{"lab": {"uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "@type": ["Lab", "Item"], "correspondence": [{"contact_email": "Yi52LnN0ZWVuc2VsQG5raS5ubA==", "@id": "/users/dd8b1cd6-93cd-41e5-b184-caf1369cb39f/", "display_title": "Bas van Steensel"}], "display_title": "Bas van Steensel, NKI", "title": "Bas van Steensel, NKI", "@id": "/labs/bas-van-steensel-lab/", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "award": {"@id": "/awards/1U54DK107965-01/", "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.", "display_title": "COMBINED CYTOLOGICAL, GENOMIC, AND FUNCTIONAL MAPPING OF NUCLEAR GENOME ORGANIZATION", "name": "1U54DK107965-01", "center_title": "NOFIC - Belmont", "uuid": "91b694c3-f4d7-4ddd-8278-16f94e15c1c5", "status": "current", "@type": ["Award", "Item"], "project": "4DN", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"@id": "/files-fastq/4DNFIZXJL2TW/", "uuid": "91c709b8-f8f0-4420-9bc6-6a53d3dcdee9", "status": "released", "file_type": "reads", "file_classification": "raw file", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFIZXJL2TW/@@download/4DNFIZXJL2TW.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIZXJL2TW", "file_size": 238571272, "display_title": "4DNFIZXJL2TW.fastq.gz", "upload_key": "91c709b8-f8f0-4420-9bc6-6a53d3dcdee9/4DNFIZXJL2TW.fastq.gz", "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/752ce923-1003-425c-b63f-196ef30fefe5/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIZXJL2TW/fastqc_report.html", "Sequence length": "65", "uuid": "752ce923-1003-425c-b63f-196ef30fefe5", "Total Sequences": 4964414, "status": "released", "display_title": "QualityMetricFastqc from 2020-07-02", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "display_title": "fastq", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"@id": "/files-fastq/4DNFIOIF8WFE/", "uuid": "6590ceb5-5c0f-44a3-9b94-7ec0afc30c01", "status": "released", "file_type": "reads", "file_classification": "raw file", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFIOIF8WFE/@@download/4DNFIOIF8WFE.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIOIF8WFE", "file_size": 2216789117, "display_title": "4DNFIOIF8WFE.fastq.gz", "upload_key": "6590ceb5-5c0f-44a3-9b94-7ec0afc30c01/4DNFIOIF8WFE.fastq.gz", "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/689e9bb7-cf38-40f1-983c-4d545c4dee6d/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIOIF8WFE/fastqc_report.html", "Sequence length": "65", "uuid": "689e9bb7-cf38-40f1-983c-4d545c4dee6d", "Total Sequences": 46082405, "status": "released", "display_title": "QualityMetricFastqc from 2020-07-02", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "display_title": "fastq", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}], "status": "released", "aliases": ["vanSteensel-lab:DamID_K562_r2_4xAP3"], "protocol": {"@id": "/protocols/4ebc8669-4d1e-4adb-9314-5e5d88b66f84/", "display_title": "4DN Standard DamID-seq protocol", "@type": ["Protocol", "Item"], "uuid": "4ebc8669-4d1e-4adb-9314-5e5d88b66f84", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEXLVPKOIM", "biosample": {"treatments_summary": "None", "modifications_summary": "None", "uuid": "fe71ebb2-2f41-4e40-bfda-508d50323401", "@id": "/biosamples/4DNBSKN91Y5M/", "biosample_type": "immortalized cells", "biosource_summary": "K562 (Tier 2)", "@type": ["Biosample", "Item"], "status": "released", "accession": "4DNBSKN91Y5M", "display_title": "4DNBSKN91Y5M", "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"status": "released", "description": "Gold biosample", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "badge_classification": "Commendation", "title": "Gold Biosample", "display_title": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "commendation": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "biosource": [{"lab": {"status": "current", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "url": "https://www.atcc.org/products/all/CCL-243.aspx", "award": {"@type": ["Award", "Item"], "status": "current", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@id": "/awards/1U01CA200059-01/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"term_id": "CL:0000081", "term_name": "blood cell", "uuid": "0d64fbe2-ed5c-43cd-a30d-d9f0320d27ed", "status": "released", "display_title": "blood cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "blood cell", "@id": "/ontology-terms/CL:0000081/", "slim_terms": [{"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["dcic:K562T2", "4dn-dcic-lab:K562T2"], "accession": "4DNSRWQFKJYO", "cell_line": {"@type": ["OntologyTerm", "Item"], "display_title": "K562", "@id": "/ontology-terms/EFO:0002067/", "status": "released", "synonyms": ["K562 cell", "K-562", "K-562 