEOME STRUCTURE AND FUNCTION BY COMPREHENSIVE MULTIMODAL DATA INTEGRATION", "status": "current", "name": "1UM1HG011593-01", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIAYH864G/", "uuid": "8a18a301-cada-4db6-bc82-72db10e04dbf", "upload_key": "8a18a301-cada-4db6-bc82-72db10e04dbf/4DNFIAYH864G.fastq.gz", "href": "/files-fastq/4DNFIAYH864G/@@download/4DNFIAYH864G.fastq.gz", "file_type_detailed": "reads (fastq)", "accession": "4DNFIAYH864G", "display_title": "4DNFIAYH864G.fastq.gz", "file_type": "reads", "file_size": 519800497, "status": "released", "quality_metric": {"@id": "/quality-metrics-fastqc/9b9a9bf6-fe21-4f3a-813e-ed5b342c4dfa/", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIAYH864G/fastqc_report.html", "Sequence length": "35-75", "status": "released", "display_title": "QualityMetricFastqc from 2021-11-01", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 10628520, "uuid": "9b9a9bf6-fe21-4f3a-813e-ed5b342c4dfa", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "status": "released", "display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI6CBOCSM/", "uuid": "a484c2e1-6c47-4210-85e4-1d6e76cd5024", "upload_key": "a484c2e1-6c47-4210-85e4-1d6e76cd5024/4DNFI6CBOCSM.fastq.gz", "href": "/files-fastq/4DNFI6CBOCSM/@@download/4DNFI6CBOCSM.fastq.gz", "file_type_detailed": "reads (fastq)", "accession": "4DNFI6CBOCSM", "display_title": "4DNFI6CBOCSM.fastq.gz", "file_type": "reads", "file_size": 501399039, "status": "released", "quality_metric": {"@id": "/quality-metrics-fastqc/95519e0d-2aed-47f3-b4c9-1003ba664fbc/", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI6CBOCSM/fastqc_report.html", "Sequence length": "35-75", "status": "released", "display_title": "QualityMetricFastqc from 2021-11-01", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 10297217, "uuid": "95519e0d-2aed-47f3-b4c9-1003ba664fbc", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "status": "released", "display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIHLQ1IPI/", "uuid": "12dda154-8538-4c30-b2f2-4f5af2c37cdf", "upload_key": "12dda154-8538-4c30-b2f2-4f5af2c37cdf/4DNFIHLQ1IPI.fastq.gz", "href": "/files-fastq/4DNFIHLQ1IPI/@@download/4DNFIHLQ1IPI.fastq.gz", "file_type_detailed": "reads (fastq)", "accession": "4DNFIHLQ1IPI", "display_title": "4DNFIHLQ1IPI.fastq.gz", "file_type": "reads", "file_size": 518872248, "status": "released", "quality_metric": {"@id": "/quality-metrics-fastqc/d9c5cf31-0033-4de1-91f3-f7c0a9fc2c92/", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIHLQ1IPI/fastqc_report.html", "Sequence length": "35-75", "status": "released", "display_title": "QualityMetricFastqc from 2021-11-01", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 10617310, "uuid": "d9c5cf31-0033-4de1-91f3-f7c0a9fc2c92", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "status": "released", "display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI5DBKCJJ/", "uuid": "8be943b1-7a89-4c17-9736-f19cc31a2b82", "upload_key": "8be943b1-7a89-4c17-9736-f19cc31a2b82/4DNFI5DBKCJJ.fastq.gz", "href": "/files-fastq/4DNFI5DBKCJJ/@@download/4DNFI5DBKCJJ.fastq.gz", "file_type_detailed": "reads (fastq)", "accession": "4DNFI5DBKCJJ", "display_title": "4DNFI5DBKCJJ.fastq.gz", "file_type": "reads", "file_size": 514282615, "status": "released", "quality_metric": {"@id": "/quality-metrics-fastqc/d4ae223e-701b-4f4d-9b15-d96333a33b02/", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI5DBKCJJ/fastqc_report.html", "Sequence length": "35-75", "status": "released", "display_title": "QualityMetricFastqc from 2021-11-01", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 10533431, "uuid": "d4ae223e-701b-4f4d-9b15-d96333a33b02", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "status": "released", "display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}], "status": "released", "aliases": ["gilbert-lab:iPSC_80kbdel_L_phase_rep1"], "antibody": {"antibody_name": "anti-BrdU", "uuid": "e01a63eb-00a8-45c0-908f-c09f24d43f9e", "antibody_product_no": "555627", "display_title": "anti-BrdU (BD Biosciences, 555627)", "@id": "/antibodys/anti-BrdU-555627/", "@type": ["Antibody", "Item"], "status": "released", "antibody_vendor": {"@type": ["Vendor", "Item"], "uuid": "75e5dd4b-c173-40d0-8373-662cc05b9d32", "title": "BD