{"lab": {"title": "Bas van Steensel, NKI", "status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "display_title": "Bas van Steensel, NKI", "correspondence": [{"contact_email": "Yi52LnN0ZWVuc2VsQG5raS5ubA==", "@id": "/users/dd8b1cd6-93cd-41e5-b184-caf1369cb39f/", "display_title": "Bas van Steensel"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "award": {"center_title": "NOFIC - Belmont", "@type": ["Award", "Item"], "status": "current", "project": "4DN", "@id": "/awards/1U54DK107965-01/", "uuid": "91b694c3-f4d7-4ddd-8278-16f94e15c1c5", "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.", "name": "1U54DK107965-01", "display_title": "COMBINED CYTOLOGICAL, GENOMIC, AND FUNCTIONAL MAPPING OF NUCLEAR GENOME ORGANIZATION", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["vanSteensel-lab:HCT116_4xAP3"], "accession": "4DNES3PG7E7F", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "description": "DamID for Nucleolus (4X-AP3) on HCT116 wildtype cells - cells were transduced with virus expressing a Dam fusion protein, gDNA was harvested after 3 or 4 days and processed for DamID-seq", "date_created": "2020-07-01T07:53:54.740490+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "DamID-seq on HCT116 cells (2020-07-01)", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-02-22T18:46:56.716916+00:00"}, "public_release": "2023-11-03", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"status": "released", "accession": "4DNEXT1WW176", "@id": "/experiments-damid/4DNEXT1WW176/", "display_title": "DamID-seq with DAM-Nucleolus on HCT116 (Tier 2) - 4DNEXT1WW176", "uuid": "33368258-3afd-4d6c-b81b-232cc0138375", "@type": ["ExperimentDamid", "Experiment", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"status": "released", "accession": "4DNEXOQ91GG3", "@id": "/experiments-damid/4DNEXOQ91GG3/", "display_title": "DamID-seq with DAM-Nucleolus on HCT116 (Tier 2) - 4DNEXOQ91GG3", "uuid": "afbc3254-14f1-4e63-996f-b8c1e7bdee76", "@type": ["ExperimentDamid", "Experiment", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 3, "tec_rep_no": 1, "replicate_exp": {"status": "released", "accession": "4DNEXOFUK2A4", "@id": "/experiments-damid/4DNEXOFUK2A4/", "display_title": "DamID-seq with DAM-Nucleolus on HCT116 (Tier 2) - 4DNEXOFUK2A4", "uuid": "07f2d9c5-2a34-4a8c-be9f-6ca7ec2bdf1c", "@type": ["ExperimentDamid", "Experiment", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"lab": {"uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "display_title": "Bas van Steensel, NKI", "status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "uuid": "e27ae6f2-3836-4896-8375-ae74a4e4d762", "display_title": "4DNES3PG7E7F - Processed files", "title": "4DNES3PG7E7F - Processed files", "filetype": "HiglassViewConfig", "@type": ["HiglassViewConfig", "UserContent", "Item"], "description": "4DNES3PG7E7F (DamID for Nucleolus (4X-AP3) on HCT116 wildtype cells - cells were transduced with virus expressing a Dam fusion protein, gDNA was harvested after 3 or 4 days and processed for DamID-seq): 4DNFIX4LBRF1, 4DNFI4HQPGVC, 4DNFIXCJPXLT, 4DNFITTGS4PV, 4DNFI75WW3X2, 4DNFI9FNWY12, 4DNFI1WJGLKY, 4DNFI31UMKYF", "contributing_labs": [], "@id": "/higlass-view-configs/e27ae6f2-3836-4896-8375-ae74a4e4d762/", "award": {"uuid": "91b694c3-f4d7-4ddd-8278-16f94e15c1c5", "@type": ["Award", "Item"], "status": "current", "@id": "/awards/1U54DK107965-01/", "display_title": "COMBINED CYTOLOGICAL, GENOMIC, AND FUNCTIONAL MAPPING OF NUCLEAR GENOME ORGANIZATION", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "name": "e27ae6f2-3836-4896-8375-ae74a4e4d762", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}, "location": "tab:processed-files", "description": "auto_generated_higlass_view_config"}], "static_headers": [{"lab": {"status": "current", "@type": ["Lab", "Item"], "@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "display_title": "Bas van Steensel, NKI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "body": "Please use caution when using this data. Nucleolar DamID has not been validated extensively. Preliminary analyses suggest a substantial difference in data quality between cell lines. We interpret this as a difference in information content along the chromosomes due to more pronounced nucleolar interactions in some cell lines.", "name": "static-header.nucleolar_damid_caution", "award": {"@id": "/awards/1U01CA200059-01/", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "status": "current", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Caution:", "status": "released", "aliases": ["4dn-dcic-lab:no_dam_id_seq_prelim_caution"], "options": {"filetype": "md", "collapsible": true, "default_open": true, "convert_ext_links": true}, "date_created": "2020-07-10T14:50:59.399365+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-11-03T14:45:16.647531+00:00"}, "schema_version": "2", "@id": "/static-sections/4dffb987-01e2-4747-866c-bafccbd014a3/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "4dffb987-01e2-4747-866c-bafccbd014a3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267227777"]}, "display_title": "Caution:", "external_references": [], "content": "Please use caution when using this data. Nucleolar DamID has not been validated extensively. Preliminary analyses suggest a substantial difference in data quality between cell lines. We interpret this as a difference in information content along the chromosomes due to more pronounced nucleolar interactions in some cell lines.", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p>Please use caution when using this data. Nucleolar DamID has not been validated extensively. Preliminary analyses suggest a substantial difference in data quality between cell lines. We interpret this as a difference in information content along the chromosomes due to more pronounced nucleolar interactions in some cell lines.</p></div>"}, {"lab": {"status": "current", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "\n**Data Use Guidelines:** This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) \nand the 4DN Data Portal paper \n([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).", "name": "item-page-headers.ExperimentSet.data-usage-guidelines", "award": {"@id": "/awards/1U01CA200059-01/", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "status": "current", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Data Usage Guidelines", "status": "released", "aliases": [], "options": {"filetype": "md", "title_icon": "exclamation-circle", "collapsible": false, "default_open": true}, "date_created": "2018-08-06T03:09:55.543206+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-05-09T09:31:34.537494+00:00"}, "schema_version": "2", "@id": "/static-sections/621e8359-3885-40ce-965d-91894aa7b758/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "621e8359-3885-40ce-965d-91894aa7b758", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267228139"]}, "display_title": "Data Usage Guidelines", "external_references": [], "content": "\n**Data Use Guidelines:** This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) \nand the 4DN Data Portal paper \n([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p><strong>Data Use Guidelines:</strong> This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n(<a href=\"https://doi.org/10.1038/nature23884\" rel=\"noopener noreferrer\" target=\"_blank\">doi:10.1038/nature23884</a>) \nand the 4DN Data Portal paper \n(<a href=\"https://doi.org/10.1038/s41467-022-29697-4\" rel=\"noopener noreferrer\" target=\"_blank\">doi:10.1038/s41467-022-29697-4</a>), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the <a href=\"mailto:support@4dnucleome.org\">Data Coordination and Integration Center</a>.</p></div>"}], "processed_files": [{"status": "released", "accession": "4DNFIX4LBRF1", "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."], "@type": ["FileProcessed", "File", "Item"], "file_format": {"status": "released", "display_title": "bw", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 949309, "href": "/files-processed/4DNFIX4LBRF1/@@download/4DNFIX4LBRF1.bw", "upload_key": "647785a0-0396-4eb5-a891-bbbcc26d5ec1/4DNFIX4LBRF1.bw", "@id": "/files-processed/4DNFIX4LBRF1/", "file_type_detailed": "normalized counts (bw)", "file_classification": "processed file", "file_type": "normalized counts", "display_title": "4DNFIX4LBRF1.bw", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/647785a0-0396-4eb5-a891-bbbcc26d5ec1/4DNFIX4LBRF1.bw", "genome_assembly": "GRCh38", "uuid": "647785a0-0396-4eb5-a891-bbbcc26d5ec1", "md5sum": "a31cfd74092d08ba24261fe817f2ef35", "higlass_uid": "61b23225-d5e7-400d-9f6f-41925a0cc848", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "uuid": "344b718a-7f51-43bf-a2dc-d5658d5c3e2f", "@id": "/higlass-view-configs/344b718a-7f51-43bf-a2dc-d5658d5c3e2f/", "display_title": "4DNFIX4LBRF1 - normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2024-02-22T17:36:37.176456+00:00"}, "track_and_facet_info": {"dataset": "DamID-seq on HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "experimental_lab": "Bas van Steensel, NKI", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "DamID-seq", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}}, {"status": "released", "accession": "4DNFI4HQPGVC", "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."], "@type": ["FileProcessed", "File", "Item"], "file_format": {"status": "released", "display_title": "bed", "@id": "/file-formats/bed/", "@type": ["FileFormat", "Item"], "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 3195, "href": "/files-processed/4DNFI4HQPGVC/@@download/4DNFI4HQPGVC.bed.gz", "upload_key": "dcdb86f1-4b94-460c-a869-99dab9d232ba/4DNFI4HQPGVC.bed.gz", "@id": "/files-processed/4DNFI4HQPGVC/", "file_type_detailed": "NADs (bed)", "file_classification": "processed file", "file_type": "NADs", "display_title": "4DNFI4HQPGVC.bed.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcdb86f1-4b94-460c-a869-99dab9d232ba/4DNFI4HQPGVC.bed.gz", "genome_assembly": "GRCh38", "uuid": "dcdb86f1-4b94-460c-a869-99dab9d232ba", "md5sum": "20daf7d0710cae4ff168d13c0ee2af92", "higlass_uid": "ZYG4UgMkQ_afKm_MciLk9A", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "uuid": "5cd193b8-5a60-41ab-a78b-b236d14a06fb", "@id": "/higlass-view-configs/5cd193b8-5a60-41ab-a78b-b236d14a06fb/", "display_title": "4DNFI4HQPGVC - NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "extra_files": [{"use_for": "visualization", "href": "/files-processed/4DNFI4HQPGVC/@@download/4DNFI4HQPGVC.beddb", "md5sum": "bb0bfc57bd11aaad6cada6ea00ddac2c", "file_format": {"@id": "/file-formats/beddb/", "display_title": "beddb", "uuid": "76dc8c06-67d8-487b-8fc8-d841752a0b60", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "beddb", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2024-02-22T17:50:42.196132+00:00"}, "track_and_facet_info": {"dataset": "DamID-seq on HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "experimental_lab": "Bas van Steensel, NKI", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "DamID-seq", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}}], "project_release": "2020-07-14", "experiments_in_set": [{"display_title": "DamID-seq with DAM-Nucleolus on HCT116 (Tier 2) - 4DNEXT1WW176", "accession": "4DNEXT1WW176", "status": "released", "@type": ["ExperimentDamid", "Experiment", "Item"], "@id": "/experiments-damid/4DNEXT1WW176/", "uuid": "33368258-3afd-4d6c-b81b-232cc0138375", "files": [{"file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFIQNIDROR/", "upload_key": "8eb7297f-8e12-49dd-898e-a12c41a1cab4/4DNFIQNIDROR.fastq.gz", "@type": ["FileFastq", "File", "Item"], "file_classification": "raw file", "md5sum": "e6ac960a9e88ea0f385a12a32d556406", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/8eb7297f-8e12-49dd-898e-a12c41a1cab4/4DNFIQNIDROR.fastq.gz", "accession": "4DNFIQNIDROR", "uuid": "8eb7297f-8e12-49dd-898e-a12c41a1cab4", "file_size": 190602622, "file_type": "reads", "status": "released", "href": "/files-fastq/4DNFIQNIDROR/@@download/4DNFIQNIDROR.fastq.gz", "display_title": "4DNFIQNIDROR.fastq.gz", "lab": {"@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "status": "current", "display_title": "Bas van Steensel, NKI", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "file_format": {"file_format": "fastq", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "raw file", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "quality_metric": {"uuid": "fe112133-e596-4cad-9598-cc698e59b538", "Total Sequences": 3971649, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "65", "@id": "/quality-metrics-fastqc/fe112133-e596-4cad-9598-cc698e59b538/", "display_title": "QualityMetricFastqc from 2020-07-02", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIQNIDROR/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFILY8YEVX/", "upload_key": "876badeb-3b39-4156-80b2-5bac4f86d262/4DNFILY8YEVX.fastq.gz", "@type": ["FileFastq", "File", "Item"], "file_classification": "raw file", "md5sum": "b26d454138acd7a7fe4f9be1a2c15504", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/876badeb-3b39-4156-80b2-5bac4f86d262/4DNFILY8YEVX.fastq.gz", "accession": "4DNFILY8YEVX", "uuid": "876badeb-3b39-4156-80b2-5bac4f86d262", "file_size": 1955900548, "file_type": "reads", "status": "released", "href": "/files-fastq/4DNFILY8YEVX/@@download/4DNFILY8YEVX.fastq.gz", "display_title": "4DNFILY8YEVX.fastq.gz", "lab": {"@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "status": "current", "display_title": "Bas van Steensel, NKI", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "file_format": {"file_format": "fastq", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "raw file", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "quality_metric": {"uuid": "a8c79c32-4d3c-498c-a5ed-1d1479eecfef", "Total Sequences": 40498318, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "65", "@id": "/quality-metrics-fastqc/a8c79c32-4d3c-498c-a5ed-1d1479eecfef/", "display_title": "QualityMetricFastqc from 