cell"], "term_name": "K562", "preferred_name": "K562", "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "uuid": "0f1257b4-30e2-4c34-b8a3-e564c65ec55a", "term_id": "EFO:0002067", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"uuid": "2a0c64b1-25f1-44c1-88c3-7da6291f5b69", "@id": "/individuals-human/4DNIN4YSFWCS/", "protected_data": false, "status": "released", "display_title": "4DNIN4YSFWCS", "@type": ["IndividualHuman", "Individual", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "references": [], "description": "K562 (CCL-243)", "date_created": "2017-04-10T01:14:06.383509+00:00", "submitted_by": {"error": "no view permissions"}, "SOP_cell_line": {"display_title": "4DN_K562_SOP_170314.pdf", "status": "released", "@id": "/protocols/d6eb1886-6427-4083-a05c-9268730f5ed6/", "uuid": "d6eb1886-6427-4083-a05c-9268730f5ed6", "@type": ["Protocol", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-06-05T14:31:58.118863+00:00"}, "modifications": [], "biosource_type": "immortalized cell line", "cell_line_tier": "Tier 2", "public_release": "2017-09-05", "schema_version": "2", "project_release": "2017-09-05", "biosource_vendor": {"uuid": "7a6f2efe-5be8-4db2-afa8-d82e9b4ad254", "status": "released", "@id": "/vendors/american-type-culture-collection/", "display_title": "American Type Culture Collection", "@type": ["Vendor", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "alternate_accessions": [], "@id": "/biosources/4DNSRWQFKJYO/", "@type": ["Biosource", "Item"], "uuid": "1032c021-c18a-49ab-90d2-fd2cc5a8e1b7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "K562 (Tier 2) - 4DNSRWQFKJYO", "external_references": [], "biosource_name": "K562 (Tier 2)", "biosource_category": ["Tier 2"], "organism": {"name": "human", "display_title": "H. sapiens", "@type": ["Organism", "Item"], "status": "released", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@id": "/organisms/9606/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pcr_cycles": 11, "description": "K562 4xAP3 replicate 2 using biosample K562_r2_4xAP3", "follows_sop": "Yes", "sop_mapping": {"has_sop": "No"}, "date_created": "2020-07-01T07:52:56.699995+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-11-03T14:45:08.447039+00:00"}, "me_pcr_cycles": 24, "sap_treatment": "No", "public_release": "2023-11-03", "schema_version": "4", "experiment_type": {"@type": ["ExperimentType", "Item"], "title": "DamID-seq", "uuid": "b777a1da-8dc8-4473-9b8d-4f7716fb0a4a", "@id": "/experiment-types/damid-seq/", "status": "released", "assay_subclass_short": "Proximity-seq", "display_title": "DamID-seq", "experiment_category": "Sequencing", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_type": "alignments", "uuid": "8334c291-e42c-4ded-b86b-f6719b21f213", "file_type_detailed": "alignments (bam)", "@type": ["FileProcessed", "File", "Item"], "file_classification": "processed file", "display_title": "4DNFIXZTDSY7.bam", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8334c291-e42c-4ded-b86b-f6719b21f213/4DNFIXZTDSY7.bam", "upload_key": "8334c291-e42c-4ded-b86b-f6719b21f213/4DNFIXZTDSY7.bam", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "file_format": {"file_format": "bam", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFIXZTDSY7", "href": "/files-processed/4DNFIXZTDSY7/@@download/4DNFIXZTDSY7.bam", "@id": "/files-processed/4DNFIXZTDSY7/", "file_size": 179472725, "status": "released", "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "processed file", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type": "alignments", "uuid": "e2d38096-6665-4848-a2c2-864907996a63", "file_type_detailed": "alignments (bam)", "@type": ["FileProcessed", "File", "Item"], "file_classification": "processed file", "display_title": "4DNFIZQAH18C.bam", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e2d38096-6665-4848-a2c2-864907996a63/4DNFIZQAH18C.bam", "upload_key": "e2d38096-6665-4848-a2c2-864907996a63/4DNFIZQAH18C.bam", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "file_format": {"file_format": "bam", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFIZQAH18C", "href": "/files-processed/4DNFIZQAH18C/@@download/4DNFIZQAH18C.bam", "@id": "/files-processed/4DNFIZQAH18C/", "file_size": 1329786961, "status": "released", "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "processed file", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type": "normalized counts", "uuid": "5441503d-ee73-49c0-9df4-179423959f86", "file_type_detailed": "normalized counts (bw)", "@type": ["FileProcessed", "File", "Item"], "file_classification": "processed file", "display_title": "4DNFISNVPFBC.bw", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/5441503d-ee73-49c0-9df4-179423959f86/4DNFISNVPFBC.bw", "upload_key": "5441503d-ee73-49c0-9df4-179423959f86/4DNFISNVPFBC.bw", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "file_format": {"file_format": "bw", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFISNVPFBC", "href": "/files-processed/4DNFISNVPFBC/@@download/4DNFISNVPFBC.bw", "@id": "/files-processed/4DNFISNVPFBC/", "file_size": 