Biosciences", "status": "released", "@id": "/vendors/bd-biosciences/", "display_title": "BD Biosciences", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "protocol": {"uuid": "5e017160-ad8b-49c1-a129-ccbd29966b6d", "display_title": "4DN Standard 2-stage Repli-seq protocol", "@type": ["Protocol", "Item"], "@id": "/protocols/5e017160-ad8b-49c1-a129-ccbd29966b6d/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEX5ZRL6AF", "biosample": {"uuid": "8a7d1849-d203-4347-900e-02f01d291840", "biosource_summary": "7889SA3.5", "status": "released", "biosample_type": "induced pluripotent stem cells", "modifications_summary": "Crispr deletion for 80KB IDS deletion", "display_title": "4DNBSNJMBVXT", "accession": "4DNBSNJMBVXT", "@type": ["Biosample", "Item"], "treatments_summary": "None", "@id": "/biosamples/4DNBSNJMBVXT/", "modifications": [{"@id": "/modifications/b58569ad-9d0a-4f3b-bfcc-e5a2d916e061/", "genomic_change": "deletion", "display_title": "Crispr deletion for 80KB IDS deletion", "modification_type": "Crispr", "description": "Deletion of 80 kb region at hg19, chrX: 148,551,953-148,636,657 including an early/late replication boundary", "uuid": "b58569ad-9d0a-4f3b-bfcc-e5a2d916e061", "status": "released", "@type": ["Modification", "Item"], "target_of_mod": [{"feature_type": {"status": "released", "uuid": "41b7a2c5-f2d9-46b4-a49d-51502fe61bb3", "@id": "/ontology-terms/SO:0000001/", "display_title": "region", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "preferred_label": "80KB IDS deletion", "organism_name": "human", "display_title": "80KB IDS deletion", "genome_location": [{"display_title": "GRCh38:X:149470422-149555112", "@id": "/genomic-regions/9e0dc5e1-83c6-4288-88b9-4c244836ac55/", "uuid": "9e0dc5e1-83c6-4288-88b9-4c244836ac55", "status": "released", "@type": ["GenomicRegion", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/bio-features/4ecbdbe9-0949-426a-bc2d-1dfa8bfce44c/", "status": "released", "uuid": "4ecbdbe9-0949-426a-bc2d-1dfa8bfce44c", "@type": ["BioFeature", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosource": [{"lab": {"display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "status": "current", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "award": {"status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "@id": "/awards/2U01CA200059-06/", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"term_id": "CL:0000034", "slim_terms": [{"display_title": "cell", "status": "current", "@type": ["OntologyTerm", "Item"], "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "status": "released", "@type": ["OntologyTerm", "Item"], "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "status": "released", "preferred_name": "stem cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000034/", "display_title": "stem cell", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "synonyms": ["animal stem cell"], "term_name": "stem cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["4dn-dcic-lab:7889SA3.5_iPS_cells"], "accession": "4DNSRIOTVJ4X", "cell_line": {"term_id": "CL:0002248", "@id": "/ontology-terms/CL:0002248/", "term_name": "pluripotent stem cell", "preferred_name": "pluripotent stem cell", "display_title": "pluripotent stem cell", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "8816a6d9-1295-4590-88fa-3dff7a2d117b", "slim_terms": [{"status": "released", "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "current", "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"display_title": "4DNINF2U62Q5", "@id": "/individuals-human/4DNINF2U62Q5/", "status": "released", "uuid": "bb407e38-3c7f-4782-9099-ed213854859f", "@type": ["IndividualHuman", "Individual", "Item"], "protected_data": false, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "Clone 3.5 of 7889SA pluripotent stem cells induced from human male fibroblasts - normal karyotype - described in PMID: 27120160", "date_created": "2021-01-20T15:02:19.468582+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-02-17T23:36:29.799426+00:00"}, "biosource_type": "induced pluripotent stem cell", "cell_line_tier": "Unclassified", "public_release": "2021-01-20", "schema_version": "2", "project_release": "2021-01-20", "biosource_vendor": {"@id": "/vendors/tessier-lavigne-lab/", "status": "released", "@type": ["Vendor", "Item"], "uuid": "41c3a683-313f-433e-b0e2-ab0ee775e55e", "display_title": "Tessier-Lavigne Lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "override_biosource_name": "7889SA3.5", "@id": "/biosources/4DNSRIOTVJ4X/", "@type": ["Biosource", "Item"], "uuid": "85b1e0d9-6d5a-4ddf-b964-3f712e7949d6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "7889SA3.5 - 4DNSRIOTVJ4X", "external_references": [], "biosource_name": "7889SA3.5", "biosource_category": ["Human stem cell"], "organism": {"@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "name": "human", "@type": ["Organism", "Item"], "display_title": "H. sapiens", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "badges": [{"messages": ["Biosample missing morphology_image"], "badge": {"status": "released", "warning": "Biosample Metadata Incomplete", "badge_icon": "/static/img/badges/biosample-icon.svg", "title": "Biosample Metadata Incomplete", "display_title": "Biosample Metadata Incomplete", "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.", "@type": ["Badge", "Item"], "@id": "/badges/biosample-metadata-incomplete/", "badge_classification": "Warning", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}]}, "dna_label": "BrdU", "description": "80 kb IZ del iPSCs Replicate 1 Late experiment", "sop_mapping": {"has_sop": "No"}, "date_created": "2021-11-01T18:12:24.359072+00:00", "submitted_by": {"error": "no view permissions"}, "labeling_time": 120, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-10-04T20:04:42.755259+00:00"}, "public_release": "2021-11-10", "schema_version": "4", "stage_fraction": "late fraction", "antibody_lot_id": "7033666", "experiment_type": {"uuid": "23e234e7-d59e-4c40-ae42-7a7d5339fa76", "experiment_category": "Sequencing", "title": "2-stage Repli-seq", "@type": ["ExperimentType", "Item"], "display_title": "2-stage Repli-seq", "@id": "/experiment-types/2-stage-repli-seq/", "assay_subclass_short": "Replication timing", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"href": "/files-processed/4DNFIQVGKN4G/@@download/4DNFIQVGKN4G.bam", "accession": "4DNFIQVGKN4G", "file_type": "alignments", "uuid": "4817637e-af28-4848-9a74-b9df045ab7a8", "display_title": "4DNFIQVGKN4G.bam", "file_format": {"@id": "/file-formats/bam/", "display_title": "bam", "file_format": "bam", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 544158037, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/4817637e-af28-4848-9a74-b9df045ab7a8/4DNFIQVGKN4G.bam", "@type": ["FileProcessed", "File", "Item"], "upload_key": "4817637e-af28-4848-9a74-b9df045ab7a8/4DNFIQVGKN4G.bam", "status": "released", "@id": "/files-processed/4DNFIQVGKN4G/", "file_type_detailed": "alignments (bam)", "file_classification": "processed file", "quality_metric": {"display_title": "QualityMetricDedupqcRepliseq from 2021-11-02", "uuid": "9ff2baae-9169-4061-a6f8-1b679447b963", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "@id": "/quality-metrics-dedupqc-repliseq/9ff2baae-9169-4061-a6f8-1b679447b963/", "status": "released", "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "9100782", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "5.021", "tooltip": "Percent of total aligned reads (=0.46m)", "numberType": "percent"}]}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "2-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "late fraction of 2 fractions", "dataset": "E/L repliseq on\u00a0engineered iPSC cells", "condition": "IZ boundary deletion late fraction", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "7889SA3.5", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"href": "/files-processed/4DNFIFBIE2XK/@@download/4DNFIFBIE2XK.bedGraph.gz", "accession": "4DNFIFBIE2XK", "file_type": "normalized counts", "uuid": "a4dce737-95b1-4ca3-9a1c-685d43c1c142", "display_title": "4DNFIFBIE2XK.bedGraph.gz", "file_format": {"@id": "/file-formats/bg/", "display_title": "bg", "file_format": "bg", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 3584613, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a4dce737-95b1-4ca3-9a1c-685d43c1c142/4DNFIFBIE2XK.bedGraph.gz", "@type": ["FileProcessed", "File", "Item"], "upload_key": "a4dce737-95b1-4ca3-9a1c-685d43c1c142/4DNFIFBIE2XK.bedGraph.gz", "status": "released", "@id": "/files-processed/4DNFIFBIE2XK/", "file_type_detailed": "normalized