2020-07-02", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFILY8YEVX/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "processed_files": [{"status": "released", "upload_key": "de903d88-893d-47b5-bcea-9b8caab83f0c/4DNFIK5T2DQB.bam", "file_size": 138271175, "href": "/files-processed/4DNFIK5T2DQB/@@download/4DNFIK5T2DQB.bam", "display_title": "4DNFIK5T2DQB.bam", "file_type": "alignments", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/de903d88-893d-47b5-bcea-9b8caab83f0c/4DNFIK5T2DQB.bam", "uuid": "de903d88-893d-47b5-bcea-9b8caab83f0c", "file_classification": "processed file", "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."], "accession": "4DNFIK5T2DQB", "@id": "/files-processed/4DNFIK5T2DQB/", "file_format": {"status": "released", "display_title": "bam", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "alignments (bam)", "md5sum": "206d9338ce3299f57ddef33ecd901e6d", "lab": {"@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "status": "current", "display_title": "Bas van Steensel, NKI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "last_modified": {"date_modified": "2024-02-22T17:46:55.539531+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"status": "released", "upload_key": "f5a0526d-081e-4786-ba0d-f194479557b9/4DNFIJHL9CX5.bam", "file_size": 1112517926, "href": "/files-processed/4DNFIJHL9CX5/@@download/4DNFIJHL9CX5.bam", "display_title": "4DNFIJHL9CX5.bam", "file_type": "alignments", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f5a0526d-081e-4786-ba0d-f194479557b9/4DNFIJHL9CX5.bam", "uuid": "f5a0526d-081e-4786-ba0d-f194479557b9", "file_classification": "processed file", "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."], "accession": "4DNFIJHL9CX5", "@id": "/files-processed/4DNFIJHL9CX5/", "file_format": {"status": "released", "display_title": "bam", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "alignments (bam)", "md5sum": "bfc04ed62f667b99b80c61dc9dc11991", "lab": {"@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "status": "current", "display_title": "Bas van Steensel, NKI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "last_modified": {"date_modified": "2024-02-22T17:46:51.598084+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"status": "released", "upload_key": "884e0b9b-6261-4dda-889b-4cbe1b3dda33/4DNFIXCJPXLT.bw", "file_size": 947044, "href": "/files-processed/4DNFIXCJPXLT/@@download/4DNFIXCJPXLT.bw", "display_title": "4DNFIXCJPXLT.bw", "file_type": "normalized counts", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/884e0b9b-6261-4dda-889b-4cbe1b3dda33/4DNFIXCJPXLT.bw", "uuid": "884e0b9b-6261-4dda-889b-4cbe1b3dda33", "file_classification": "processed file", "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."], "accession": "4DNFIXCJPXLT", "higlass_uid": "67356b89-8129-44e4-961d-73a441bc33e7", "@id": "/files-processed/4DNFIXCJPXLT/", "file_format": {"status": "released", "display_title": "bw", "@type": ["FileFormat", "Item"], "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "normalized counts (bw)", "md5sum": "9fedc0ea7339ed6eb2dfebb0eca7f3d6", "lab": {"@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "status": "current", "display_title": "Bas van Steensel, NKI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"uuid": "4a9c10a2-9dc3-4f25-a811-ffe55ba32473", "@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/4a9c10a2-9dc3-4f25-a811-ffe55ba32473/", "status": "released", "display_title": "4DNFIXCJPXLT - normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "last_modified": {"date_modified": "2024-02-22T17:37:08.535247+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"status": "released", "upload_key": "8c68d7fd-a8ed-4f30-9fc0-d1db2d8023f2/4DNFITTGS4PV.bed.gz", "file_size": 2467, "href": "/files-processed/4DNFITTGS4PV/@@download/4DNFITTGS4PV.bed.gz", "display_title": "4DNFITTGS4PV.bed.gz", "file_type": "NADs", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8c68d7fd-a8ed-4f30-9fc0-d1db2d8023f2/4DNFITTGS4PV.bed.gz", "uuid": "8c68d7fd-a8ed-4f30-9fc0-d1db2d8023f2", "file_classification": "processed file", "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."], "accession": "4DNFITTGS4PV", "higlass_uid": "a03WQVaRShuc-q36e_5RMA", "@id": "/files-processed/4DNFITTGS4PV/", "file_format": {"status": "released", "display_title": "bed", "@type": ["FileFormat", "Item"], "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "@id": "/file-formats/bed/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "NADs (bed)", "md5sum": "afe4743ac9327a75a8f3ee9cb62fe994", "lab": {"@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "status": "current", "display_title": "Bas van Steensel, NKI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "extra_files": [{"md5sum": "d56ec6adfe84ad12f31a3296b07f3729", "use_for": "visualization", "href": "/files-processed/4DNFITTGS4PV/@@download/4DNFITTGS4PV.beddb", "file_format": {"file_format": "beddb", "display_title": "beddb", "@type": ["FileFormat", "Item"], "status": "released", "uuid": "76dc8c06-67d8-487b-8fc8-d841752a0b60", "@id": "/file-formats/beddb/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"uuid": "cf315f3c-6304-445f-bb3b-ab1dfdd51ae2", "@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/cf315f3c-6304-445f-bb3b-ab1dfdd51ae2/", "status": "released", "display_title": "4DNFITTGS4PV - NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "last_modified": {"date_modified": "2024-02-22T17:29:35.273313+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}], "biosample": {"treatments_summary": "None", "@type": ["Biosample", "Item"], "biosample_category": ["Tier 2"], "modifications_summary": "None", "biosource_summary": "HCT116 (Tier 2)", "biosample_type": "immortalized cells", "display_title": "4DNBSAH3ZFBQ", "status": "released", "accession": "4DNBSAH3ZFBQ", "@id": "/biosamples/4DNBSAH3ZFBQ/", "uuid": "254089d6-a30b-4493-8940-c6afefb854c9", "biosource": [{"@type": ["Biosource", "Item"], "@id": "/biosources/4DNSRMYUIVGD/", "display_title": "HCT116 (Tier 2) - 4DNSRMYUIVGD", "biosource_type": "immortalized cell line", "accession": "4DNSRMYUIVGD", "cell_line_tier": "Tier 2", "status": "released", "uuid": "393880ea-f928-406d-a4bf-78435b8975ef", "cell_line": {"status": "released", "preferred_name": "HCT116", "term_name": "HCT116", "synonyms": ["HCT-116 cell", "HCT116 cell"], "@type": ["OntologyTerm", "Item"], "term_id": "EFO:0002824", "@id": "/ontology-terms/EFO:0002824/", "display_title": "HCT116", "uuid": "49d090b2-5326-40ce-9c19-7a214c682272", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"term_name": "colon", "synonyms": ["large bowel", "posterior intestine"], "status": "released", "preferred_name": "colon", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0001155/", "display_title": "colon", "uuid": "3e39f551-bc0b-4bee-b932-29d71956fb94", "term_id": "UBERON:0001155", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000059/", "status": "released", "display_title": "large intestine", "uuid": "111174bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0001007/", "status": "released", "display_title": "digestive system", "uuid": "111129bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"scientific_name": "Homo sapiens", "@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "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": {"commendation": "Gold Biosample", "display_title": "Gold Biosample", "@id": "/badges/gold-biosample/", "status": "released", "@type": ["Badge", "Item"], "badge_classification": "Commendation", "title": "Gold Biosample", "description": "Gold biosample", "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "cell_culture_details": [{"status": "released", "@id": "/biosample-cell-cultures/5f130d8c-2538-4a94-a888-2c276f99f892/", "uuid": "5f130d8c-2538-4a94-a888-2c276f99f892", "in_vitro_differentiated": "No", "@type": ["BiosampleCellCulture", "Item"], "display_title": "BiosampleCellCulture from 2020-07-01", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"tissue_source": "colon", "organ_system": ["large intestine", "digestive system"]}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "other_processed_files": [{"type": "supplementary", "description": "The files associated with the gatc bin size processing of data for DamID-seq on HCT116 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam", "title": "gatc binned files", "files": [{"md5sum": "13caf2fe36f1f9b186fbe861ab6350e3", "href": "/files-processed/4DNFIRAWS3SL/@@download/4DNFIRAWS3SL.txt.gz", "display_title": "4DNFIRAWS3SL.txt.gz", "status": "released", "accession": "4DNFIRAWS3SL", "uuid": "018ca136-1f82-45e2-8187-99df3ef8bfc1", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/018ca136-1f82-45e2-8187-99df3ef8bfc1/4DNFIRAWS3SL.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIRAWS3SL/", "file_size": 50226103, "file_type_detailed": "counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:47:25.680354+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "e4274b6360e7da2310924af1217a94ca", "href": "/files-processed/4DNFIEWY1TD4/@@download/4DNFIEWY1TD4.txt.gz", "display_title": "4DNFIEWY1TD4.txt.gz", "status": "released", "accession": "4DNFIEWY1TD4", "uuid": "b452b57d-078c-4c94-8ccb-0c9000da72f9", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/b452b57d-078c-4c94-8ccb-0c9000da72f9/4DNFIEWY1TD4.txt.gz", "genome_assembly": "GRCh38", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIEWY1TD4/", "file_size": 59240261, "file_type_detailed": "normalized counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:40:58.047031+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "ee6c3c54b49e6aa48c0bb75551e9b0ab", "href": "/files-processed/4DNFICBWU93Z/@@download/4DNFICBWU93Z.bw", "display_title": "4DNFICBWU93Z.bw", "status": "released", "accession": "4DNFICBWU93Z", "higlass_uid": "c6ea8a75-6c5f-459b-acc7-7e221066b3c9", "uuid": "d133bb11-e12a-4832-a7ed-f4368a3cc27e", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/d133bb11-e12a-4832-a7ed-f4368a3cc27e/4DNFICBWU93Z.bw", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFICBWU93Z/", "file_size": 40459110, "file_type_detailed": "counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFICBWU93Z", "@id": "/higlass-view-configs/20b54fc0-69b4-4b78-b55c-37267abc04c0/", "uuid": "20b54fc0-69b4-4b78-b55c-37267abc04c0", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:41:13.683914+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "3f9b50f697a4509516bef49376409dae", "href": "/files-processed/4DNFI2NS3J7Q/@@download/4DNFI2NS3J7Q.bw", "display_title": "4DNFI2NS3J7Q.bw", "status": "released", "accession": "4DNFI2NS3J7Q", "higlass_uid": "02c49890-02e8-4ae2-808c-4dae0f476499", "uuid": "782fff11-57d5-4ff7-80d7-731a23274b0a", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/782fff11-57d5-4ff7-80d7-731a23274b0a/4DNFI2NS3J7Q.bw", "genome_assembly": "GRCh38", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFI2NS3J7Q/", "file_size": 23978914, "file_type_detailed": "normalized counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFI2NS3J7Q", "@id": "/higlass-view-configs/79df53b1-0f34-4ddd-b692-84785b711f91/", "uuid": "79df53b1-0f34-4ddd-b692-84785b711f91", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:36:49.544722+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, {"type": "supplementary", "description": "The files associated with the 25kb bin size processing of data for DamID-seq on HCT116 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam", "title": "25kb binned files", "files": [{"md5sum": "282eaace827bc4957ff933b5297164ef", "href": "/files-processed/4DNFISPYXHS4/@@download/4DNFISPYXHS4.txt.gz", "display_title": "4DNFISPYXHS4.txt.gz", "status": "released", "accession": "4DNFISPYXHS4", "uuid": "0076fbd9-4cd3-4bd2-87e3-9495c97f783a", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/0076fbd9-4cd3-4bd2-87e3-9495c97f783a/4DNFISPYXHS4.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFISPYXHS4/", "file_size": 739742, "file_type_detailed": "counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:42:18.267112+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "c41a674482a18fc79c0bcdfeea254085", "href": "/files-processed/4DNFI6M66HYU/@@download/4DNFI6M66HYU.txt.gz", "display_title": "4DNFI6M66HYU.txt.gz", "status": "released", "accession": "4DNFI6M66HYU", "uuid": "4c67f721-0b77-42cd-bb43-0f3a710f82b3", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/4c67f721-0b77-42cd-bb43-0f3a710f82b3/4DNFI6M66HYU.txt.gz", "genome_assembly": "GRCh38", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFI6M66HYU/", "file_size": 1641667, "file_type_detailed": "normalized counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:42:22.154379+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "ba96d28ffab374be913535e982f3188e", "href": "/files-processed/4DNFIMRKMND4/@@download/4DNFIMRKMND4.bw", "display_title": "4DNFIMRKMND4.bw", "status": "released", "accession": "4DNFIMRKMND4", "higlass_uid": "f0868de5-b5cd-4dca-9772-3cec5f01867d", "uuid": "84a2f947-6664-4738-8a83-bb36c921287b", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/84a2f947-6664-4738-8a83-bb36c921287b/4DNFIMRKMND4.bw", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIMRKMND4/", "file_size": 1068364, "file_type_detailed": "counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFIMRKMND4", "@id": "/higlass-view-configs/9c2425a6-cb74-4b36-b912-efad948c1fe9/", "uuid": "9c2425a6-cb74-4b36-b912-efad948c1fe9", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:39:29.847202+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "ccd60c5302b1e1d358ba9adb4cd8b5b6", "href": "/files-processed/4DNFII9K12IF/@@download/4DNFII9K12IF.bw", "display_title": "4DNFII9K12IF.bw", "status": "released", "accession": "4DNFII9K12IF", "higlass_uid": "ce139459-de2b-41ca-a652-fb32f804e1d2", "uuid": "9b93e201-261f-411e-a40e-792e4592229c", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/9b93e201-261f-411e-a40e-792e4592229c/4DNFII9K12IF.bw", "genome_assembly": "GRCh38", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFII9K12IF/", "file_size": 1825779, "file_type_detailed": "normalized counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFII9K12IF", "@id": "/higlass-view-configs/7aacebc0-ebce-48aa-ab24-3a4c074b2f0a/", "uuid": "7aacebc0-ebce-48aa-ab24-3a4c074b2f0a", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:35:32.122112+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "939820cf53df061fc61347a734d2217c", "href": "/files-processed/4DNFIITHD9DQ/@@download/4DNFIITHD9DQ.txt.gz", "display_title": "4DNFIITHD9DQ.txt.gz", "status": "released", "accession": "4DNFIITHD9DQ", "uuid": "4eaa9dd3-b8b0-4134-9230-73b81e84121a", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/4eaa9dd3-b8b0-4134-9230-73b81e84121a/4DNFIITHD9DQ.txt.gz", "genome_assembly": "GRCh38", "file_type": "NADs", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIITHD9DQ/", "file_size": 513337, "file_type_detailed": "NADs (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:37:36.057431+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "dda6e77b20d0b2b62706e86b601c8c0d", "href": "/files-processed/4DNFISFC6QFV/@@download/4DNFISFC6QFV.bed.gz", "display_title": "4DNFISFC6QFV.bed.gz", "status": "released", "accession": "4DNFISFC6QFV", "higlass_uid": "Yc8aZ9-lQ2iZeQ6-6Cgerg", "uuid": "12d32954-4093-4e1d-add2-5d1c93b29218", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/12d32954-4093-4e1d-add2-5d1c93b29218/4DNFISFC6QFV.bed.gz", "genome_assembly": "GRCh38", "file_type": "NADs", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFISFC6QFV/", "file_size": 3058, "file_type_detailed": "NADs (bed)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFISFC6QFV - NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "@id": "/higlass-view-configs/57f03656-d9a0-4fa9-b91f-b9e4a0f2ec11/", "uuid": "57f03656-d9a0-4fa9-b91f-b9e4a0f2ec11", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bed", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "file_format": "bed", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bed/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:36:24.190444+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, {"type": "supplementary", "description": "Additional files associated with the 50kb bin size processing of data for DamID-seq on HCT116 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam", "title": "Additional 50kb binned files", "files": [{"md5sum": "5c7cff0283b3fba670fe567e7ca534a9", "href": "/files-processed/4DNFIZRANC32/@@download/4DNFIZRANC32.txt.gz", "display_title": "4DNFIZRANC32.txt.gz", "status": "released", "accession": "4DNFIZRANC32", "uuid": "efe15375-46ab-4c54-aa12-87e1667cc3bd", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/efe15375-46ab-4c54-aa12-87e1667cc3bd/4DNFIZRANC32.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIZRANC32/", "file_size": 371864, "file_type_detailed": "counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:40:44.845899+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "3cd4a5f16fee06b6fef819e30c833cf6", "href": "/files-processed/4DNFICKPWEP5/@@download/4DNFICKPWEP5.txt.gz", "display_title": "4DNFICKPWEP5.txt.gz", "status": "released", "accession": "4DNFICKPWEP5", "uuid": "7c236747-cb0e-437b-babe-ca9f1f3d0283", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/7c236747-cb0e-437b-babe-ca9f1f3d0283/4DNFICKPWEP5.txt.gz", "genome_assembly": "GRCh38", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFICKPWEP5/", "file_size": 820660, "file_type_detailed": "normalized counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:41:17.584114+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "f21e034b3e6d988c423b487de4c6b6da", "href": "/files-processed/4DNFIIGISD8K/@@download/4DNFIIGISD8K.bw", "display_title": "4DNFIIGISD8K.bw", "status": "released", "accession": "4DNFIIGISD8K", "higlass_uid": "ee47f9b3-5080-40c3-bb0b-1ae5f27c41db", "uuid": "f3735ff9-79d6-403e-83b7-32d06ff6acbb", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f3735ff9-79d6-403e-83b7-32d06ff6acbb/4DNFIIGISD8K.bw", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIIGISD8K/", "file_size": 583409, "file_type_detailed": "counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFIIGISD8K", "@id": "/higlass-view-configs/74360120-44c5-47a1-a846-9ce3162c6343/", "uuid": "74360120-44c5-47a1-a846-9ce3162c6343", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:40:33.298152+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "32c240a2d53e864c4867b27c0a62edd9", "href": "/files-processed/4DNFI1XCTUB8/@@download/4DNFI1XCTUB8.txt.gz", "display_title": "4DNFI1XCTUB8.txt.gz", "status": "released", "accession": "4DNFI1XCTUB8", "uuid": "8703202a-c6a9-4979-878c-6b65d68d4f92", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8703202a-c6a9-4979-878c-6b65d68d4f92/4DNFI1XCTUB8.txt.gz", "genome_assembly": "GRCh38", "file_type": "NADs", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFI1XCTUB8/", "file_size": 250922, "file_type_detailed": "NADs (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:36:30.081012+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, {"type": "supplementary", "description": "The files associated with the 100kb bin size processing of data for DamID-seq on HCT116 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam", "title": "100kb binned files", "files": [{"md5sum": "c1267a3ee9a0ada709ca6a857b138e91", "href": "/files-processed/4DNFIQCEXKDF/@@download/4DNFIQCEXKDF.txt.gz", "display_title": "4DNFIQCEXKDF.txt.gz", "status": "released", "accession": "4DNFIQCEXKDF", "uuid": "2c531f29-f292-42d5-a6cc-ad5e2977c387", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/2c531f29-f292-42d5-a6cc-ad5e2977c387/4DNFIQCEXKDF.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIQCEXKDF/", "file_size": 185466, "file_type_detailed": "counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:42:10.489302+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "7becffde1d7bb450257693023dd6cec2", "href": "/files-processed/4DNFIVD9EDXP/@@download/4DNFIVD9EDXP.txt.gz", "display_title": "4DNFIVD9EDXP.txt.gz", "status": "released", "accession": "4DNFIVD9EDXP", "uuid": "f45cc3fe-604a-41c1-8089-d5b8586613b8", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f45cc3fe-604a-41c1-8089-d5b8586613b8/4DNFIVD9EDXP.txt.gz", "genome_assembly": "GRCh38", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIVD9EDXP/", "file_size": 412151, "file_type_detailed": "normalized counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:40:12.640634+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "308445b3d182a2e2379b192c61157cb7", "href": "/files-processed/4DNFI7HB4OPE/@@download/4DNFI7HB4OPE.bw", "display_title": "4DNFI7HB4OPE.bw", "status": "released", "accession": "4DNFI7HB4OPE", "higlass_uid": "112f73cf-edba-414e-90f4-79ced1ef89fc", "uuid": "55c671fa-dacd-4785-8b72-e0c8946c4c9d", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/55c671fa-dacd-4785-8b72-e0c8946c4c9d/4DNFI7HB4OPE.bw", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFI7HB4OPE/", "file_size": 321915, "file_type_detailed": "counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFI7HB4OPE", "@id": "/higlass-view-configs/374e5192-79ef-4ad2-87a9-e21d2003c5d4/", "uuid": "374e5192-79ef-4ad2-87a9-e21d2003c5d4", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:38:01.773439+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "504fcce7e6bcefc3ef9d160999917c2c", "href": "/files-processed/4DNFIWULR2U2/@@download/4DNFIWULR2U2.bw", "display_title": "4DNFIWULR2U2.bw", "status": "released", "accession": "4DNFIWULR2U2", "higlass_uid": "cdad404b-2eb8-473f-a96b-ded61650d59f", "uuid": "082a775e-b4d8-4cd6-ab6b-677664286172", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/082a775e-b4d8-4cd6-ab6b-677664286172/4DNFIWULR2U2.bw", "genome_assembly": "GRCh38", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIWULR2U2/", "file_size": 495503, "file_type_detailed": "normalized counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFIWULR2U2 - normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "@id": "/higlass-view-configs/b5c49754-855c-4ffd-8a0f-db238d36d859/", "uuid": "b5c49754-855c-4ffd-8a0f-db238d36d859", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:36:00.917662+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "8ed2b7d96957edea6ce53fd1acfe3773", "href": "/files-processed/4DNFIAM1ZREF/@@download/4DNFIAM1ZREF.txt.gz", "display_title": "4DNFIAM1ZREF.txt.gz", "status": "released", "accession": "4DNFIAM1ZREF", "uuid": "73a083dc-f831-496e-99ac-90e11a58c1c4", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/73a083dc-f831-496e-99ac-90e11a58c1c4/4DNFIAM1ZREF.txt.gz", "genome_assembly": "GRCh38", "file_type": "NADs", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIAM1ZREF/", "file_size": 127829, "file_type_detailed": "NADs (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:35:23.989947+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "1e66314a0b5caf374ec55e24b46244dd", "href": "/files-processed/4DNFIAO7XCXI/@@download/4DNFIAO7XCXI.bed.gz", "display_title": "4DNFIAO7XCXI.bed.gz", "status": "released", "accession": "4DNFIAO7XCXI", "higlass_uid": "X7myZGb6QOmoseqb2xIEMg", "uuid": "7a777ca2-acd2-4bae-841d-ead61fcc5095", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/7a777ca2-acd2-4bae-841d-ead61fcc5095/4DNFIAO7XCXI.bed.gz", "genome_assembly": "GRCh38", "file_type": "NADs", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIAO7XCXI/", "file_size": 2021, "file_type_detailed": "NADs (bed)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFIAO7XCXI - NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "@id": "/higlass-view-configs/842c7779-bd86-4492-a17f-139688ce8422/", "uuid": "842c7779-bd86-4492-a17f-139688ce8422", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bed", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "file_format": "bed", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bed/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:50:12.434650+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, {"type": "supplementary", "description": "Non-bin specific files for DamID-seq on HCT116 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam", "title": "Other files - non-binned", "files": [{"md5sum": "559d59b5dda4f7528a72688645a35e0c", "href": "/files-processed/4DNFIPRJ3ZWQ/@@download/4DNFIPRJ3ZWQ.html", "display_title": "4DNFIPRJ3ZWQ.html", "status": "released", "accession": "4DNFIPRJ3ZWQ", "uuid": "9d3b9ace-9f3a-44d4-ac69-3ddeb23218b4", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/9d3b9ace-9f3a-44d4-ac69-3ddeb23218b4/4DNFIPRJ3ZWQ.html", "genome_assembly": "GRCh38", "file_type": "other", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIPRJ3ZWQ/", "file_size": 2656615, "file_type_detailed": "other (html)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "html", "uuid": "8bd6fe41-6af8-43c9-b24a-d74241898f09", "file_format": "html", "@type": ["FileFormat", "Item"], "@id": "/file-formats/html/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:32:06.939104+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}], "experiment_type": {"assay_subclassification": "Proximity to Cellular Component", "assay_subclass_short": "Proximity-seq", "other_tags": ["1D"], "@type": ["ExperimentType", "Item"], "display_title": "DamID-seq", "uuid": "b777a1da-8dc8-4473-9b8d-4f7716fb0a4a", "title": "DamID-seq", "@id": "/experiment-types/damid-seq/", "experiment_category": "Sequencing", "status": "released", "assay_classification": "Linear DNA Enrichment", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "last_modified": {"date_modified": "2023-11-03T14:45:14.972789+00:00"}, "experiment_categorizer": {"field": "Target", "value": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "combined": "Target: Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "DamID-seq with DAM-Nucleolus on HCT116 (Tier 2) - 4DNEXOQ91GG3", "accession": "4DNEXOQ91GG3", "status": "released", "@type": ["ExperimentDamid", "Experiment", "Item"], "@id": "/experiments-damid/4DNEXOQ91GG3/", "uuid": "afbc3254-14f1-4e63-996f-b8c1e7bdee76", "files": [{"file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFI8RHK5LP/", "upload_key": "a10ade01-8f5b-4a96-829d-84f3973626da/4DNFI8RHK5LP.fastq.gz", "@type": ["FileFastq", "File", "Item"], "file_classification": "raw file", "md5sum": "d51f6f227c336dc1c32e916d01f892c1", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/a10ade01-8f5b-4a96-829d-84f3973626da/4DNFI8RHK5LP.fastq.gz", "accession": "4DNFI8RHK5LP", "uuid": "a10ade01-8f5b-4a96-829d-84f3973626da", "file_size": 257453567, "file_type": "reads", "status": "released", "href": "/files-fastq/4DNFI8RHK5LP/@@download/4DNFI8RHK5LP.fastq.gz", "display_title": "4DNFI8RHK5LP.fastq.gz", "lab": {"@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "status": "current", "display_title": "Bas van Steensel, NKI", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "file_format": {"file_format": "fastq", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "raw file", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "quality_metric": {"uuid": "14920876-50d0-4fc3-9a03-b69028be0bc7", "Total Sequences": 5407800, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "65", "@id": "/quality-metrics-fastqc/14920876-50d0-4fc3-9a03-b69028be0bc7/", "display_title": "QualityMetricFastqc from 2020-07-02", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI8RHK5LP/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFISJO8KT6/", "upload_key": "0103f59a-b4ef-4ef5-9d8f-48233f91b517/4DNFISJO8KT6.fastq.gz", "@type": ["FileFastq", "File", "Item"], "file_classification": "raw file", "md5sum": "9776b59d05109bd27555eadf49e2ba3d", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/0103f59a-b4ef-4ef5-9d8f-48233f91b517/4DNFISJO8KT6.fastq.gz", "accession": "4DNFISJO8KT6", "uuid": "0103f59a-b4ef-4ef5-9d8f-48233f91b517", "file_size": 1946240574, "file_type": "reads", "status": "released", "href": "/files-fastq/4DNFISJO8KT6/@@download/4DNFISJO8KT6.fastq.gz", "display_title": "4DNFISJO8KT6.fastq.gz", "lab": {"@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "status": "current", "display_title": "Bas van Steensel, NKI", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "file_format": {"file_format": "fastq", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "raw file", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "quality_metric": {"uuid": "58c4ed7f-9aff-43b3-8865-b12e47f46dfc", "Total Sequences": 40450604, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "65", "@id": "/quality-metrics-fastqc/58c4ed7f-9aff-43b3-8865-b12e47f46dfc/", "display_title": "QualityMetricFastqc from 2020-07-02", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFISJO8KT6/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "processed_files": [{"status": "released", "upload_key": "ee8974a8-6a18-4132-818e-e856600ec123/4DNFIFBR7Z3I.bam", "file_size": 190482756, "href": "/files-processed/4DNFIFBR7Z3I/@@download/4DNFIFBR7Z3I.bam", "display_title": "4DNFIFBR7Z3I.bam", "file_type": "alignments", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ee8974a8-6a18-4132-818e-e856600ec123/4DNFIFBR7Z3I.bam", "uuid": "ee8974a8-6a18-4132-818e-e856600ec123", "file_classification": "processed file", "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."], "accession": "4DNFIFBR7Z3I", "@id": "/files-processed/4DNFIFBR7Z3I/", "file_format": {"status": "released", "display_title": "bam", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "alignments (bam)", "md5sum": "3ceb0f412a67465118bafdb8cf7b38cf", "lab": {"@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "status": "current", "display_title": "Bas van Steensel, NKI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "last_modified": {"date_modified": "2024-02-22T17:46:28.115157+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"status": "released", "upload_key": "247e4ff9-7d87-481c-af0f-00f5ad211194/4DNFIQJLAHSI.bam", "file_size": 1163619023, "href": "/files-processed/4DNFIQJLAHSI/@@download/4DNFIQJLAHSI.bam", "display_title": "4DNFIQJLAHSI.bam", "file_type": "alignments", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/247e4ff9-7d87-481c-af0f-00f5ad211194/4DNFIQJLAHSI.bam", "uuid": "247e4ff9-7d87-481c-af0f-00f5ad211194", "file_classification": "processed file", "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."], "accession": "4DNFIQJLAHSI", "@id": "/files-processed/4DNFIQJLAHSI/", "file_format": {"status": "released", "display_title": "bam", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "alignments (bam)", "md5sum": "1371332b31b576092d8d5623762e563c", "lab": {"@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "status": "current", "display_title": "Bas van Steensel, NKI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "last_modified": {"date_modified": "2024-02-22T17:46:23.995184+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"status": "released", "upload_key": "d3ea4d3d-75e8-44db-9604-242f6b94ff52/4DNFI75WW3X2.bw", "file_size": 947567, "href": "/files-processed/4DNFI75WW3X2/@@download/4DNFI75WW3X2.bw", "display_title": "4DNFI75WW3X2.bw", "file_type": "normalized counts", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/d3ea4d3d-75e8-44db-9604-242f6b94ff52/4DNFI75WW3X2.bw", "uuid": "d3ea4d3d-75e8-44db-9604-242f6b94ff52", "file_classification": "processed file", "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."], "accession": "4DNFI75WW3X2", "higlass_uid": "8b1779b3-0a78-4332-9e65-8133ce701faa", "@id": "/files-processed/4DNFI75WW3X2/", "file_format": {"status": "released", "display_title": "bw", "@type": ["FileFormat", "Item"], "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "normalized counts (bw)", "md5sum": "fbb4a48cb97640f852582d249a184de5", "lab": {"@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "status": "current", "display_title": "Bas van Steensel, NKI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"uuid": "c2221f6f-6022-45f1-9591-d7f00dac6498", "@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/c2221f6f-6022-45f1-9591-d7f00dac6498/", "status": "released", "display_title": "4DNFI75WW3X2 - normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "last_modified": {"date_modified": "2024-02-22T17:37:05.800113+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"status": "released", "upload_key": "23757a6b-734a-407a-a344-3e418a082bf6/4DNFI9FNWY12.bed.gz", "file_size": 3028, "href": "/files-processed/4DNFI9FNWY12/@@download/4DNFI9FNWY12.bed.gz", "display_title": "4DNFI9FNWY12.bed.gz", "file_type": "NADs", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/23757a6b-734a-407a-a344-3e418a082bf6/4DNFI9FNWY12.bed.gz", "uuid": "23757a6b-734a-407a-a344-3e418a082bf6", "file_classification": "processed file", "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."], "accession": "4DNFI9FNWY12", "higlass_uid": "RerjPiavQq2Ra_mLUS_c5w", "@id": "/files-processed/4DNFI9FNWY12/", "file_format": {"status": "released", "display_title": "bed", "@type": ["FileFormat", "Item"], "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "@id": "/file-formats/bed/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "NADs (bed)", "md5sum": "d3b0dc22f8912dd5f8f969682c3f624b", "lab": {"@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "status": "current", "display_title": "Bas van Steensel, NKI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "extra_files": [{"md5sum": "c49d1525714da9762ef6758f2c4f2bd1", "use_for": "visualization", "href": "/files-processed/4DNFI9FNWY12/@@download/4DNFI9FNWY12.beddb", "file_format": {"file_format": "beddb", "display_title": "beddb", "@type": ["FileFormat", "Item"], "status": "released", "uuid": "76dc8c06-67d8-487b-8fc8-d841752a0b60", "@id": "/file-formats/beddb/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"uuid": "bfbb78f9-6fa7-4f5b-b57f-77bd203a4afd", "@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/bfbb78f9-6fa7-4f5b-b57f-77bd203a4afd/", "status": "released", "display_title": "4DNFI9FNWY12 - NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "last_modified": {"date_modified": "2024-02-22T17:29:31.020023+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}], "biosample": {"treatments_summary": "None", "@type": ["Biosample", "Item"], "biosample_category": ["Tier 2"], "modifications_summary": "None", "biosource_summary": "HCT116 (Tier 2)", "biosample_type": "immortalized cells", "display_title": "4DNBSA3GV3KY", "status": "released", "accession": "4DNBSA3GV3KY", "@id": "/biosamples/4DNBSA3GV3KY/", "uuid": "77e3b4c4-6f8c-4977-a7e2-e17673c44818", "biosource": [{"@type": ["Biosource", "Item"], "@id": "/biosources/4DNSRMYUIVGD/", "display_title": "HCT116 (Tier 2) - 4DNSRMYUIVGD", "biosource_type": "immortalized cell line", "accession": "4DNSRMYUIVGD", "cell_line_tier": "Tier 2", "status": "released", "uuid": "393880ea-f928-406d-a4bf-78435b8975ef", "cell_line": {"status": "released", "preferred_name": "HCT116", "term_name": "HCT116", "synonyms": ["HCT-116 cell", "HCT116 cell"], "@type": ["OntologyTerm", "Item"], "term_id": "EFO:0002824", "@id": "/ontology-terms/EFO:0002824/", "display_title": "HCT116", "uuid": "49d090b2-5326-40ce-9c19-7a214c682272", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"term_name": "colon", "synonyms": ["large bowel", "posterior intestine"], "status": "released", "preferred_name": "colon", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0001155/", "display_title": "colon", "uuid": "3e39f551-bc0b-4bee-b932-29d71956fb94", "term_id": "UBERON:0001155", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000059/", "status": "released", "display_title": "large intestine", "uuid": "111174bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0001007/", "status": "released", "display_title": "digestive system", "uuid": "111129bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"scientific_name": "Homo sapiens", "@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "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": {"commendation": "Gold Biosample", "display_title": "Gold Biosample", "@id": "/badges/gold-biosample/", "status": "released", "@type": ["Badge", "Item"], "badge_classification": "Commendation", "title": "Gold Biosample", "description": "Gold biosample", "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "cell_culture_details": [{"status": "released", "@id": "/biosample-cell-cultures/643810e1-9fc1-490d-8db6-108517c9b38b/", "uuid": "643810e1-9fc1-490d-8db6-108517c9b38b", "in_vitro_differentiated": "No", "@type": ["BiosampleCellCulture", "Item"], "display_title": "BiosampleCellCulture from 2020-07-01", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"tissue_source": "colon", "organ_system": ["large intestine", "digestive system"]}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "other_processed_files": [{"type": "supplementary", "description": "The files associated with the gatc bin size processing of data for DamID-seq on HCT116 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam", "title": "gatc binned files", "files": [{"md5sum": "47036c0ae5e0399b475e3783058a35b4", "href": "/files-processed/4DNFIEYYP1B4/@@download/4DNFIEYYP1B4.txt.gz", "display_title": "4DNFIEYYP1B4.txt.gz", "status": "released", "accession": "4DNFIEYYP1B4", "uuid": "9036a139-a533-4c7c-aa32-978fefc028a3", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/9036a139-a533-4c7c-aa32-978fefc028a3/4DNFIEYYP1B4.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIEYYP1B4/", "file_size": 50999296, "file_type_detailed": "counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:47:19.509452+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "6260ed73ffef311800be668b15224c43", "href": "/files-processed/4DNFIB76LROJ/@@download/4DNFIB76LROJ.txt.gz", "display_title": "4DNFIB76LROJ.txt.gz", "status": "released", "accession": "4DNFIB76LROJ", "uuid": "c2732142-9938-47fa-b32e-08a6ce66b21d", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c2732142-9938-47fa-b32e-08a6ce66b21d/4DNFIB76LROJ.txt.gz", "genome_assembly": "GRCh38", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIB76LROJ/", "file_size": 60928251, "file_type_detailed": "normalized counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:40:54.762728+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "16a66e7ef019bda1fc17101ba6bbdc5e", "href": "/files-processed/4DNFIZSIBBUU/@@download/4DNFIZSIBBUU.bw", "display_title": "4DNFIZSIBBUU.bw", "status": "released", "accession": "4DNFIZSIBBUU", "higlass_uid": "e9f3e955-44ac-4b72-b329-d90666bfb796", "uuid": "e0216c23-6f49-4b4e-906a-6813e166dc74", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e0216c23-6f49-4b4e-906a-6813e166dc74/4DNFIZSIBBUU.bw", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIZSIBBUU/", "file_size": 41107874, "file_type_detailed": "counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFIZSIBBUU", "@id": "/higlass-view-configs/4a8e90a0-71d3-41fe-b7f7-d2e8429ef6d5/", "uuid": "4a8e90a0-71d3-41fe-b7f7-d2e8429ef6d5", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:41:07.401120+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "fd58734008d35ef760dd00ef9b317b8b", "href": "/files-processed/4DNFIUXQ6I3L/@@download/4DNFIUXQ6I3L.bw", "display_title": "4DNFIUXQ6I3L.bw", "status": "released", "accession": "4DNFIUXQ6I3L", "higlass_uid": "241ce99a-ef74-457a-be96-a1a33fb29a91", "uuid": "c837ce7b-77bb-48a8-8a3b-8dff23ffcf1d", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c837ce7b-77bb-48a8-8a3b-8dff23ffcf1d/4DNFIUXQ6I3L.bw", "genome_assembly": "GRCh38", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIUXQ6I3L/", "file_size": 26290125, "file_type_detailed": "normalized counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFIUXQ6I3L", "@id": "/higlass-view-configs/41a68138-e1ac-4085-8106-56ec4ba0cb0d/", "uuid": "41a68138-e1ac-4085-8106-56ec4ba0cb0d", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:36:46.692786+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, {"type": "supplementary", "description": "The files associated with the 25kb bin size processing of data for DamID-seq on HCT116 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam", "title": "25kb binned files", "files": [{"md5sum": "c9f67e7d6a6fd86997f157163bad3f7e", "href": "/files-processed/4DNFIMMXSM99/@@download/4DNFIMMXSM99.txt.gz", "display_title": "4DNFIMMXSM99.txt.gz", "status": "released", "accession": "4DNFIMMXSM99", "uuid": "8969d60f-a1a9-46b1-8159-fb0f3e451044", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8969d60f-a1a9-46b1-8159-fb0f3e451044/4DNFIMMXSM99.