940713, "status": "released", "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "processed file", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "normalized counts for K562 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "external_references": [], "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"uuid": "e2feeb71-0040-4aec-8652-c4126caf6415", "@id": "/higlass-view-configs/e2feeb71-0040-4aec-8652-c4126caf6415/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFISNVPFBC - normalized counts for K562 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type": "NADs", "uuid": "87834a89-e4de-4e1c-a8c5-a1333894c74b", "file_type_detailed": "NADs (bed)", "@type": ["FileProcessed", "File", "Item"], "file_classification": "processed file", "display_title": "4DNFIHNYZL1B.bed.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/87834a89-e4de-4e1c-a8c5-a1333894c74b/4DNFIHNYZL1B.bed.gz", "upload_key": "87834a89-e4de-4e1c-a8c5-a1333894c74b/4DNFIHNYZL1B.bed.gz", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "file_format": {"file_format": "bed", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "bed", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "@id": "/file-formats/bed/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNFIHNYZL1B", "href": "/files-processed/4DNFIHNYZL1B/@@download/4DNFIHNYZL1B.bed.gz", "@id": "/files-processed/4DNFIHNYZL1B/", "file_size": 6003, "status": "released", "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "processed file", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "NADs for K562 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "external_references": [], "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"uuid": "2953afef-c993-4ce5-bc94-9a2787cf28bd", "@id": "/higlass-view-configs/2953afef-c993-4ce5-bc94-9a2787cf28bd/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIHNYZL1B - NADs for K562 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "project_release": "2020-07-14", "targeted_factor": [{"status": "released", "uuid": "f126f470-4fff-40d2-b2b3-842e50ea5cfb", "display_title": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "@id": "/bio-features/f126f470-4fff-40d2-b2b3-842e50ea5cfb/", "@type": ["BioFeature", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosample_quantity": 0.5, "authentication_docs": [{"@id": "/protocols/a250e974-8558-4030-b7c8-39dab2e27f02/", "@type": ["Protocol", "Item"], "display_title": "ts171019_mePCRs_K562.pdf", "uuid": "a250e974-8558-4030-b7c8-39dab2e27f02", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_relation": [{"experiment": {"display_title": "DamID-seq on K562 (Tier 2) - 4DNEXSZ95DTY", "@type": ["ExperimentDamid", "Experiment", "Item"], "@id": "/experiments-damid/4DNEXSZ95DTY/", "uuid": "d1649c26-8afd-4376-abd7-2219022a3168", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "controlled by"}], "me_pcr_library_date": "2017-10-19", "y_ligation_dna_input": 200.0, "other_processed_files": [{"type": "supplementary", "files": [{"file_type_detailed": "counts (compressed_txt)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/072b82cc-8f00-45ea-9179-232df853e5ad/4DNFI7NQJ2ME.txt.gz", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "file_size": 50771421, "@id": "/files-processed/4DNFI7NQJ2ME/", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "href": "/files-processed/4DNFI7NQJ2ME/@@download/4DNFI7NQJ2ME.txt.gz", "status": "released", "accession": "4DNFI7NQJ2ME", "uuid": "072b82cc-8f00-45ea-9179-232df853e5ad", "display_title": "4DNFI7NQJ2ME.txt.gz", "file_format": {"status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "@id": "/file-formats/compressed_txt/", "file_format": "compressed_txt", "display_title": "compressed_txt", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "gatc binned files", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "last_modified": {"date_modified": "2024-02-22T17:48:02.708725+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "normalized counts (compressed_txt)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/2b209db5-ea35-428c-a847-aefd449ca34b/4DNFI9ZJIZYU.txt.gz", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "file_size": 60010752, "@id": "/files-processed/4DNFI9ZJIZYU/", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "href": "/files-processed/4DNFI9ZJIZYU/@@download/4DNFI9ZJIZYU.txt.gz", "status": "released", "accession": "4DNFI9ZJIZYU", "uuid": "2b209db5-ea35-428c-a847-aefd449ca34b", "display_title": "4DNFI9ZJIZYU.txt.gz", "file_format": {"status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "@id": "/file-formats/compressed_txt/", "file_format": "compressed_txt", "display_title": "compressed_txt", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "gatc