counts (bg)", "file_classification": "processed file", "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "2-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "late fraction of 2 fractions", "dataset": "E/L repliseq on\u00a0engineered iPSC cells", "condition": "IZ boundary deletion late fraction", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "7889SA3.5", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for 7889SA3.5 2-stage Repli-seq late fraction of 2 fractions"}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"display_title": "4DNFIFBIE2XK - normalized counts for 7889SA3.5 2-stage Repli-seq late fraction of 2 fractions", "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "d7f975be-6fae-401f-ae90-640bdf9ff570", "status": "released", "@id": "/higlass-view-configs/d7f975be-6fae-401f-ae90-640bdf9ff570/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"href": "/files-processed/4DNFIY39QFPP/@@download/4DNFIY39QFPP.bam", "accession": "4DNFIY39QFPP", "file_type": "alignments", "uuid": "ac4499dc-22ce-4993-bc78-15073bc70b18", "display_title": "4DNFIY39QFPP.bam", "file_format": {"@id": "/file-formats/bam/", "display_title": "bam", "file_format": "bam", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 526460169, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ac4499dc-22ce-4993-bc78-15073bc70b18/4DNFIY39QFPP.bam", "@type": ["FileProcessed", "File", "Item"], "upload_key": "ac4499dc-22ce-4993-bc78-15073bc70b18/4DNFIY39QFPP.bam", "status": "released", "@id": "/files-processed/4DNFIY39QFPP/", "file_type_detailed": "alignments (bam)", "file_classification": "processed file", "quality_metric": {"display_title": "QualityMetricDedupqcRepliseq from 2021-11-02", "uuid": "b879b78c-a0a6-45d9-8972-0e1b86cc0efc", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "@id": "/quality-metrics-dedupqc-repliseq/b879b78c-a0a6-45d9-8972-0e1b86cc0efc/", "status": "released", "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "8822128", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "4.889", "tooltip": "Percent of total aligned reads (=0.43m)", "numberType": "percent"}]}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "2-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "late fraction of 2 fractions", "dataset": "E/L repliseq on\u00a0engineered iPSC cells", "condition": "IZ boundary deletion late fraction", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "7889SA3.5", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"href": "/files-processed/4DNFISW7RCC8/@@download/4DNFISW7RCC8.bedGraph.gz", "accession": "4DNFISW7RCC8", "file_type": "normalized counts", "uuid": "76f7010e-4807-4cb4-8124-08f852ef3590", "display_title": "4DNFISW7RCC8.bedGraph.gz", "file_format": {"@id": "/file-formats/bg/", "display_title": "bg", "file_format": "bg", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 3584385, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/76f7010e-4807-4cb4-8124-08f852ef3590/4DNFISW7RCC8.bedGraph.gz", "@type": ["FileProcessed", "File", "Item"], "upload_key": "76f7010e-4807-4cb4-8124-08f852ef3590/4DNFISW7RCC8.bedGraph.gz", "status": "released", "@id": "/files-processed/4DNFISW7RCC8/", "file_type_detailed": "normalized counts (bg)", "file_classification": "processed file", "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "2-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "late fraction of 2 fractions", "dataset": "E/L repliseq on\u00a0engineered iPSC cells", "condition": "IZ boundary deletion late fraction", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "7889SA3.5", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for 7889SA3.5 2-stage Repli-seq late fraction of 2 fractions"}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"display_title": "4DNFISW7RCC8 - normalized counts for 7889SA3.5 2-stage Repli-seq late fraction of 2 fractions", "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "0b9dc1bf-ce64-45c6-8d64-127d58fe0182", "status": "released", "@id": "/higlass-view-configs/0b9dc1bf-ce64-45c6-8d64-127d58fe0182/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"href": "/files-processed/4DNFII6KG6JS/@@download/4DNFII6KG6JS.bam", "accession": "4DNFII6KG6JS", "file_type": "alignments", "uuid": "8848f9fa-20f2-47cc-b1b4-35aa2c1beba9", "display_title": "4DNFII6KG6JS.bam", "file_format": {"@id": "/file-formats/bam/", "display_title": "bam", "file_format": "bam", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 