{"lab": {"uuid": "b2c2deeb-e883-4ac0-b9e2-906e598884d6", "display_title": "Andrew Belmont, ILLINOIS", "title": "Andrew Belmont, ILLINOIS", "@type": ["Lab", "Item"], "correspondence": [{"contact_email": "YXNiZWxAaWxsaW5vaXMuZWR1", "@id": "/users/92f90aed-7df1-4bd9-9e74-a472cb50d663/", "display_title": "Andrew Belmont"}], "status": "current", "@id": "/labs/andrew-belmont-lab/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b2c2deeb-e883-4ac0-b9e2-906e598884d6"]}}, "award": {"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.", "center_title": "CDIMV - Ma", "display_title": "MULTISCALE ANALYSES OF 4D NUCLEOME STRUCTURE AND FUNCTION BY COMPREHENSIVE MULTIMODAL DATA INTEGRATION", "name": "1UM1HG011593-01", "@id": "/awards/1UM1HG011593-01/", "@type": ["Award", "Item"], "status": "current", "uuid": "9f6d9e4a-9542-49c7-8a54-c6c9a1862d90", "project": "4DN", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"uuid": "ae743679-4649-46d6-90de-a322c4ff8e19", "file_size": 2853909210, "upload_key": "ae743679-4649-46d6-90de-a322c4ff8e19/4DNFIMEQDH69.fastq.gz", "file_classification": "raw file", "href": "/files-fastq/4DNFIMEQDH69/@@download/4DNFIMEQDH69.fastq.gz", "accession": "4DNFIMEQDH69", "file_type": "reads", "display_title": "4DNFIMEQDH69.fastq.gz", "@id": "/files-fastq/4DNFIMEQDH69/", "@type": ["FileFastq", "File", "Item"], "status": "released", "file_type_detailed": "reads (fastq)", "quality_metric": {"uuid": "a443bf0e-6333-42f2-a184-024232e90272", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2025-03-15", "status": "released", "@id": "/quality-metrics-fastqc/a443bf0e-6333-42f2-a184-024232e90272/", "Total Sequences": 60483896, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "100", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIMEQDH69/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"status": "released", "display_title": "fastq", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "status": "released", "aliases": ["belmont-lab:TSA-seq_CenpB_F121-9_condE_bio2_PC_20230823"], "antibody": {"status": "released", "uuid": "c8e061c8-1f7b-412d-a4bd-9fc8ec4a98d0", "@type": ["Antibody", "Item"], "@id": "/antibodys/anti-CENPB-ab25734/", "display_title": "anti-CENPB (Abcam, ab25734)", "antibody_name": "anti-CENPB", "antibody_product_no": "ab25734", "antibody_vendor": {"display_title": "Abcam", "uuid": "13540f71-312d-441e-a2dc-ea0dfa7e0841", "status": "released", "@type": ["Vendor", "Item"], "title": "Abcam", "@id": "/vendors/abcam/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "protocol": {"@type": ["Protocol", "Item"], "uuid": "c023d600-5195-4af2-81c7-356cb3095d06", "status": "released", "@id": "/protocols/c023d600-5195-4af2-81c7-356cb3095d06/", "display_title": "TSA-Seq-Protocol-201912.pdf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEX81MLG2D", "biosample": {"status": "released", "display_title": "4DNBSIIARRL1", "modifications_summary": "None", "biosource_summary": "F121-9-CASTx129 (Tier 2)", "@id": "/biosamples/4DNBSIIARRL1/", "biosample_type": "stem cells", "uuid": "dc92740d-d03b-45b3-a634-2f4a8d453801", "accession": "4DNBSIIARRL1", "@type": ["Biosample", "Item"], "treatments_summary": "None", "biosource": [{"lab": {"@id": "/labs/4dn-dcic-lab/", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "award": {"display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "status": "current", "@id": "/awards/1U01CA200059-01/", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "term_name": "stem cell", "synonyms": ["animal stem cell"], "preferred_name": "stem cell", "display_title": "stem