binned files", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "last_modified": {"date_modified": "2024-02-22T17:41:17.565307+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "counts (bw)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/30445a32-6a8b-442d-87c3-736a2a205b7d/4DNFIZRAFW3Z.bw", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "file_size": 40868080, "@id": "/files-processed/4DNFIZRAFW3Z/", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "higlass_uid": "c933bfe6-91c8-4575-9807-9f14d0092fae", "href": "/files-processed/4DNFIZRAFW3Z/@@download/4DNFIZRAFW3Z.bw", "status": "released", "accession": "4DNFIZRAFW3Z", "uuid": "30445a32-6a8b-442d-87c3-736a2a205b7d", "display_title": "4DNFIZRAFW3Z.bw", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"@id": "/higlass-view-configs/39cd1c97-fa18-45db-84b6-3c91892a2063/", "display_title": "4DNFIZRAFW3Z", "uuid": "39cd1c97-fa18-45db-84b6-3c91892a2063", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "file_format": {"status": "released", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bw/", "file_format": "bw", "display_title": "bw", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "gatc binned files", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for K562 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "last_modified": {"date_modified": "2024-02-22T17:41:52.199833+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "normalized counts (bw)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/3e8d1eef-20b9-42e2-9450-9dec5a38b522/4DNFI1TMYT9I.bw", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "file_size": 23593982, "@id": "/files-processed/4DNFI1TMYT9I/", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "higlass_uid": "1b3203ab-00e3-46da-b361-471ab98d0bd6", "href": "/files-processed/4DNFI1TMYT9I/@@download/4DNFI1TMYT9I.bw", "status": "released", "accession": "4DNFI1TMYT9I", "uuid": "3e8d1eef-20b9-42e2-9450-9dec5a38b522", "display_title": "4DNFI1TMYT9I.bw", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"@id": "/higlass-view-configs/2dab60e9-eedf-48b3-b2f6-13e08f983d3c/", "display_title": "4DNFI1TMYT9I", "uuid": "2dab60e9-eedf-48b3-b2f6-13e08f983d3c", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "file_format": {"status": "released", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bw/", "file_format": "bw", "display_title": "bw", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "gatc binned files", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "normalized counts for K562 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "last_modified": {"date_modified": "2024-02-22T17:37:09.078449+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "title": "gatc binned files", "description": "The files associated with the gatc bin size processing of data for DamID-seq on K562 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam"}, {"type": "supplementary", "files": [{"file_type_detailed": "counts (compressed_txt)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/11bb3d8e-498e-4b36-ad82-857e369e181c/4DNFI4DAP4LW.txt.gz", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "file_size": 740379, "@id": "/files-processed/4DNFI4DAP4LW/", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "href": "/files-processed/4DNFI4DAP4LW/@@download/4DNFI4DAP4LW.txt.gz", "status": "released", "accession": "4DNFI4DAP4LW", "uuid": "11bb3d8e-498e-4b36-ad82-857e369e181c", "display_title": "4DNFI4DAP4LW.txt.gz", "file_format": {"status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "@id": "/file-formats/compressed_txt/", "file_format": "compressed_txt", "display_title": "compressed_txt", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "25kb binned files", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "last_modified": {"date_modified": "2024-02-22T17:46:11.947319+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "normalized counts (compressed_txt)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8c96a612-c8d0-43b1-8271-fbed7ee65011/4DNFI5R56KE8.txt.gz", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "file_size": 1623988, "@id": "/files-processed/4DNFI5R56KE8/", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "href": "/files-processed/4DNFI5R56KE8/@@download/4DNFI5R56KE8.txt.gz", "status": "released", "accession": "4DNFI5R56KE8", "uuid": "8c96a612-c8d0-43b1-8271-fbed7ee65011", "display_title": "4DNFI5R56KE8.txt.gz", "file_format": {"status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "@id": "/file-formats/compressed_txt/", "file_format": "compressed_txt", "display_title": "compressed_txt", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "25kb