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIMMXSM99/", "file_size": 741122, "file_type_detailed": "counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:42:13.528441+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "fd0bb709b42c89ee0654d1aa20234d8b", "href": "/files-processed/4DNFIBIVMMVB/@@download/4DNFIBIVMMVB.txt.gz", "display_title": "4DNFIBIVMMVB.txt.gz", "status": "released", "accession": "4DNFIBIVMMVB", "uuid": "e56d5ccd-98fe-4d06-b3fa-9136b87d6640", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e56d5ccd-98fe-4d06-b3fa-9136b87d6640/4DNFIBIVMMVB.txt.gz", "genome_assembly": "GRCh38", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIBIVMMVB/", "file_size": 1640189, "file_type_detailed": "normalized counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:42:19.896141+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "e7350fd636b99ce16185ece056fb3db2", "href": "/files-processed/4DNFI73XSF9D/@@download/4DNFI73XSF9D.bw", "display_title": "4DNFI73XSF9D.bw", "status": "released", "accession": "4DNFI73XSF9D", "higlass_uid": "61c00f63-71a8-4fd7-b365-12234a0de333", "uuid": "90cd2fa1-e498-44b3-8919-f6015a5ecac3", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/90cd2fa1-e498-44b3-8919-f6015a5ecac3/4DNFI73XSF9D.bw", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFI73XSF9D/", "file_size": 1069923, "file_type_detailed": "counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFI73XSF9D", "@id": "/higlass-view-configs/2db5a9f9-8755-48ba-adfb-7eefcbf8d97e/", "uuid": "2db5a9f9-8755-48ba-adfb-7eefcbf8d97e", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:42:03.408192+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "4177140b1173e5262f95de8017e752cd", "href": "/files-processed/4DNFIBAQL8C3/@@download/4DNFIBAQL8C3.bw", "display_title": "4DNFIBAQL8C3.bw", "status": "released", "accession": "4DNFIBAQL8C3", "higlass_uid": "f68ab5f8-c460-4eb3-838c-ffb7abe00833", "uuid": "ac756878-4b35-40c5-bfbe-9a8130f6541f", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ac756878-4b35-40c5-bfbe-9a8130f6541f/4DNFIBAQL8C3.bw", "genome_assembly": "GRCh38", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIBAQL8C3/", "file_size": 1827111, "file_type_detailed": "normalized counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFIBAQL8C3", "@id": "/higlass-view-configs/0719d5be-b865-40e6-8a3d-64a948eff015/", "uuid": "0719d5be-b865-40e6-8a3d-64a948eff015", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:35:29.325949+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "0375ad988ed9fac179981eac44a7a732", "href": "/files-processed/4DNFIWTEERD1/@@download/4DNFIWTEERD1.txt.gz", "display_title": "4DNFIWTEERD1.txt.gz", "status": "released", "accession": "4DNFIWTEERD1", "uuid": "3d802ba1-077f-4ad7-a638-2825fdc54d81", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/3d802ba1-077f-4ad7-a638-2825fdc54d81/4DNFIWTEERD1.txt.gz", "genome_assembly": "GRCh38", "file_type": "NADs", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIWTEERD1/", "file_size": 516325, "file_type_detailed": "NADs (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:37:33.712893+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "b7af293149385893fe4177d436077b2d", "href": "/files-processed/4DNFITFC2SPD/@@download/4DNFITFC2SPD.bed.gz", "display_title": "4DNFITFC2SPD.bed.gz", "status": "released", "accession": "4DNFITFC2SPD", "higlass_uid": "SoZtxZ5KShCN3isrzsJpQQ", "uuid": "74ec05e8-a7e4-4fa9-9638-5b3a402ece66", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/74ec05e8-a7e4-4fa9-9638-5b3a402ece66/4DNFITFC2SPD.bed.gz", "genome_assembly": "GRCh38", "file_type": "NADs", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFITFC2SPD/", "file_size": 4425, "file_type_detailed": "NADs (bed)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFITFC2SPD - NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "@id": "/higlass-view-configs/af04abb4-8e2a-48df-8ead-c4a61edb7938/", "uuid": "af04abb4-8e2a-48df-8ead-c4a61edb7938", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bed", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "file_format": "bed", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bed/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:36:19.878377+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, {"type": "supplementary", "description": "Additional files associated with the 50kb bin size processing of data for DamID-seq on HCT116 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam", "title": "Additional 50kb binned files", "files": [{"md5sum": "39772aeab6f0e67074dd8668d81106d6", "href": "/files-processed/4DNFIAJVT7K3/@@download/4DNFIAJVT7K3.txt.gz", "display_title": "4DNFIAJVT7K3.txt.gz", "status": "released", "accession": "4DNFIAJVT7K3", "uuid": "d1f4246b-d481-4e18-a2a7-d8d9b2bd1f07", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/d1f4246b-d481-4e18-a2a7-d8d9b2bd1f07/4DNFIAJVT7K3.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIAJVT7K3/", "file_size": 372394, "file_type_detailed": "counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:40:40.166268+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "922689b3d3438f18aead15b405eaf4c8", "href": "/files-processed/4DNFI2TEHTST/@@download/4DNFI2TEHTST.txt.gz", "display_title": "4DNFI2TEHTST.txt.gz", "status": "released", "accession": "4DNFI2TEHTST", "uuid": "70543a4c-806f-425a-bdb5-08f68cc1ab83", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/70543a4c-806f-425a-bdb5-08f68cc1ab83/4DNFI2TEHTST.txt.gz", "genome_assembly": "GRCh38", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFI2TEHTST/", "file_size": 819418, "file_type_detailed": "normalized counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:41:15.220970+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "d5bd2cb9668ef1421cde623acfcbb839", "href": "/files-processed/4DNFIRNA2NL6/@@download/4DNFIRNA2NL6.bw", "display_title": "4DNFIRNA2NL6.bw", "status": "released", "accession": "4DNFIRNA2NL6", "higlass_uid": "58a97b8e-57ee-4d41-b42e-13eb48b61944", "uuid": "468dc810-edb7-412b-a087-d3ffb97a58c4", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/468dc810-edb7-412b-a087-d3ffb97a58c4/4DNFIRNA2NL6.bw", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIRNA2NL6/", "file_size": 583996, "file_type_detailed": "counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFIRNA2NL6", "@id": "/higlass-view-configs/bb080229-04ea-4f2c-b228-d88d5ed597b5/", "uuid": "bb080229-04ea-4f2c-b228-d88d5ed597b5", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:40:28.590153+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "cefdc9db89d714a4a44ce910e99c4242", "href": "/files-processed/4DNFICQQKZU1/@@download/4DNFICQQKZU1.txt.gz", "display_title": "4DNFICQQKZU1.txt.gz", "status": "released", "accession": "4DNFICQQKZU1", "uuid": "c0984815-b4be-4eeb-87f9-84309e3c8b85", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c0984815-b4be-4eeb-87f9-84309e3c8b85/4DNFICQQKZU1.txt.gz", "genome_assembly": "GRCh38", "file_type": "NADs", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFICQQKZU1/", "file_size": 250693, "file_type_detailed": "NADs (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:36:26.842908+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, {"type": "supplementary", "description": "The files associated with the 100kb bin size processing of data for DamID-seq on HCT116 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam", "title": "100kb binned files", "files": [{"md5sum": "65248cad0407fa07639edbbcc03ef3e3", "href": "/files-processed/4DNFIFO8WKCJ/@@download/4DNFIFO8WKCJ.txt.gz", "display_title": "4DNFIFO8WKCJ.txt.gz", "status": "released", "accession": "4DNFIFO8WKCJ", "uuid": "eddb5dc6-4826-4a91-bf74-7903c214f6db", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/eddb5dc6-4826-4a91-bf74-7903c214f6db/4DNFIFO8WKCJ.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIFO8WKCJ/", "file_size": 185483, "file_type_detailed": "counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:42:05.629860+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "dbce3b4417c897ee95f579a750987c96", "href": "/files-processed/4DNFIVBO7B52/@@download/4DNFIVBO7B52.txt.gz", "display_title": "4DNFIVBO7B52.txt.gz", "status": "released", "accession": "4DNFIVBO7B52", "uuid": "35281376-b2c1-4a96-96c7-8c7260c1dec5", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/35281376-b2c1-4a96-96c7-8c7260c1dec5/4DNFIVBO7B52.txt.gz", "genome_assembly": "GRCh38", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIVBO7B52/", "file_size": 411848, "file_type_detailed": "normalized counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:40:09.933980+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "741fdfcb2149cff294c54bedc24ea705", "href": "/files-processed/4DNFIR35OEPK/@@download/4DNFIR35OEPK.bw", "display_title": "4DNFIR35OEPK.bw", "status": "released", "accession": "4DNFIR35OEPK", "higlass_uid": "40400936-8dce-4dd8-9a58-c6e0896e96b9", "uuid": "47ddc988-230c-455b-8d84-a57dd285f79f", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/47ddc988-230c-455b-8d84-a57dd285f79f/4DNFIR35OEPK.bw", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIR35OEPK/", "file_size": 322299, "file_type_detailed": "counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFIR35OEPK", "@id": "/higlass-view-configs/4db441ed-db47-47e2-8cee-086b4ca1afa4/", "uuid": "4db441ed-db47-47e2-8cee-086b4ca1afa4", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:37:56.263817+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "56f3a482bda85c751ee083a5ec0e3521", "href": "/files-processed/4DNFI44ZMJSR/@@download/4DNFI44ZMJSR.bw", "display_title": "4DNFI44ZMJSR.bw", "status": "released", "accession": "4DNFI44ZMJSR", "higlass_uid": "666368f2-e229-47f9-b79e-d65fa6d86aa9", "uuid": "5ca2a28b-37b7-4800-a2be-23b24fc4799d", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/5ca2a28b-37b7-4800-a2be-23b24fc4799d/4DNFI44ZMJSR.bw", "genome_assembly": "GRCh38", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFI44ZMJSR/", "file_size": 495281, "file_type_detailed": "normalized counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFI44ZMJSR - normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "@id": "/higlass-view-configs/d165c97e-118b-424b-9bd0-741e8cae1a21/", "uuid": "d165c97e-118b-424b-9bd0-741e8cae1a21", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:35:58.471497+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "4daa547ffd6693230bd20978380aa00c", "href": "/files-processed/4DNFIBINMC7O/@@download/4DNFIBINMC7O.txt.gz", "display_title": "4DNFIBINMC7O.txt.gz", "status": "released", "accession": "4DNFIBINMC7O", "uuid": "b7ea299d-ac6f-4caa-8fce-6482bd91b289", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/b7ea299d-ac6f-4caa-8fce-6482bd91b289/4DNFIBINMC7O.txt.gz", "genome_assembly": "GRCh38", "file_type": "NADs", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIBINMC7O/", "file_size": 127685, "file_type_detailed": "NADs (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:35:21.710877+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "6e1096a28070426db3881f723457c3df", "href": "/files-processed/4DNFI65LBV4I/@@download/4DNFI65LBV4I.bed.gz", "display_title": "4DNFI65LBV4I.bed.gz", "status": "released", "accession": "4DNFI65LBV4I", "higlass_uid": "ApdWAx4rTPCI05ba0h-XDg", "uuid": "a480cb8b-6a0e-49e5-9dab-8d9b247c4ce5", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a480cb8b-6a0e-49e5-9dab-8d9b247c4ce5/4DNFI65LBV4I.bed.gz", "genome_assembly": "GRCh38", "file_type": "NADs", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFI65LBV4I/", "file_size": 2080, "file_type_detailed": "NADs (bed)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFI65LBV4I - NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "@id": "/higlass-view-configs/ffd33dcd-0715-46f4-97f0-ec8fcc007393/", "uuid": "ffd33dcd-0715-46f4-97f0-ec8fcc007393", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bed", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "file_format": "bed", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bed/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:50:09.810498+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, {"type": "supplementary", "description": "Non-bin specific files for DamID-seq on HCT116 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam", "title": "Other files - non-binned", "files": [{"md5sum": "ff7cc653553f0b1fbcf03a2a9099b605", "href": "/files-processed/4DNFIKW1D9JV/@@download/4DNFIKW1D9JV.html", "display_title": "4DNFIKW1D9JV.html", "status": "released", "accession": "4DNFIKW1D9JV", "uuid": "ad23b9fe-3148-4ec0-a7d2-d28eb778a419", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ad23b9fe-3148-4ec0-a7d2-d28eb778a419/4DNFIKW1D9JV.html", "genome_assembly": "GRCh38", "file_type": "other", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIKW1D9JV/", "file_size": 2624699, "file_type_detailed": "other (html)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "html", "uuid": "8bd6fe41-6af8-43c9-b24a-d74241898f09", "file_format": "html", "@type": ["FileFormat", "Item"], "@id": "/file-formats/html/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:32:04.173800+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}], "experiment_type": {"assay_subclassification": "Proximity to Cellular Component", "assay_subclass_short": "Proximity-seq", "other_tags": ["1D"], "@type": ["ExperimentType", "Item"], "display_title": "DamID-seq", "uuid": "b777a1da-8dc8-4473-9b8d-4f7716fb0a4a", "title": "DamID-seq", "@id": "/experiment-types/damid-seq/", "experiment_category": "Sequencing", "status": "released", "assay_classification": "Linear DNA Enrichment", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "last_modified": {"date_modified": "2023-11-03T14:45:05.998203+00:00"}, "experiment_categorizer": {"field": "Target", "value": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "combined": "Target: Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "DamID-seq with DAM-Nucleolus on HCT116 (Tier 2) - 4DNEXOFUK2A4", "accession": "4DNEXOFUK2A4", "status": "released", "@type": ["ExperimentDamid", "Experiment", "Item"], "@id": "/experiments-damid/4DNEXOFUK2A4/", "uuid": "07f2d9c5-2a34-4a8c-be9f-6ca7ec2bdf1c", "files": [{"file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFIB7EFCA6/", "upload_key": "d5c7abc5-8443-4234-8ece-bddd0541ba84/4DNFIB7EFCA6.fastq.gz", "@type": ["FileFastq", "File", "Item"], "file_classification": "raw file", "md5sum": "ebd956e9429c6d12a1b87cbad3f673aa", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/d5c7abc5-8443-4234-8ece-bddd0541ba84/4DNFIB7EFCA6.fastq.gz", "accession": "4DNFIB7EFCA6", "uuid": "d5c7abc5-8443-4234-8ece-bddd0541ba84", "file_size": 2262638370, "file_type": "reads", "status": "released", "href": "/files-fastq/4DNFIB7EFCA6/@@download/4DNFIB7EFCA6.fastq.gz", "display_title": "4DNFIB7EFCA6.fastq.gz", "lab": {"@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "status": "current", "display_title": "Bas van Steensel, NKI", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "file_format": {"file_format": "fastq", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "raw file", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "dataset": "DamID-seq on HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "quality_metric": {"uuid": "c87acbbb-852a-44f3-9dfc-5d76eab42c3c", "Total Sequences": 48012314, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "65", "@id": "/quality-metrics-fastqc/c87acbbb-852a-44f3-9dfc-5d76eab42c3c/", "display_title": "QualityMetricFastqc from 2020-07-02", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIB7EFCA6/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "processed_files": [{"status": "released", "upload_key": "a5ee8ef3-9398-4948-8799-e8de9bdc5873/4DNFI554WH37.bam", "file_size": 1263157228, "href": "/files-processed/4DNFI554WH37/@@download/4DNFI554WH37.bam", "display_title": "4DNFI554WH37.bam", "file_type": "alignments", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a5ee8ef3-9398-4948-8799-e8de9bdc5873/4DNFI554WH37.bam", "uuid": "a5ee8ef3-9398-4948-8799-e8de9bdc5873", "file_classification": "processed