cell", "@id": "/ontology-terms/CL:0000034/", "slim_terms": [{"display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "term_id": "CL:0000034", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["dcic:f1219castx129T1", "4dn-dcic-lab:f1219castx129T2"], "accession": "4DNSRMG5APUM", "cell_line": {"display_title": "F121-9-CASTx129", "term_name": "F121-9-CASTx129", "term_id": "4DN:0000002", "preferred_name": "F121-9-CASTx129", "uuid": "111201bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/4DN:0000002/", "status": "released", "slim_terms": [{"@id": "/ontology-terms/CLO:0000031/", "status": "released", "@type": ["OntologyTerm", "Item"], "uuid": "f9483d7e-4731-47d1-b8e0-1aac05ba2b49", "display_title": "cell line", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"uuid": "cade1337-728d-4b5d-99f5-ed08b621cd7b", "display_title": "4DNINSF32UE9", "status": "released", "@type": ["IndividualMouse", "Individual", "Item"], "@id": "/individuals-mouse/4DNINSF32UE9/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "references": [], "description": "Castx129 female mouse hybrid ES cells - clone F121-9.  Maternal 129/Sv, Paternal CAST - Tier 2 cell line", "date_created": "2017-04-10T01:14:03.935702+00:00", "submitted_by": {"error": "no view permissions"}, "SOP_cell_line": {"uuid": "cb03c0c6-4ba6-4bbe-9210-c430ee4fdb2c", "@id": "/protocols/cb03c0c6-4ba6-4bbe-9210-c430ee4fdb2c/", "@type": ["Protocol", "Item"], "status": "released", "display_title": "4DN_F121-9_SOP_180913.pdf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-09-19T19:54:45.519400+00:00"}, "modifications": [], "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 2", "public_release": "2017-04-10T01:14:03.935702+00:00", "schema_version": "2", "project_release": "2017-04-10T01:14:03.935702+00:00", "biosource_vendor": {"@id": "/vendors/gilbert-lab/", "uuid": "b5770c30-923d-4f04-b486-f6bfdab6f89d", "@type": ["Vendor", "Item"], "status": "released", "display_title": "Gilbert Lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "alternate_accessions": [], "@id": "/biosources/4DNSRMG5APUM/", "@type": ["Biosource", "Item"], "uuid": "f01caf67-dd73-40ae-9476-940f0762b9c2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "F121-9-CASTx129 (Tier 2) - 4DNSRMG5APUM", "external_references": [], "biosource_name": "F121-9-CASTx129 (Tier 2)", "biosource_category": ["Tier 2", "Mouse stem cell"], "organism": {"@type": ["Organism", "Item"], "name": "mouse", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "status": "released", "display_title": "M. musculus", "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "badges": [{"messages": ["Tiered cell line cultured after 2022-05-10 missing 4DN specified FBS vendor and lot info"], "badge": {"warning": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "display_title": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "status": "released", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "badge_classification": "Warning", "@type": ["Badge", "Item"], "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "documents": [{"@id": "/documents/e7a97845-0606-49d0-9d27-49e169c18e3c/", "display_title": "expt_details_CenpB_F121-9_condE_bio2_PC_20230823.xlsx", "@type": ["Document", "Item"], "uuid": "e7a97845-0606-49d0-9d27-49e169c18e3c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "pcr_cycles": 10, "resolution": "Medium", "description": "CenpB TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition E (1:300 tyramide-biotin, 30 minute reaction) on F121-9 ES cells replicate 2", "follows_sop": "Yes", "sop_mapping": {"has_sop": "No"}, "date_created": "2025-03-14T19:01:51.168012+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-09-30T18:51:34.486629+00:00"}, "reaction_time": 30.0, "public_release": "2025-09-30", "schema_version": "3", "affinity_rounds": 