binned files", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "last_modified": {"date_modified": "2024-02-22T17:39:53.527318+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "counts (bw)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/1aafec63-7757-4b2d-9a23-45b123b431a5/4DNFIUZBQKNN.bw", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "file_size": 1079668, "@id": "/files-processed/4DNFIUZBQKNN/", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "higlass_uid": "dec48041-d796-4aad-b380-7fc559141724", "href": "/files-processed/4DNFIUZBQKNN/@@download/4DNFIUZBQKNN.bw", "status": "released", "accession": "4DNFIUZBQKNN", "uuid": "1aafec63-7757-4b2d-9a23-45b123b431a5", "display_title": "4DNFIUZBQKNN.bw", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"@id": "/higlass-view-configs/9328c9c8-3609-4cd2-ad05-c7c3888fb38e/", "display_title": "4DNFIUZBQKNN", "uuid": "9328c9c8-3609-4cd2-ad05-c7c3888fb38e", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "file_format": {"status": "released", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bw/", "file_format": "bw", "display_title": "bw", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "25kb binned files", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for K562 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "last_modified": {"date_modified": "2024-02-22T17:39:58.009218+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "normalized counts (bw)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/5814344d-f9b4-4c48-b9c4-3e2a45065210/4DNFIUGQGPJ6.bw", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "file_size": 1813437, "@id": "/files-processed/4DNFIUGQGPJ6/", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "higlass_uid": "2645634c-5db0-4f28-a518-68018953f65b", "href": "/files-processed/4DNFIUGQGPJ6/@@download/4DNFIUGQGPJ6.bw", "status": "released", "accession": "4DNFIUGQGPJ6", "uuid": "5814344d-f9b4-4c48-b9c4-3e2a45065210", "display_title": "4DNFIUGQGPJ6.bw", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"@id": "/higlass-view-configs/2e49ab39-02d7-4ab8-8bac-eb050cdb019c/", "display_title": "4DNFIUGQGPJ6", "uuid": "2e49ab39-02d7-4ab8-8bac-eb050cdb019c", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "file_format": {"status": "released", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bw/", "file_format": "bw", "display_title": "bw", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "25kb binned files", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "normalized counts for K562 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "last_modified": {"date_modified": "2024-02-22T17:35:47.693054+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "NADs (compressed_txt)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/bec266b3-55bf-455a-a34c-4b4da6ac96ba/4DNFI863Q6N9.txt.gz", "file_type": "NADs", "@type": ["FileProcessed", "File", "Item"], "file_size": 516055, "@id": "/files-processed/4DNFI863Q6N9/", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "href": "/files-processed/4DNFI863Q6N9/@@download/4DNFI863Q6N9.txt.gz", "status": "released", "accession": "4DNFI863Q6N9", "uuid": "bec266b3-55bf-455a-a34c-4b4da6ac96ba", "display_title": "4DNFI863Q6N9.txt.gz", "file_format": {"status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "@id": "/file-formats/compressed_txt/", "file_format": "compressed_txt", "display_title": "compressed_txt", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "25kb binned files", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "last_modified": {"date_modified": "2024-02-22T17:35:09.838423+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "NADs (bed)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/28518a96-d96a-48a1-aa48-3d7f4244e443/4DNFITEXXR2O.bed.gz", "file_type": "NADs", "@type": ["FileProcessed", "File", "Item"], "file_size": 6944, "@id": "/files-processed/4DNFITEXXR2O/", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "higlass_uid": "dSD0brd5QxOAdfsXmnSClA", "href": "/files-processed/4DNFITEXXR2O/@@download/4DNFITEXXR2O.bed.gz", "status": "released", "accession": "4DNFITEXXR2O", "uuid": "28518a96-d96a-48a1-aa48-3d7f4244e443", "display_title": "4DNFITEXXR2O.bed.gz", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"@id": "/higlass-view-configs/e4ba735f-2e1f-4626-ad68-1438425c83f5/", "display_title": "4DNFITEXXR2O - NADs for K562 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "uuid": "e4ba735f-2e1f-4626-ad68-1438425c83f5", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "file_format": {"status": "released", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "@id": "/file-formats/bed/", "file_format": "bed", "display_title": "bed", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "25kb