file", "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."], "accession": "4DNFI554WH37", "@id": "/files-processed/4DNFI554WH37/", "file_format": {"status": "released", "display_title": "bam", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "alignments (bam)", "md5sum": "d465d6358a2387ffcccb19497a29cc3f", "lab": {"@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "status": "current", "display_title": "Bas van Steensel, NKI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "last_modified": {"date_modified": "2024-02-22T17:50:49.260377+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"status": "released", "upload_key": "e2e45343-755d-45e8-a5a7-098b1a33bc31/4DNFI1WJGLKY.bw", "file_size": 947178, "href": "/files-processed/4DNFI1WJGLKY/@@download/4DNFI1WJGLKY.bw", "display_title": "4DNFI1WJGLKY.bw", "file_type": "normalized counts", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e2e45343-755d-45e8-a5a7-098b1a33bc31/4DNFI1WJGLKY.bw", "uuid": "e2e45343-755d-45e8-a5a7-098b1a33bc31", "file_classification": "processed file", "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."], "accession": "4DNFI1WJGLKY", "higlass_uid": "c0b3181d-5074-4fa2-9b18-336911dc522d", "@id": "/files-processed/4DNFI1WJGLKY/", "file_format": {"status": "released", "display_title": "bw", "@type": ["FileFormat", "Item"], "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "normalized counts (bw)", "md5sum": "cfed65182eb4173bd62ab6fbe68b5efe", "lab": {"@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "status": "current", "display_title": "Bas van Steensel, NKI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"uuid": "5b5bb938-a0e6-4575-97d3-0363ac003dc9", "@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/5b5bb938-a0e6-4575-97d3-0363ac003dc9/", "status": "released", "display_title": "4DNFI1WJGLKY - normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "last_modified": {"date_modified": "2024-02-22T17:37:03.267719+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"status": "released", "upload_key": "78d46930-36b9-466d-a0ca-b7f47e0ad9e6/4DNFI31UMKYF.bed.gz", "file_size": 4080, "href": "/files-processed/4DNFI31UMKYF/@@download/4DNFI31UMKYF.bed.gz", "display_title": "4DNFI31UMKYF.bed.gz", "file_type": "NADs", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/78d46930-36b9-466d-a0ca-b7f47e0ad9e6/4DNFI31UMKYF.bed.gz", "uuid": "78d46930-36b9-466d-a0ca-b7f47e0ad9e6", "file_classification": "processed file", "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."], "accession": "4DNFI31UMKYF", "higlass_uid": "OByAS4jqQ7ixuiSGAkOfXw", "@id": "/files-processed/4DNFI31UMKYF/", "file_format": {"status": "released", "display_title": "bed", "@type": ["FileFormat", "Item"], "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "@id": "/file-formats/bed/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "NADs (bed)", "md5sum": "78c09e8f2c73a5320e618803880cc020", "lab": {"@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "status": "current", "display_title": "Bas van Steensel, NKI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "extra_files": [{"md5sum": "4b9b15ebe3fce8881b0abc317ac59b22", "use_for": "visualization", "href": "/files-processed/4DNFI31UMKYF/@@download/4DNFI31UMKYF.beddb", "file_format": {"file_format": "beddb", "display_title": "beddb", "@type": ["FileFormat", "Item"], "status": "released", "uuid": "76dc8c06-67d8-487b-8fc8-d841752a0b60", "@id": "/file-formats/beddb/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"uuid": "a1810b4d-b27a-4d9a-b0b9-f7226d95785c", "@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/a1810b4d-b27a-4d9a-b0b9-f7226d95785c/", "status": "released", "display_title": "4DNFI31UMKYF - NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "last_modified": {"date_modified": "2024-02-22T17:29:26.724089+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}], "biosample": {"treatments_summary": "None", "@type": ["Biosample", "Item"], "biosample_category": ["Tier 2"], "modifications_summary": "None", "biosource_summary": "HCT116 (Tier 2)", "biosample_type": "immortalized cells", "display_title": "4DNBS54371JN", "status": "released", "accession": "4DNBS54371JN", "@id": "/biosamples/4DNBS54371JN/", "uuid": "260af42d-fd85-45e8-95ce-e921157b9e0c", "biosource": [{"@type": ["Biosource", "Item"], "@id": "/biosources/4DNSRMYUIVGD/", "display_title": "HCT116 (Tier 2) - 4DNSRMYUIVGD", "biosource_type": "immortalized cell line", "accession": "4DNSRMYUIVGD", "cell_line_tier": "Tier 2", "status": "released", "uuid": "393880ea-f928-406d-a4bf-78435b8975ef", "cell_line": {"status": "released", "preferred_name": "HCT116", "term_name": "HCT116", "synonyms": ["HCT-116 cell", "HCT116 cell"], "@type": ["OntologyTerm", "Item"], "term_id": "EFO:0002824", "@id": "/ontology-terms/EFO:0002824/", "display_title": "HCT116", "uuid": "49d090b2-5326-40ce-9c19-7a214c682272", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"term_name": "colon", "synonyms": ["large bowel", "posterior intestine"], "status": "released", "preferred_name": "colon", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0001155/", "display_title": "colon", "uuid": "3e39f551-bc0b-4bee-b932-29d71956fb94", "term_id": "UBERON:0001155", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000059/", "status": "released", "display_title": "large intestine", "uuid": "111174bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0001007/", "status": "released", "display_title": "digestive system", "uuid": "111129bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"scientific_name": "Homo sapiens", "@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "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": {"commendation": "Gold Biosample", "display_title": "Gold Biosample", "@id": "/badges/gold-biosample/", "status": "released", "@type": ["Badge", "Item"], "badge_classification": "Commendation", "title": "Gold Biosample", "description": "Gold biosample", "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "cell_culture_details": [{"status": "released", "@id": "/biosample-cell-cultures/6e8f546e-6be8-4e63-8aeb-c52b62b9c814/", "uuid": "6e8f546e-6be8-4e63-8aeb-c52b62b9c814", "in_vitro_differentiated": "No", "@type": ["BiosampleCellCulture", "Item"], "display_title": "BiosampleCellCulture from 2020-07-01", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"tissue_source": "colon", "organ_system": ["large intestine", "digestive system"]}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "other_processed_files": [{"type": "supplementary", "description": "The files associated with the gatc bin size processing of data for DamID-seq on HCT116 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam", "title": "gatc binned files", "files": [{"md5sum": "de8d15874dbf8cfc45b9e0ed507679a1", "href": "/files-processed/4DNFI54ID87M/@@download/4DNFI54ID87M.txt.gz", "display_title": "4DNFI54ID87M.txt.gz", "status": "released", "accession": "4DNFI54ID87M", "uuid": "e4311b17-34cb-41e9-a270-3317f5e0a28b", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e4311b17-34cb-41e9-a270-3317f5e0a28b/4DNFI54ID87M.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFI54ID87M/", "file_size": 51630733, "file_type_detailed": "counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:47:12.995472+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "c9cc532cf3368806588df21c5a04fd1b", "href": "/files-processed/4DNFIGPZKLLL/@@download/4DNFIGPZKLLL.txt.gz", "display_title": "4DNFIGPZKLLL.txt.gz", "status": "released", "accession": "4DNFIGPZKLLL", "uuid": "296b6d45-5a48-4cba-96fd-b630279d5203", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/296b6d45-5a48-4cba-96fd-b630279d5203/4DNFIGPZKLLL.txt.gz", "genome_assembly": "GRCh38", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIGPZKLLL/", "file_size": 60088169, "file_type_detailed": "normalized counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:40:51.691737+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "e26a7f84a8ba4c8774d8ad58bb8ea17a", "href": "/files-processed/4DNFIHP58N8E/@@download/4DNFIHP58N8E.bw", "display_title": "4DNFIHP58N8E.bw", "status": "released", "accession": "4DNFIHP58N8E", "higlass_uid": "549aa9f5-183a-47d1-96ea-cdbc64e87fc0", "uuid": "fd427801-7b5a-4d73-b215-b047090b93fe", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/fd427801-7b5a-4d73-b215-b047090b93fe/4DNFIHP58N8E.bw", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIHP58N8E/", "file_size": 41374342, "file_type_detailed": "counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFIHP58N8E", "@id": "/higlass-view-configs/78d2fe11-4644-44b9-81f0-f20721fd50f8/", "uuid": "78d2fe11-4644-44b9-81f0-f20721fd50f8", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:41:01.325749+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "7228c8b56e32f977b54d7abe431c60df", "href": "/files-processed/4DNFIOZPJSIH/@@download/4DNFIOZPJSIH.bw", "display_title": "4DNFIOZPJSIH.bw", "status": "released", "accession": "4DNFIOZPJSIH", "higlass_uid": "b28073b0-2168-4032-835c-6757bdf6f2ce", "uuid": "cd42f82d-600e-478d-8677-2d01a9bfb57d", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/cd42f82d-600e-478d-8677-2d01a9bfb57d/4DNFIOZPJSIH.bw", "genome_assembly": "GRCh38", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIOZPJSIH/", "file_size": 26546090, "file_type_detailed": "normalized counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFIOZPJSIH", "@id": "/higlass-view-configs/ff0bd3a0-ffa5-4455-85b5-70971ed17d06/", "uuid": "ff0bd3a0-ffa5-4455-85b5-70971ed17d06", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:36:43.212381+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, {"type": "supplementary", "description": "The files associated with the 25kb bin size processing of data for DamID-seq on HCT116 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam", "title": "25kb binned files", "files": [{"md5sum": "f090a888bf662c0389c0428ddec1e70d", "href": "/files-processed/4DNFINAZX3C1/@@download/4DNFINAZX3C1.txt.gz", "display_title": "4DNFINAZX3C1.txt.gz", "status": "released", "accession": "4DNFINAZX3C1", "uuid": "c916e464-004f-48a2-8bb0-5edc93417e05", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c916e464-004f-48a2-8bb0-5edc93417e05/4DNFINAZX3C1.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFINAZX3C1/", "file_size": 739679, "file_type_detailed": "counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:42:09.224907+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "f52fbf407281b9a1835951d2e357241e", "href": "/files-processed/4DNFIMEY2C17/@@download/4DNFIMEY2C17.txt.gz", "display_title": "4DNFIMEY2C17.txt.gz", "status": "released", "accession": "4DNFIMEY2C17", "uuid": "98796916-a09f-4c7a-bc24-1dd602d8f17e", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/98796916-a09f-4c7a-bc24-1dd602d8f17e/4DNFIMEY2C17.txt.gz", "genome_assembly": "GRCh38", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIMEY2C17/", "file_size": 1633830, "file_type_detailed": "normalized counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:42:17.534443+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "68752c5e868d716155fc47b7fb4fb64e", "href": "/files-processed/4DNFIZYBGEY7/@@download/4DNFIZYBGEY7.bw", "display_title": "4DNFIZYBGEY7.bw", "status": "released", "accession": "4DNFIZYBGEY7", "higlass_uid": "02e9d683-7ce9-4428-b32a-fe81e2530329", "uuid": "21acb580-498f-4fe1-afb4-9128bba02031", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/21acb580-498f-4fe1-afb4-9128bba02031/4DNFIZYBGEY7.bw", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIZYBGEY7/", "file_size": 1065470, "file_type_detailed": "counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFIZYBGEY7", "@id": "/higlass-view-configs/bd14fedf-50f1-4cd9-a1fb-3da8ea52deea/", "uuid": "bd14fedf-50f1-4cd9-a1fb-3da8ea52deea", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:41:58.421402+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "de145f83a79118a1ed9be44575467bb4", "href": "/files-processed/4DNFIQZYGJBX/@@download/4DNFIQZYGJBX.bw", "display_title": "4DNFIQZYGJBX.bw", "status": "released", "accession": "4DNFIQZYGJBX", "higlass_uid": "fb7f7bd6-6a46-4b78-8441-5e87f5777ba9", "uuid": "18e98574-1d20-4f92-b1e7-34376cb9a963", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/18e98574-1d20-4f92-b1e7-34376cb9a963/4DNFIQZYGJBX.bw", "genome_assembly": "GRCh38", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIQZYGJBX/", "file_size": 1826658, "file_type_detailed": "normalized counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFIQZYGJBX", "@id": "/higlass-view-configs/ce1ca02c-5cc4-431b-bbda-66e42b0e032c/", "uuid": "ce1ca02c-5cc4-431b-bbda-66e42b0e032c", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:35:26.910219+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "aa175f6c1ba1e00367710db4adb2ae90", "href": "/files-processed/4DNFISA46SYT/@@download/4DNFISA46SYT.txt.gz", "display_title": "4DNFISA46SYT.txt.gz", "status": "released", "accession": "4DNFISA46SYT", "uuid": "c7b30fc7-e1c9-4f6f-8ab8-95fa80f83b38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c7b30fc7-e1c9-4f6f-8ab8-95fa80f83b38/4DNFISA46SYT.txt.gz", "genome_assembly": "GRCh38", "file_type": "NADs", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFISA46SYT/", "file_size": 521189, "file_type_detailed": "NADs (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:37:31.198764+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "b542e78959a1ebe139e30015250d10f0", "href": "/files-processed/4DNFI4ZWNFWV/@@download/4DNFI4ZWNFWV.bed.gz", "display_title": "4DNFI4ZWNFWV.bed.gz", "status": "released", "accession": "4DNFI4ZWNFWV", "higlass_uid": "f0aRUvI_Q3iML2lBukEbMw", "uuid": "f2e6d320-5f9a-42bb-a6b1-8907d52c2748", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f2e6d320-5f9a-42bb-a6b1-8907d52c2748/4DNFI4ZWNFWV.bed.gz", "genome_assembly": "GRCh38", "file_type": "NADs", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFI4ZWNFWV/", "file_size": 6749, "file_type_detailed": "NADs (bed)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFI4ZWNFWV - NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "@id": "/higlass-view-configs/cce2a615-bc87-467f-9dfb-be6d3997a3a0/", "uuid": "cce2a615-bc87-467f-9dfb-be6d3997a3a0", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bed", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "file_format": "bed", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bed/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:36:15.276926+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, {"type": "supplementary", "description": "Additional files associated with the 50kb bin size processing of data for DamID-seq on HCT116 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam", "title": "Additional 50kb binned files", "files": [{"md5sum": "250eaf71f0ef55898f7078726f0903a0", "href": "/files-processed/4DNFIMKWN76L/@@download/4DNFIMKWN76L.txt.gz", "display_title": "4DNFIMKWN76L.txt.gz", "status": "released", "accession": "4DNFIMKWN76L", "uuid": "29021344-c664-451a-a9b0-ae148b7df425", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/29021344-c664-451a-a9b0-ae148b7df425/4DNFIMKWN76L.