1, "antibody_lot_id": "GR3424432-1", "experiment_type": {"uuid": "75d7181c-e329-463e-b776-a467433aa4db", "experiment_category": "Sequencing", "assay_subclass_short": "Proximity-seq", "@type": ["ExperimentType", "Item"], "title": "TSA-seq", "status": "released", "display_title": "TSA-seq", "@id": "/experiment-types/tsa-seq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_type_detailed": "normalized counts (bw)", "upload_key": "a5e66ba5-36bd-4ba4-909a-7329d081b6ba/4DNFIZ4K9TG6.bw", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a5e66ba5-36bd-4ba4-909a-7329d081b6ba/4DNFIZ4K9TG6.bw", "display_title": "4DNFIZ4K9TG6.bw", "file_format": {"@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "bw", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "a5e66ba5-36bd-4ba4-909a-7329d081b6ba", "@type": ["FileProcessed", "File", "Item"], "file_type": "normalized counts", "status": "released", "file_size": 1013218, "@id": "/files-processed/4DNFIZ4K9TG6/", "file_classification": "processed file", "href": "/files-processed/4DNFIZ4K9TG6/@@download/4DNFIZ4K9TG6.bw", "accession": "4DNFIZ4K9TG6", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFIZ4K9TG6 - normalized counts for F121-9-CASTx129 (Tier 2) TSA-seq Cenpb mouse protein", "@id": "/higlass-view-configs/e7ede862-020a-4454-8b93-5fe855bd6a94/", "status": "released", "uuid": "e7ede862-020a-4454-8b93-5fe855bd6a94", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "external_references": [], "track_and_facet_info": {"experimental_lab": "Andrew Belmont, ILLINOIS", "experiment_type": "TSA-seq", "experiment_bucket": "processed file", "assay_info": "Cenpb mouse protein", "dataset": "TSA-seq CenpB in F121-9 ES cells", "condition": "condition2 - conditionE - anti-CenpB", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "F121-9-CASTx129 (Tier 2)", "lab_name": "Andrew Belmont, ILLINOIS", "track_title": "normalized counts for F121-9-CASTx129 (Tier 2) TSA-seq Cenpb mouse protein"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "project_release": "2025-09-30", "reaction_buffer": "50% Sucrose", "targeted_factor": [{"@id": "/bio-features/99f88fb4-24bc-43a8-a4eb-cd296c76c006/", "status": "released", "display_title": "Cenpb mouse protein", "uuid": "99f88fb4-24bc-43a8-a4eb-cd296c76c006", "@type": ["BioFeature", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "protocol_version": "2.0", "antibody_dilution": "1:1000", "biosample_quantity": 52000000.0, "secondary_antibody": {"@type": ["Antibody", "Item"], "antibody_product_no": "111-035-144", "@id": "/antibodys/goat-anti-rabbit-IgG-111-035-144/", "uuid": "c1ec3af7-813c-4bea-850b-a8a4648b38ad", "antibody_name": "goat anti-rabbit IgG", "status": "released", "display_title": "goat anti-rabbit IgG (Jackson ImmunoResearch, 111-035-144)", "antibody_vendor": {"title": "Jackson ImmunoResearch", "status": "released", "uuid": "295a05e5-fa7c-498d-9cd6-fa0586d430b9", "@id": "/vendors/jackson-immunoresearch/", "display_title": "Jackson ImmunoResearch", "@type": ["Vendor", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "authentication_docs": [{"@id": "/protocols/7aa713ef-a695-4697-b607-f8f8846af0d5/", "@type": ["Protocol", "Item"], "status": "released", "display_title": "image_CenpB_F121-9_condE_bio2_PC_20230823.pdf", "uuid": "7aa713ef-a695-4697-b607-f8f8846af0d5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/protocols/00018e32-3afb-4105-86ba-dc1af6595fe6/", "@type": ["Protocol", "Item"], "status": "released", "display_title": "dotBlot_CenpB_F121-9_condE_bio2_PC_20230823.pdf", "uuid": "00018e32-3afb-4105-86ba-dc1af6595fe6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_relation": [{"experiment": {"display_title": "TSA-seq