binned files", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "NADs for K562 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "last_modified": {"date_modified": "2024-02-22T17:36:52.638482+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "title": "25kb binned files", "description": "The files associated with the 25kb bin size processing of data for DamID-seq on K562 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam"}, {"type": "supplementary", "files": [{"file_type_detailed": "counts (compressed_txt)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/9dbf009c-9c46-4cb9-92ea-12c7e1e30273/4DNFILRVOJF9.txt.gz", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "file_size": 371509, "@id": "/files-processed/4DNFILRVOJF9/", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "href": "/files-processed/4DNFILRVOJF9/@@download/4DNFILRVOJF9.txt.gz", "status": "released", "accession": "4DNFILRVOJF9", "uuid": "9dbf009c-9c46-4cb9-92ea-12c7e1e30273", "display_title": "4DNFILRVOJF9.txt.gz", "file_format": {"status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "@id": "/file-formats/compressed_txt/", "file_format": "compressed_txt", "display_title": "compressed_txt", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "Additional 50kb binned files", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "last_modified": {"date_modified": "2024-02-22T17:41:15.205888+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "normalized counts (compressed_txt)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/65260d1e-adcc-4b12-8cc3-bd30512adf96/4DNFIM4STVGL.txt.gz", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "file_size": 813297, "@id": "/files-processed/4DNFIM4STVGL/", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "href": "/files-processed/4DNFIM4STVGL/@@download/4DNFIM4STVGL.txt.gz", "status": "released", "accession": "4DNFIM4STVGL", "uuid": "65260d1e-adcc-4b12-8cc3-bd30512adf96", "display_title": "4DNFIM4STVGL.txt.gz", "file_format": {"status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "@id": "/file-formats/compressed_txt/", "file_format": "compressed_txt", "display_title": "compressed_txt", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "Additional 50kb binned files", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "last_modified": {"date_modified": "2024-02-22T17:41:32.523138+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "counts (bw)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a78f0932-5cd2-4b19-8165-3abea9ebd58b/4DNFICNN1HU7.bw", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "file_size": 588413, "@id": "/files-processed/4DNFICNN1HU7/", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "higlass_uid": "ae3fde7d-4534-4cfd-baff-4fb1200ebe91", "href": "/files-processed/4DNFICNN1HU7/@@download/4DNFICNN1HU7.bw", "status": "released", "accession": "4DNFICNN1HU7", "uuid": "a78f0932-5cd2-4b19-8165-3abea9ebd58b", "display_title": "4DNFICNN1HU7.bw", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"@id": "/higlass-view-configs/c2a05dd3-bd7b-4ce7-84b2-47308d31cd50/", "display_title": "4DNFICNN1HU7", "uuid": "c2a05dd3-bd7b-4ce7-84b2-47308d31cd50", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "file_format": {"status": "released", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bw/", "file_format": "bw", "display_title": "bw", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "Additional 50kb binned files", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for K562 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "last_modified": {"date_modified": "2024-02-22T17:41:02.823823+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "NADs (compressed_txt)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/3fb683e6-8dd0-473c-90e9-9fa589735b19/4DNFIXG4QZQ5.txt.gz", "file_type": "NADs", "@type": ["FileProcessed", "File", "Item"], "file_size": 252602, "@id": "/files-processed/4DNFIXG4QZQ5/", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "href": "/files-processed/4DNFIXG4QZQ5/@@download/4DNFIXG4QZQ5.txt.gz", "status": "released", "accession": "4DNFIXG4QZQ5", "uuid": "3fb683e6-8dd0-473c-90e9-9fa589735b19", "display_title": "4DNFIXG4QZQ5.txt.gz", "file_format": {"status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "@id": "/file-formats/compressed_txt/", "file_format": "compressed_txt", "display_title": "compressed_txt", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "Additional 50kb binned files", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "last_modified": {"date_modified": "2024-02-22T17:36:45.191540+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "title": "Additional 50kb binned files", "description": "Additional files associated with the 50kb bin size processing of data for DamID-seq on K562 