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIMKWN76L/", "file_size": 371789, "file_type_detailed": "counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:40:35.453859+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "086bcce419bb57d9f54acba9189e9ce9", "href": "/files-processed/4DNFIVONWWAS/@@download/4DNFIVONWWAS.txt.gz", "display_title": "4DNFIVONWWAS.txt.gz", "status": "released", "accession": "4DNFIVONWWAS", "uuid": "e49eae9c-01b8-4ace-a27c-8b5e37bf3abd", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e49eae9c-01b8-4ace-a27c-8b5e37bf3abd/4DNFIVONWWAS.txt.gz", "genome_assembly": "GRCh38", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIVONWWAS/", "file_size": 817797, "file_type_detailed": "normalized counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:41:12.698017+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "8ea278681db2f9d3ee7e944c1c8e51b7", "href": "/files-processed/4DNFIKDYUWDQ/@@download/4DNFIKDYUWDQ.bw", "display_title": "4DNFIKDYUWDQ.bw", "status": "released", "accession": "4DNFIKDYUWDQ", "higlass_uid": "2287546e-5052-4a77-b836-c4488fa83cfa", "uuid": "84685c57-f6de-46f8-bf47-6b5f9f11e6bc", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/84685c57-f6de-46f8-bf47-6b5f9f11e6bc/4DNFIKDYUWDQ.bw", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIKDYUWDQ/", "file_size": 582104, "file_type_detailed": "counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFIKDYUWDQ", "@id": "/higlass-view-configs/7c89da58-268b-4c5a-a700-8a4ae9b84711/", "uuid": "7c89da58-268b-4c5a-a700-8a4ae9b84711", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:40:23.608965+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "a54c46d97db007690754c6eac487611b", "href": "/files-processed/4DNFI35UO5MA/@@download/4DNFI35UO5MA.txt.gz", "display_title": "4DNFI35UO5MA.txt.gz", "status": "released", "accession": "4DNFI35UO5MA", "uuid": "11411670-95ab-4034-b2ca-22b58daad977", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/11411670-95ab-4034-b2ca-22b58daad977/4DNFI35UO5MA.txt.gz", "genome_assembly": "GRCh38", "file_type": "NADs", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFI35UO5MA/", "file_size": 252319, "file_type_detailed": "NADs (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:36:24.151260+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, {"type": "supplementary", "description": "The files associated with the 100kb bin size processing of data for DamID-seq on HCT116 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam", "title": "100kb binned files", "files": [{"md5sum": "5bf4e8145ff1cb0c6112d2ee0f216f2d", "href": "/files-processed/4DNFIE3H7GK6/@@download/4DNFIE3H7GK6.txt.gz", "display_title": "4DNFIE3H7GK6.txt.gz", "status": "released", "accession": "4DNFIE3H7GK6", "uuid": "9e071e16-9a68-4af2-a19e-fcf510d44dba", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/9e071e16-9a68-4af2-a19e-fcf510d44dba/4DNFIE3H7GK6.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIE3H7GK6/", "file_size": 185347, "file_type_detailed": "counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:42:00.854705+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "b1bcb2c9bc3d6b7c3ae317267ffe38a6", "href": "/files-processed/4DNFIKRKLFZW/@@download/4DNFIKRKLFZW.txt.gz", "display_title": "4DNFIKRKLFZW.txt.gz", "status": "released", "accession": "4DNFIKRKLFZW", "uuid": "bd1dfbd0-ec8d-48f8-a9bb-30d37abd2dcb", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/bd1dfbd0-ec8d-48f8-a9bb-30d37abd2dcb/4DNFIKRKLFZW.txt.gz", "genome_assembly": "GRCh38", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIKRKLFZW/", "file_size": 411250, "file_type_detailed": "normalized counts (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:40:06.974372+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "4fede88d4e8f952b46651778d659f571", "href": "/files-processed/4DNFI3N1Z2NM/@@download/4DNFI3N1Z2NM.bw", "display_title": "4DNFI3N1Z2NM.bw", "status": "released", "accession": "4DNFI3N1Z2NM", "higlass_uid": "8a5a3f7f-8b08-4698-9e69-7ac5c3aca67a", "uuid": "96a0ac76-3d49-4a10-abb0-05c93df05f3d", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/96a0ac76-3d49-4a10-abb0-05c93df05f3d/4DNFI3N1Z2NM.bw", "genome_assembly": "GRCh38", "file_type": "counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFI3N1Z2NM/", "file_size": 321863, "file_type_detailed": "counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFI3N1Z2NM", "@id": "/higlass-view-configs/d3209c5b-4242-426d-aed9-d1c01b3b15bd/", "uuid": "d3209c5b-4242-426d-aed9-d1c01b3b15bd", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:37:51.370630+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "38cd34cd96f8d3796aa5c98dcd8a0673", "href": "/files-processed/4DNFIH79T93A/@@download/4DNFIH79T93A.bw", "display_title": "4DNFIH79T93A.bw", "status": "released", "accession": "4DNFIH79T93A", "higlass_uid": "9629d335-5c7d-4d28-9d63-461881eb0a24", "uuid": "c4312d54-28b2-4fa3-83ad-6e884f70be9e", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c4312d54-28b2-4fa3-83ad-6e884f70be9e/4DNFIH79T93A.bw", "genome_assembly": "GRCh38", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIH79T93A/", "file_size": 495064, "file_type_detailed": "normalized counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFIH79T93A - normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "@id": "/higlass-view-configs/56632da9-6b58-45b6-bdf2-78245e840e91/", "uuid": "56632da9-6b58-45b6-bdf2-78245e840e91", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:35:55.586972+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "45b129576124e5cf2e2478844515a091", "href": "/files-processed/4DNFIT8RUC8M/@@download/4DNFIT8RUC8M.txt.gz", "display_title": "4DNFIT8RUC8M.txt.gz", "status": "released", "accession": "4DNFIT8RUC8M", "uuid": "340287aa-97a3-4869-be62-ad91b90265e5", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/340287aa-97a3-4869-be62-ad91b90265e5/4DNFIT8RUC8M.txt.gz", "genome_assembly": "GRCh38", "file_type": "NADs", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIT8RUC8M/", "file_size": 128495, "file_type_detailed": "NADs (compressed_txt)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "compressed_txt", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:35:19.070182+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "ff7c78b58bb981e625401d395be04a0b", "href": "/files-processed/4DNFIK29WD47/@@download/4DNFIK29WD47.bed.gz", "display_title": "4DNFIK29WD47.bed.gz", "status": "released", "accession": "4DNFIK29WD47", "higlass_uid": "F3Jn_dF-QiqOsCM_-p55WA", "uuid": "e6dd06ea-aaa1-4106-82d5-b753a9e023e6", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e6dd06ea-aaa1-4106-82d5-b753a9e023e6/4DNFIK29WD47.bed.gz", "genome_assembly": "GRCh38", "file_type": "NADs", "@type": ["FileProcessed", "File", "Item"], "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."], "@id": "/files-processed/4DNFIK29WD47/", "file_size": 2767, "file_type_detailed": "NADs (bed)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFIK29WD47 - NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "@id": "/higlass-view-configs/e00e386f-37b9-4171-82a5-4d77fd330f84/", "uuid": "e00e386f-37b9-4171-82a5-4d77fd330f84", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "file_format": {"status": "released", "display_title": "bed", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "file_format": "bed", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bed/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:50:07.349838+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, {"type": "supplementary", "description": "Non-bin specific files for DamID-seq on HCT116 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam", "title": "Other files - non-binned", "files": [{"md5sum": "7e095184a8ed2cf6c4be9d65715a4dfa", "href": "/files-processed/4DNFIOITTDRN/@@download/4DNFIOITTDRN.html", "display_title": "4DNFIOITTDRN.html", "status": "released", "accession": "4DNFIOITTDRN", "uuid": "d9553ca9-ee8c-4cd7-836a-958669bcaea1", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/d9553ca9-ee8c-4cd7-836a-958669bcaea1/4DNFIOITTDRN.html", "genome_assembly": "GRCh38", "file_type": "other", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIOITTDRN/", "file_size": 2582365, "file_type_detailed": "other (html)", "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 HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "file_format": {"status": "released", "display_title": "html", "uuid": "8bd6fe41-6af8-43c9-b24a-d74241898f09", "file_format": "html", "@type": ["FileFormat", "Item"], "@id": "/file-formats/html/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "status": "current", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:32:01.600106+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}], "experiment_type": {"assay_subclassification": "Proximity to Cellular Component", "assay_subclass_short": "Proximity-seq", "other_tags": ["1D"], "@type": ["ExperimentType", "Item"], "display_title": "DamID-seq", "uuid": "b777a1da-8dc8-4473-9b8d-4f7716fb0a4a", "title": "DamID-seq", "@id": "/experiment-types/damid-seq/", "experiment_category": "Sequencing", "status": "released", "assay_classification": "Linear DNA Enrichment", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "last_modified": {"date_modified": "2023-11-03T14:45:09.304007+00:00"}, "experiment_categorizer": {"field": "Target", "value": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "combined": "Target: Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experimentset_type": "replicate", "other_processed_files": [{"type": "supplementary", "files": [{"@id": "/files-processed/4DNFIJAJRPVD/", "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."], "accession": "4DNFIJAJRPVD", "md5sum": "acccbc2938eb55d671eef4e10905c141", "display_title": "4DNFIJAJRPVD.txt.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c3a66fc3-dfad-45db-a3f8-f8697606ed4f/4DNFIJAJRPVD.txt.gz", "file_format": {"display_title": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFIJAJRPVD/@@download/4DNFIJAJRPVD.txt.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "c3a66fc3-dfad-45db-a3f8-f8697606ed4f", "status": "released", "genome_assembly": "GRCh38", "file_type": "normalized counts", "file_size": 70240734, "file_type_detailed": "normalized counts (compressed_txt)", "lab": {"display_title": "Bas van Steensel, NKI", "@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "status": "current", "@type": ["Lab", "Item"], "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:40:18.733100+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "DamID-seq on HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "experimental_lab": "Bas van Steensel, NKI", "replicate_info": "merged replicates", "experiment_bucket": "gatc binned files", "experiment_type": "DamID-seq", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}}, {"@id": "/files-processed/4DNFIJ2W3L79/", "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."], "accession": "4DNFIJ2W3L79", "md5sum": "42962bf2a7d51d8658b5efa059f86e37", "display_title": "4DNFIJ2W3L79.bw", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f4120bb6-749f-4a8f-821f-d734e9e5247e/4DNFIJ2W3L79.bw", "file_format": {"display_title": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "status": "released", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFIJ2W3L79/@@download/4DNFIJ2W3L79.bw", "@type": ["FileProcessed", "File", "Item"], "uuid": "f4120bb6-749f-4a8f-821f-d734e9e5247e", "higlass_uid": "f88cc3fe-0d5b-4062-85ec-1c8c109a9fe8", "status": "released", "genome_assembly": "GRCh38", "file_type": "normalized counts", "file_size": 34723261, "file_type_detailed": "normalized counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"status": "released", "@id": "/higlass-view-configs/a26ea583-6f2b-4ca3-9c26-f4b62bd85e5b/", "uuid": "a26ea583-6f2b-4ca3-9c26-f4b62bd85e5b", "display_title": "4DNFIJ2W3L79", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "lab": {"display_title": "Bas van Steensel, NKI", "@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "status": "current", "@type": ["Lab", "Item"], "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:36:11.252730+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "DamID-seq on HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "experimental_lab": "Bas van Steensel, NKI", "replicate_info": "merged replicates", "experiment_bucket": "gatc binned files", "experiment_type": "DamID-seq", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}}], "title": "gatc binned files", "description": "The files associated with the gatc bin size processing of data for DamID-seq on HCT116 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam", "higlass_view_config": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "32c103f2-6fa2-47f5-b6a7-afc3b824fa1c", "description": "Supplementary Files (gatc binned files) for 4DNES3PG7E7F (DamID for Nucleolus (4X-AP3) on HCT116 wildtype cells - cells were transduced with virus expressing a Dam fusion protein, gDNA was harvested after 3 or 4 days and processed for DamID-seq): 4DNFIJ2W3L79", "@id": "/higlass-view-configs/32c103f2-6fa2-47f5-b6a7-afc3b824fa1c/", "status": "released", "display_title": "4DNES3PG7E7F - gatc binned files", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}, "last_modified": {"date_modified": "2024-02-23T06:03:57.721965+00:00"}}}, {"type": "supplementary", "files": [{"@id": "/files-processed/4DNFI72A3L1I/", "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."], "accession": "4DNFI72A3L1I", "md5sum": "cffd5bc32a2c66a88e68a83d2cd40e04", "display_title": "4DNFI72A3L1I.txt.