against Cenpb mouse protein on F121-9-CASTx129 (Tier 2) - 4DNEXXGSHCYL", "@id": "/experiments-tsaseq/4DNEXXGSHCYL/", "uuid": "be97c65f-44fa-471f-b108-f51d066d76e0", "status": "released", "@type": ["ExperimentTsaseq", "Experiment", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "has input"}], "fragment_size_range": "100-600", "average_biotin_range": "25-100", "fragmentation_method": "sonication", "reaction_temperature": 25.0, "average_fragment_size": 350, "other_processed_files": [{"type": "preliminary", "files": [{"status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/537fe93c-f71f-45e7-a424-82cfcacbe48d/4DNFIFLNRH28.bam", "display_title": "4DNFIFLNRH28.bam", "file_type_detailed": "alignments (bam)", "accession": "4DNFIFLNRH28", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIFLNRH28/", "genome_assembly": "GRCm38", "file_type": "alignments", "href": "/files-processed/4DNFIFLNRH28/@@download/4DNFIFLNRH28.bam", "file_size": 2175335363, "uuid": "537fe93c-f71f-45e7-a424-82cfcacbe48d", "quality_metric": {"display_title": "QualityMetricDedupqcRepliseq from 2025-03-17", "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "uuid": "3c423552-5761-4264-9b55-27dadf9e3028", "@id": "/quality-metrics-dedupqc-repliseq/3c423552-5761-4264-9b55-27dadf9e3028/", "quality_metric_summary": [{"title": "Total Aligned", "value": "45493674", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "22.024", "tooltip": "Percent of total aligned reads (=10.02m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "file_format": "bam", "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2025-10-25T04:23:07.440902+00:00"}, "track_and_facet_info": {"experimental_lab": "Andrew Belmont, ILLINOIS", "experiment_type": "TSA-seq", "experiment_bucket": "Repli-Seq Pipeline - Preliminary Files", "assay_info": "Cenpb mouse protein", "dataset": "TSA-seq CenpB in F121-9 ES cells", "condition": "condition2 - conditionE - anti-CenpB", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "F121-9-CASTx129 (Tier 2)", "lab_name": "4DN DCIC, HMS"}}, {"higlass_uid": "e755099b-f051-4bb6-87f0-adf2a74d55d0", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/5c5742c7-af29-4667-912d-c4b1cc674959/4DNFIGBNN1RM.bedGraph.gz", "display_title": "4DNFIGBNN1RM.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "accession": "4DNFIGBNN1RM", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIGBNN1RM/", "genome_assembly": "GRCm38", "file_type": "normalized counts", "href": "/files-processed/4DNFIGBNN1RM/@@download/4DNFIGBNN1RM.bedGraph.gz", "file_size": 764729, "uuid": "5c5742c7-af29-4667-912d-c4b1cc674959", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/bg/", "@type": ["FileFormat", "Item"], "file_format": "bg", "display_title": "bg", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIGBNN1RM - normalized counts for F121-9-CASTx129 (Tier 2) TSA-seq Cenpb mouse protein", "@id": "/higlass-view-configs/fd9ca527-8f71-4997-a777-bddb7bf9f503/", "uuid": "fd9ca527-8f71-4997-a777-bddb7bf9f503", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "last_modified": {"date_modified": "2025-10-25T04:48:35.855399+00:00"}, "track_and_facet_info": {"experimental_lab": "Andrew Belmont, ILLINOIS", "experiment_type": "TSA-seq", "experiment_bucket": "Repli-Seq Pipeline - Preliminary Files", "assay_info": "Cenpb mouse protein", "dataset": "TSA-seq CenpB in F121-9 ES cells", "condition": "condition2 - conditionE - anti-CenpB", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "F121-9-CASTx129 (Tier 2)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for F121-9-CASTx129 (Tier 2) TSA-seq Cenpb mouse