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam"}, {"type": "supplementary", "files": [{"file_type_detailed": "counts (compressed_txt)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8a95159e-6c66-4fac-91ea-887541e2797f/4DNFI8TOYOOP.txt.gz", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "file_size": 186194, "@id": "/files-processed/4DNFI8TOYOOP/", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "href": "/files-processed/4DNFI8TOYOOP/@@download/4DNFI8TOYOOP.txt.gz", "status": "released", "accession": "4DNFI8TOYOOP", "uuid": "8a95159e-6c66-4fac-91ea-887541e2797f", "display_title": "4DNFI8TOYOOP.txt.gz", "file_format": {"status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "@id": "/file-formats/compressed_txt/", "file_format": "compressed_txt", "display_title": "compressed_txt", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "100kb binned files", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "last_modified": {"date_modified": "2024-02-22T17:42:38.689969+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "normalized counts (compressed_txt)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c66caab5-20ac-459e-a44e-c237be47cfcf/4DNFIQ45ZSTR.txt.gz", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "file_size": 409093, "@id": "/files-processed/4DNFIQ45ZSTR/", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "href": "/files-processed/4DNFIQ45ZSTR/@@download/4DNFIQ45ZSTR.txt.gz", "status": "released", "accession": "4DNFIQ45ZSTR", "uuid": "c66caab5-20ac-459e-a44e-c237be47cfcf", "display_title": "4DNFIQ45ZSTR.txt.gz", "file_format": {"status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "@id": "/file-formats/compressed_txt/", "file_format": "compressed_txt", "display_title": "compressed_txt", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "100kb binned files", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "last_modified": {"date_modified": "2024-02-22T17:40:27.514526+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "counts (bw)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/317012d0-78d0-421c-826f-a6427daf354c/4DNFI7CDQLNY.bw", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "file_size": 322147, "@id": "/files-processed/4DNFI7CDQLNY/", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "higlass_uid": "a06e1157-3434-4f07-b2a8-f3873fe400cb", "href": "/files-processed/4DNFI7CDQLNY/@@download/4DNFI7CDQLNY.bw", "status": "released", "accession": "4DNFI7CDQLNY", "uuid": "317012d0-78d0-421c-826f-a6427daf354c", "display_title": "4DNFI7CDQLNY.bw", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"@id": "/higlass-view-configs/30383937-ebe8-498c-a77b-bd32ea216385/", "display_title": "4DNFI7CDQLNY", "uuid": "30383937-ebe8-498c-a77b-bd32ea216385", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "file_format": {"status": "released", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bw/", "file_format": "bw", "display_title": "bw", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "100kb binned files", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for K562 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "last_modified": {"date_modified": "2024-02-22T17:39:28.811287+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "normalized counts (bw)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/33b3b9b2-6316-4887-8ec8-8b8306a108c7/4DNFIQYQVWJO.bw", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "file_size": 492579, "@id": "/files-processed/4DNFIQYQVWJO/", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "higlass_uid": "bedb8c0e-ae70-4e87-a38f-df6900b02ecd", "href": "/files-processed/4DNFIQYQVWJO/@@download/4DNFIQYQVWJO.bw", "status": "released", "accession": "4DNFIQYQVWJO", "uuid": "33b3b9b2-6316-4887-8ec8-8b8306a108c7", "display_title": "4DNFIQYQVWJO.bw", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"@id": "/higlass-view-configs/ee443867-e991-4293-87df-a241245df591/", "display_title": "4DNFIQYQVWJO - normalized counts for K562 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "uuid": "ee443867-e991-4293-87df-a241245df591", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "file_format": {"status": "released", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bw/", "file_format": "bw", "display_title": "bw", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "100kb binned files", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "normalized counts for K562 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "last_modified": {"date_modified": "2024-02-22T17:36:16.259000+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "NADs (compressed_txt)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dddb36c3-cdfa-4f36-bd54-f5d0ae626c3a/4DNFIYZ72ZBD.txt.gz", "file_type": "NADs", "@type": ["FileProcessed", "File", "Item"], "file_size": 