542601966, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8848f9fa-20f2-47cc-b1b4-35aa2c1beba9/4DNFII6KG6JS.bam", "@type": ["FileProcessed", "File", "Item"], "upload_key": "8848f9fa-20f2-47cc-b1b4-35aa2c1beba9/4DNFII6KG6JS.bam", "status": "released", "@id": "/files-processed/4DNFII6KG6JS/", "file_type_detailed": "alignments (bam)", "file_classification": "processed file", "quality_metric": {"display_title": "QualityMetricDedupqcRepliseq from 2021-11-02", "uuid": "e6d8dbfc-c30b-4bcc-bb20-c63d46810f9a", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "@id": "/quality-metrics-dedupqc-repliseq/e6d8dbfc-c30b-4bcc-bb20-c63d46810f9a/", "status": "released", "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "9091071", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "5.113", "tooltip": "Percent of total aligned reads (=0.46m)", "numberType": "percent"}]}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "2-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "late fraction of 2 fractions", "dataset": "E/L repliseq on\u00a0engineered iPSC cells", "condition": "IZ boundary deletion late fraction", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "7889SA3.5", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"href": "/files-processed/4DNFICLLAZZU/@@download/4DNFICLLAZZU.bedGraph.gz", "accession": "4DNFICLLAZZU", "file_type": "normalized counts", "uuid": "2da128b0-1b11-403c-a184-bf8f06c40d12", "display_title": "4DNFICLLAZZU.bedGraph.gz", "file_format": {"@id": "/file-formats/bg/", "display_title": "bg", "file_format": "bg", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 3580350, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/2da128b0-1b11-403c-a184-bf8f06c40d12/4DNFICLLAZZU.bedGraph.gz", "@type": ["FileProcessed", "File", "Item"], "upload_key": "2da128b0-1b11-403c-a184-bf8f06c40d12/4DNFICLLAZZU.bedGraph.gz", "status": "released", "@id": "/files-processed/4DNFICLLAZZU/", "file_type_detailed": "normalized counts (bg)", "file_classification": "processed file", "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "2-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "late fraction of 2 fractions", "dataset": "E/L repliseq on\u00a0engineered iPSC cells", "condition": "IZ boundary deletion late fraction", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "7889SA3.5", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for 7889SA3.5 2-stage Repli-seq late fraction of 2 fractions"}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"display_title": "4DNFICLLAZZU - normalized counts for 7889SA3.5 2-stage Repli-seq late fraction of 2 fractions", "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "846a3b91-e965-4a29-99a8-a8c1a976e7a4", "status": "released", "@id": "/higlass-view-configs/846a3b91-e965-4a29-99a8-a8c1a976e7a4/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"href": "/files-processed/4DNFID2PUM5L/@@download/4DNFID2PUM5L.bam", "accession": "4DNFID2PUM5L", "file_type": "alignments", "uuid": "0717d6ed-0581-486b-a18d-c69cb3f6449e", "display_title": "4DNFID2PUM5L.bam", "file_format": {"@id": "/file-formats/bam/", "display_title": "bam", "file_format": "bam", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 538292544, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/0717d6ed-0581-486b-a18d-c69cb3f6449e/4DNFID2PUM5L.bam", "@type": ["FileProcessed", "File", "Item"], "upload_key": "0717d6ed-0581-486b-a18d-c69cb3f6449e/4DNFID2PUM5L.bam", "status": "released", "@id": "/files-processed/4DNFID2PUM5L/", "file_type_detailed": "alignments (bam)", "file_classification": "processed file", "quality_metric": {"display_title": "QualityMetricDedupqcRepliseq from 2021-11-02", "uuid": "ad75a75d-dc43-4d62-b99d-eeb78eba58c2", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "@id": "/quality-metrics-dedupqc-repliseq/ad75a75d-dc43-4d62-b99d-eeb78eba58c2/", "status": "released", "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "9024375", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "5.064", "tooltip": "Percent of total aligned reads (=0.46m)", "numberType": "percent"}]}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "2-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "late fraction of 2 fractions", "dataset": "E/L repliseq on\u00a0engineered iPSC cells", "condition": "IZ boundary deletion late fraction", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "7889SA3.5", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"href": "/files-processed/4DNFIQDNJ6FY/@@download/4DNFIQDNJ6FY.bedGraph.gz", "accession": "4DNFIQDNJ6FY", "file_type": "normalized counts", "uuid": "c67a21c3-a98e-4f27-a85d-90e15c81ad54", "display_title": "4DNFIQDNJ6FY.bedGraph.gz", "file_format": {"@id": "/file-formats/bg/", "display_title": "bg", "file_format": "bg", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 3591370, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c67a21c3-a98e-4f27-a85d-90e15c81ad54/4DNFIQDNJ6FY.bedGraph.gz", "@type": ["FileProcessed", "File", "Item"], "upload_key": "c67a21c3-a98e-4f27-a85d-90e15c81ad54/4DNFIQDNJ6FY.bedGraph.gz", "status": "released", "@id": "/files-processed/4DNFIQDNJ6FY/", "file_type_detailed": "normalized counts (bg)", "file_classification": "processed file", "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "2-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "late fraction of 2 fractions", "dataset": "E/L repliseq on\u00a0engineered iPSC cells", "condition": "IZ boundary deletion late fraction", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "7889SA3.5", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for 7889SA3.5 2-stage Repli-seq late fraction of 2 fractions"}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"display_title": "4DNFIQDNJ6FY - normalized counts for 7889SA3.5 2-stage Repli-seq late fraction of 2 fractions", "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "4cedc950-d48f-4b6e-8dad-aee5bbf6eb20", "status": "released", "@id": "/higlass-view-configs/4cedc950-d48f-4b6e-8dad-aee5bbf6eb20/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "project_release": "2021-11-10", "cell_cycle_phase": "S", "antibody_dilution": "1:600", "contributing_labs": [{"@id": "/labs/jennifer-cremins-lab/", "status": "current", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "correspondence": [{"contact_email": "amNyZW1pbnNAc2Vhcy51cGVubi5lZHU=", "@id": "/users/8773d50c-1716-4153-9a18-d0f5ff2aa5ee/", "display_title": "Jennifer Phillips-Cremins"}], "display_title": "Jennifer Cremins, UPENN", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}], "biosample_quantity": 40000, "fragment_size_range": "200-600", "fragmentation_method": "see protocol document", "average_fragment_size": 200, "total_fractions_in_exp": 2, "biosample_quantity_units": "cells", "fragment_size_selection_method": "see document", "@id": "/experiments-repliseq/4DNEX5ZRL6AF/", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "uuid": "00d57689-e60a-4b76-b748-a6a7ce6c6ff0", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "2-stage Repli-seq on 7889SA3.5 S-phase late fraction - 4DNEX5ZRL6AF", "external_references": [], "experiment_sets": [{"accession": "4DNES4XLT839", "status": "released", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "experimentset_type": "replicate", "display_title": "4DNES4XLT839", "uuid": "e8688227-1e06-4853-91df-ea55070d5379", "@id": "/experiment-set-replicates/4DNES4XLT839/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNESE3WCUAQ", "status": "released", "@type": ["ExperimentSet", "Item"], "experimentset_type": "custom", "display_title": "4DNESE3WCUAQ", "uuid": "c6350dbf-46e7-45fb-8f23-535e23182b2a", "@id": "/experiment-sets/4DNESE3WCUAQ/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"date_published": "2022-06-08", "status": "current", "authors": ["Emerson DJ", "Zhao PA", "Cook AL", "Barnett RJ", "Klein KN", "Saulebekova D", "Ge C", "Zhou L", "Simandi Z", "Minsk MK", "Titus KR", "Wang W", "Gong W", "Zhang D", "Yang L", "Venev SV", "Gibcus JH", "Yang H", "Sasaki T", "Kanemaki MT", "Yue F", "Dekker J", "Chen CL", "Gilbert DM", "Phillips-Cremins JE"], "@type": ["Publication", "Item"], "journal": "Nature", "ID": "PMID:35676475", "@id": "/publications/ee8db237-9a92-4b72-8292-a66028a95b5b/", "short_attribution": "Emerson DJ et al. (2022)", "title": "Cohesin-mediated loop anchors confine the locations of human replication origins.", "uuid": "ee8db237-9a92-4b72-8292-a66028a95b5b", "abstract": "DNA