protein"}}, {"higlass_uid": "bac25275-dbab-4e4b-8169-4f27812c56d4", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c9d1d991-7199-4a88-ba87-53025bb34bcc/4DNFI1O4YPMA.bedGraph.gz", "display_title": "4DNFI1O4YPMA.bedGraph.gz", "file_type_detailed": "counts (bg)", "accession": "4DNFI1O4YPMA", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI1O4YPMA/", "genome_assembly": "GRCm38", "file_type": "counts", "href": "/files-processed/4DNFI1O4YPMA/@@download/4DNFI1O4YPMA.bedGraph.gz", "file_size": 659774, "uuid": "c9d1d991-7199-4a88-ba87-53025bb34bcc", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/bg/", "@type": ["FileFormat", "Item"], "file_format": "bg", "display_title": "bg", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFI1O4YPMA - counts for F121-9-CASTx129 (Tier 2) TSA-seq Cenpb mouse protein", "@id": "/higlass-view-configs/dbec32a5-41e6-4f6c-8ede-963a28ddace2/", "uuid": "dbec32a5-41e6-4f6c-8ede-963a28ddace2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "last_modified": {"date_modified": "2025-10-25T04:48:34.152213+00:00"}, "track_and_facet_info": {"experimental_lab": "Andrew Belmont, ILLINOIS", "experiment_type": "TSA-seq", "experiment_bucket": "Repli-Seq Pipeline - Preliminary Files", "assay_info": "Cenpb mouse protein", "dataset": "TSA-seq CenpB in F121-9 ES cells", "condition": "condition2 - conditionE - anti-CenpB", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "F121-9-CASTx129 (Tier 2)", "lab_name": "4DN DCIC, HMS", "track_title": "counts for F121-9-CASTx129 (Tier 2) TSA-seq Cenpb mouse protein"}}], "title": "Repli-Seq Pipeline - Preliminary Files"}], "tyramide_concentration": "1:300", "biosample_quantity_units": "cells", "library_preparation_date": "2023-08-25", "secondary_antibody_lot_id": "154205", "biotinylated_spikein_source": "drosophila_48E12_L_BiodT_primer_set: GAAACATCGC/iBiodT/GCCCATAAT--AGAAGCAGCTACGCTCCTCA", "secondary_antibody_dilution": "1:1000", "biotinylated_spikein_sequences": {"status": "released", "display_title": "4DNFIQ3495RN.fasta", "@id": "/files-reference/4DNFIQ3495RN/", "uuid": "bf96e7b1-d2e1-4758-8a31-7549f72f3c59", "@type": ["FileReference", "File", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "fragment_size_selection_method": "none", "non_biotinylated_spikein_source": "drosophila_48E12_LL_RR_primer_set: CCAATGCGATGGATATGTCA--GCGAGGTTTCATTTTTGGAA", "non_biotinylated_spikein_sequences": {"status": "released", "@type": ["FileReference", "File", "Item"], "@id": "/files-reference/4DNFIJS7RJAS/", "uuid": "1cc39697-bcd2-4db7-8276-b33d8fa74bbd", "display_title": "4DNFIJS7RJAS.fasta", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/experiments-tsaseq/4DNEX81MLG2D/", "@type": ["ExperimentTsaseq", "Experiment", "Item"], "uuid": "0a476ba9-11e0-4d54-8093-8b2f1dccb58a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "TSA-seq against Cenpb mouse protein on F121-9-CASTx129 (Tier 2) - 4DNEX81MLG2D", "external_references": [], "experiment_sets": [{"experimentset_type": "replicate", "status": "released", "accession": "4DNESE4AGSRL", "uuid": "887b5ff4-27bb-477a-8d4f-575506054974", "display_title": "4DNESE4AGSRL", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNESE4AGSRL/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "publications_of_exp": [], "experiment_categorizer": {"field": "Target", "value": "Cenpb mouse protein", "combined": "Target: Cenpb mouse protein"}, "experiment_summary": "TSA-seq against Cenpb mouse protein on F121-9-CASTx129 (Tier 2)", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSIIARRL1/", "embedded_path": "biosample.badges", "item": {"messages": ["Tiered cell line cultured after 2022-05-10 missing 4DN specified FBS vendor and lot info"], "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": []}