127514, "@id": "/files-processed/4DNFIYZ72ZBD/", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "href": "/files-processed/4DNFIYZ72ZBD/@@download/4DNFIYZ72ZBD.txt.gz", "status": "released", "accession": "4DNFIYZ72ZBD", "uuid": "dddb36c3-cdfa-4f36-bd54-f5d0ae626c3a", "display_title": "4DNFIYZ72ZBD.txt.gz", "file_format": {"status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "@id": "/file-formats/compressed_txt/", "file_format": "compressed_txt", "display_title": "compressed_txt", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "100kb binned files", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "last_modified": {"date_modified": "2024-02-22T17:35:38.946782+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "NADs (bed)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/db074579-d7fd-41c5-98d2-f7f7025e399e/4DNFIDPAFEZI.bed.gz", "file_type": "NADs", "@type": ["FileProcessed", "File", "Item"], "file_size": 3140, "@id": "/files-processed/4DNFIDPAFEZI/", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "higlass_uid": "HG93a5scQtOJyWt-oHoz1w", "href": "/files-processed/4DNFIDPAFEZI/@@download/4DNFIDPAFEZI.bed.gz", "status": "released", "accession": "4DNFIDPAFEZI", "uuid": "db074579-d7fd-41c5-98d2-f7f7025e399e", "display_title": "4DNFIDPAFEZI.bed.gz", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"@id": "/higlass-view-configs/1059cb7c-9150-476d-bde6-18a49b5c79e5/", "display_title": "4DNFIDPAFEZI - NADs for K562 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "uuid": "1059cb7c-9150-476d-bde6-18a49b5c79e5", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "file_format": {"status": "released", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "@id": "/file-formats/bed/", "file_format": "bed", "display_title": "bed", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "100kb binned files", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "NADs for K562 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "last_modified": {"date_modified": "2024-02-22T17:50:25.191347+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "title": "100kb binned files", "description": "The files associated with the 100kb bin size processing of data for DamID-seq on K562 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam"}, {"type": "supplementary", "files": [{"file_type_detailed": "other (html)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/45e1e24c-b0f7-4f15-80a7-c58069648dc5/4DNFIY4AE9BA.html", "file_type": "other", "@type": ["FileProcessed", "File", "Item"], "file_size": 2534071, "@id": "/files-processed/4DNFIY4AE9BA/", "href": "/files-processed/4DNFIY4AE9BA/@@download/4DNFIY4AE9BA.html", "status": "released", "accession": "4DNFIY4AE9BA", "uuid": "45e1e24c-b0f7-4f15-80a7-c58069648dc5", "display_title": "4DNFIY4AE9BA.html", "file_format": {"status": "released", "uuid": "8bd6fe41-6af8-43c9-b24a-d74241898f09", "@id": "/file-formats/html/", "file_format": "html", "display_title": "html", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "Other files - non-binned", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on K562 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "last_modified": {"date_modified": "2024-02-22T17:32:22.276101+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "title": "Other files - non-binned", "description": "Non-bin specific files for DamID-seq on K562 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam"}], "biosample_quantity_units": "\u03bcg", "library_preparation_date": "2017-10-17", "@id": "/experiments-damid/4DNEXLVPKOIM/", "@type": ["ExperimentDamid", "Experiment", "Item"], "uuid": "1d643c34-a1ba-4e3c-bf81-c7065b69f161", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "DamID-seq with DAM-Nucleolus on K562 (Tier 2) - 4DNEXLVPKOIM", "external_references": [], "experiment_sets": [{"@id": "/experiment-set-replicates/4DNESR65C7PI/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "status": "released", "accession": "4DNESR65C7PI", "display_title": "4DNESR65C7PI", "uuid": "0689a95a-548d-4cdb-983e-191f57602939", "experimentset_type": "replicate", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "publications_of_exp": [], "experiment_categorizer": {"field": "Target", "value": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "combined": "Target: Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "experiment_summary": "DamID-seq with DAM-Nucleolus on K562 (Tier 2)", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSKN91Y5M/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "warning": null, "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "@id": "/badges/gold-biosample/", "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "description": "Gold biosample"}}}]}, "validation-errors": []}