replication occurs through an intricately regulated series of molecular events and is fundamental for genome stability(1,2). At present, it is unknown how the locations of replication origins are determined in the human genome. Here we dissect the role of topologically associating domains (TADs)(3-6), subTADs(7)  and loops(8) in the positioning of replication initiation zones (IZs). We stratify TADs and subTADs by the presence of corner-dots indicative of loops and  the orientation of CTCF motifs. We find that high-efficiency, early replicating IZs localize to boundaries between adjacent corner-dot TADs anchored by high-density arrays of divergently and convergently oriented CTCF motifs. By contrast, low-efficiency IZs localize to weaker dotless boundaries. Following ablation of cohesin-mediated loop extrusion during G1, high-efficiency IZs become diffuse and delocalized at boundaries with complex CTCF motif orientations. Moreover, G1 knockdown of the cohesin unloading factor WAPL results in gained long-range loops and narrowed localization of IZs at the same boundaries. Finally, targeted deletion or insertion of specific boundaries causes local replication timing shifts consistent with IZ loss or gain, respectively. Our data support a model in which cohesin-mediated loop extrusion and stalling at a subset of genetically encoded TAD and subTAD boundaries is an essential determinant of the locations of replication origins in human S phase.", "display_title": "Emerson DJ et al. (2022) PMID:35676475", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"ID": "PMID:35676475", "authors": ["Emerson DJ", "Zhao PA", "Cook AL", "Barnett RJ", "Klein KN", "Saulebekova D", "Ge C", "Zhou L", "Simandi Z", "Minsk MK", "Titus KR", "Wang W", "Gong W", "Zhang D", "Yang L", "Venev SV", "Gibcus JH", "Yang H", "Sasaki T", "Kanemaki MT", "Yue F", "Dekker J", "Chen CL", "Gilbert DM", "Phillips-Cremins JE"], "title": "Cohesin-mediated loop anchors confine the locations of human replication origins.", "uuid": "ee8db237-9a92-4b72-8292-a66028a95b5b", "abstract": "DNA replication occurs through an intricately regulated series of molecular events and is fundamental for genome stability(1,2). At present, it is unknown how the locations of replication origins are determined in the human genome. Here we dissect the role of topologically associating domains (TADs)(3-6), subTADs(7)  and loops(8) in the positioning of replication initiation zones (IZs). We stratify TADs and subTADs by the presence of corner-dots indicative of loops and  the orientation of CTCF motifs. We find that high-efficiency, early replicating IZs localize to boundaries between adjacent corner-dot TADs anchored by high-density arrays of divergently and convergently oriented CTCF motifs. By contrast, low-efficiency IZs localize to weaker dotless boundaries. Following ablation of cohesin-mediated loop extrusion during G1, high-efficiency IZs become diffuse and delocalized at boundaries with complex CTCF motif orientations. Moreover, G1 knockdown of the cohesin unloading factor WAPL results in gained long-range loops and narrowed localization of IZs at the same boundaries. Finally, targeted deletion or insertion of specific boundaries causes local replication timing shifts consistent with IZ loss or gain, respectively. Our data support a model in which cohesin-mediated loop extrusion and stalling at a subset of genetically encoded TAD and subTAD boundaries is an essential determinant of the locations of replication origins in human S phase.", "date_published": "2022-06-08", "journal": "Nature", "display_title": "Emerson DJ et al. (2022) PMID:35676475", "@type": ["Publication", "Item"], "status": "current", "short_attribution": "Emerson DJ et al. (2022)", "@id": "/publications/ee8db237-9a92-4b72-8292-a66028a95b5b/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Fraction", "value": "late fraction of 2 fractions", "combined": "Fraction: late fraction of 2 fractions"}, "experiment_summary": "2-stage Repli-seq on 7889SA3.5 S-phase late fraction", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSNJMBVXT/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample missing morphology_image"], "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": []}