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a092a106-ac07-4cbb-87df-f1f4c97d62f3/4DNFI72A3L1I.txt.gz", "file_format": {"display_title": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFI72A3L1I/@@download/4DNFI72A3L1I.txt.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "a092a106-ac07-4cbb-87df-f1f4c97d62f3", "status": "released", "genome_assembly": "GRCh38", "file_type": "normalized counts", "file_size": 1646724, "file_type_detailed": "normalized counts (compressed_txt)", "lab": {"display_title": "Bas van Steensel, NKI", "@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "status": "current", "@type": ["Lab", "Item"], "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:41:53.257505+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "DamID-seq on HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "experimental_lab": "Bas van Steensel, NKI", "replicate_info": "merged replicates", "experiment_bucket": "25kb binned files", "experiment_type": "DamID-seq", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}}, {"@id": "/files-processed/4DNFIRKQUNBY/", "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."], "accession": "4DNFIRKQUNBY", "md5sum": "ab3aa3f2028e19a01453379aa205e291", "display_title": "4DNFIRKQUNBY.bw", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/1dd3f1fd-ee1c-46b7-b7c6-f6784624bca6/4DNFIRKQUNBY.bw", "file_format": {"display_title": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "status": "released", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFIRKQUNBY/@@download/4DNFIRKQUNBY.bw", "@type": ["FileProcessed", "File", "Item"], "uuid": "1dd3f1fd-ee1c-46b7-b7c6-f6784624bca6", "higlass_uid": "93422b6d-f7c1-4b77-b154-e6028a66d125", "status": "released", "genome_assembly": "GRCh38", "file_type": "normalized counts", "file_size": 1835418, "file_type_detailed": "normalized counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"status": "released", "@id": "/higlass-view-configs/6a7d0fdf-d651-4497-92cc-ad5062632d13/", "uuid": "6a7d0fdf-d651-4497-92cc-ad5062632d13", "display_title": "4DNFIRKQUNBY - normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "lab": {"display_title": "Bas van Steensel, NKI", "@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "status": "current", "@type": ["Lab", "Item"], "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:37:44.337273+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "DamID-seq on HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "experimental_lab": "Bas van Steensel, NKI", "replicate_info": "merged replicates", "experiment_bucket": "25kb binned files", "experiment_type": "DamID-seq", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}}, {"@id": "/files-processed/4DNFIYL1759Q/", "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."], "accession": "4DNFIYL1759Q", "md5sum": "6daae788843dc2f06e71ff742bc0fc18", "display_title": "4DNFIYL1759Q.txt.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/5627c70f-82c7-4074-9a8a-6d7e19277840/4DNFIYL1759Q.txt.gz", "file_format": {"display_title": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFIYL1759Q/@@download/4DNFIYL1759Q.txt.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "5627c70f-82c7-4074-9a8a-6d7e19277840", "status": "released", "genome_assembly": "GRCh38", "file_type": "NADs", "file_size": 517321, "file_type_detailed": "NADs (compressed_txt)", "lab": {"display_title": "Bas van Steensel, NKI", "@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "status": "current", "@type": ["Lab", "Item"], "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:37:05.792999+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "DamID-seq on HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "experimental_lab": "Bas van Steensel, NKI", "replicate_info": "merged replicates", "experiment_bucket": "25kb binned files", "experiment_type": "DamID-seq", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}}, {"@id": "/files-processed/4DNFIS85UL13/", "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."], "accession": "4DNFIS85UL13", "md5sum": "8e0178195b1010d23e2f47f0ecad5ae5", "display_title": "4DNFIS85UL13.bed.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/01b24212-ef8f-4d56-a0e3-c4f48479a5c0/4DNFIS85UL13.bed.gz", "file_format": {"display_title": "bed", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bed/", "status": "released", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFIS85UL13/@@download/4DNFIS85UL13.bed.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "01b24212-ef8f-4d56-a0e3-c4f48479a5c0", "higlass_uid": "W4atbNhvQGSbPaOFB4Hwsw", "status": "released", "genome_assembly": "GRCh38", "file_type": "NADs", "file_size": 5353, "file_type_detailed": "NADs (bed)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"status": "released", "@id": "/higlass-view-configs/bc914439-33d1-4709-8d1c-18732dcaa0ad/", "uuid": "bc914439-33d1-4709-8d1c-18732dcaa0ad", "display_title": "4DNFIS85UL13 - NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "lab": {"display_title": "Bas van Steensel, NKI", "@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "status": "current", "@type": ["Lab", "Item"], "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:35:27.620841+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "DamID-seq on HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "experimental_lab": "Bas van Steensel, NKI", "replicate_info": "merged replicates", "experiment_bucket": "25kb binned files", "experiment_type": "DamID-seq", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}}], "title": "25kb binned files", "description": "The files associated with the 25kb bin size processing of data for DamID-seq on HCT116 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam", "higlass_view_config": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "6ceb4026-8bbc-4ef8-a821-b33d829e855e", "description": "Supplementary Files (25kb binned files) for 4DNES3PG7E7F (DamID for Nucleolus (4X-AP3) on HCT116 wildtype cells - cells were transduced with virus expressing a Dam fusion protein, gDNA was harvested after 3 or 4 days and processed for DamID-seq): 4DNFIRKQUNBY, 4DNFIS85UL13", "@id": "/higlass-view-configs/6ceb4026-8bbc-4ef8-a821-b33d829e855e/", "status": "released", "display_title": "4DNES3PG7E7F - 25kb binned files", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}, "last_modified": {"date_modified": "2024-02-23T06:03:59.272329+00:00"}}}, {"type": "supplementary", "files": [{"@id": "/files-processed/4DNFIOTUDJSG/", "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."], "accession": "4DNFIOTUDJSG", "md5sum": "bf77f66842579ef828ca5ee8a1fe4059", "display_title": "4DNFIOTUDJSG.txt.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/6ed13dbf-bc7f-4e13-8263-860f26ab2766/4DNFIOTUDJSG.txt.gz", "file_format": {"display_title": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFIOTUDJSG/@@download/4DNFIOTUDJSG.txt.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "6ed13dbf-bc7f-4e13-8263-860f26ab2766", "status": "released", "genome_assembly": "GRCh38", "file_type": "normalized counts", "file_size": 819903, "file_type_detailed": "normalized counts (compressed_txt)", "lab": {"display_title": "Bas van Steensel, NKI", "@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "status": "current", "@type": ["Lab", "Item"], "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:40:47.636299+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "DamID-seq on HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "experimental_lab": "Bas van Steensel, NKI", "replicate_info": "merged replicates", "experiment_bucket": "Additional 50kb binned files", "experiment_type": "DamID-seq", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}}, {"@id": "/files-processed/4DNFI4Z1RPLM/", "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."], "accession": "4DNFI4Z1RPLM", "md5sum": "be8b07a12e82adda428f6f8ccaa6d571", "display_title": "4DNFI4Z1RPLM.txt.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/2c2eed20-3e8e-4793-a323-03b7caf4c192/4DNFI4Z1RPLM.txt.gz", "file_format": {"display_title": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFI4Z1RPLM/@@download/4DNFI4Z1RPLM.txt.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "2c2eed20-3e8e-4793-a323-03b7caf4c192", "status": "released", "genome_assembly": "GRCh38", "file_type": "NADs", "file_size": 251576, "file_type_detailed": "NADs (compressed_txt)", "lab": {"display_title": "Bas van Steensel, NKI", "@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "status": "current", "@type": ["Lab", "Item"], "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:35:58.506441+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "DamID-seq on HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "experimental_lab": "Bas van Steensel, NKI", "replicate_info": "merged replicates", "experiment_bucket": "Additional 50kb binned files", "experiment_type": "DamID-seq", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}}], "title": "Additional 50kb binned files", "description": "Additional files associated with the 50kb bin size processing of data for DamID-seq on HCT116 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam", "higlass_view_config": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "3181f22a-fb42-4658-9ae5-7f250ce82052", "description": "Supplementary Files (Additional 50kb binned files) for 4DNES3PG7E7F (DamID for Nucleolus (4X-AP3) on HCT116 wildtype cells - cells were transduced with virus expressing a Dam fusion protein, gDNA was harvested after 3 or 4 days and processed for DamID-seq): 4DNFIIGISD8K, 4DNFIRNA2NL6, 4DNFIKDYUWDQ", "@id": "/higlass-view-configs/3181f22a-fb42-4658-9ae5-7f250ce82052/", "status": "released", "display_title": "4DNES3PG7E7F - Additional 50kb binned files", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}, "last_modified": {"date_modified": "2023-11-03T14:44:37.020085+00:00"}}}, {"type": "supplementary", "files": [{"@id": "/files-processed/4DNFIWFLLT78/", "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."], "accession": "4DNFIWFLLT78", "md5sum": "01622eb1574d34ae696c0d10de95dea7", "display_title": "4DNFIWFLLT78.txt.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/24a173bb-8819-401d-a3ef-be3b18638b7f/4DNFIWFLLT78.txt.gz", "file_format": {"display_title": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFIWFLLT78/@@download/4DNFIWFLLT78.txt.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "24a173bb-8819-401d-a3ef-be3b18638b7f", "status": "released", "genome_assembly": "GRCh38", "file_type": "normalized counts", "file_size": 411755, "file_type_detailed": "normalized counts (compressed_txt)", "lab": {"display_title": "Bas van Steensel, NKI", "@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "status": "current", "@type": ["Lab", "Item"], "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:42:33.900743+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "DamID-seq on HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "experimental_lab": "Bas van Steensel, NKI", "replicate_info": "merged replicates", "experiment_bucket": "100kb binned files", "experiment_type": "DamID-seq", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}}, {"@id": "/files-processed/4DNFIRTSEB3U/", "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."], "accession": "4DNFIRTSEB3U", "md5sum": "bcb110a46b5fa24851e3cde90fc8b2a3", "display_title": "4DNFIRTSEB3U.bw", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/4b6a064e-99fb-4562-9100-09e3ed4d0592/4DNFIRTSEB3U.bw", "file_format": {"display_title": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "status": "released", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFIRTSEB3U/@@download/4DNFIRTSEB3U.bw", "@type": ["FileProcessed", "File", "Item"], "uuid": "4b6a064e-99fb-4562-9100-09e3ed4d0592", "higlass_uid": "1dce52e7-a8bb-4876-9829-43ab0c7efc25", "status": "released", "genome_assembly": "GRCh38", "file_type": "normalized counts", "file_size": 495920, "file_type_detailed": "normalized counts (bw)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"status": "released", "@id": "/higlass-view-configs/fc77291c-191e-4b8b-bdd6-93dffee53b0a/", "uuid": "fc77291c-191e-4b8b-bdd6-93dffee53b0a", "display_title": "4DNFIRTSEB3U - normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "lab": {"display_title": "Bas van Steensel, NKI", "@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "status": "current", "@type": ["Lab", "Item"], "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:35:29.564457+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "DamID-seq on HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "experimental_lab": "Bas van Steensel, NKI", "replicate_info": "merged replicates", "experiment_bucket": "100kb binned files", "experiment_type": "DamID-seq", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "normalized counts for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}}, {"@id": "/files-processed/4DNFIRT5DLD4/", "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."], "accession": "4DNFIRT5DLD4", "md5sum": "ccc78e82891098428d128a3e1e60cf5f", "display_title": "4DNFIRT5DLD4.txt.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/7c013156-a9f4-401a-8c99-24dd1e6c134d/4DNFIRT5DLD4.txt.gz", "file_format": {"display_title": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFIRT5DLD4/@@download/4DNFIRT5DLD4.txt.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "7c013156-a9f4-401a-8c99-24dd1e6c134d", "status": "released", "genome_assembly": "GRCh38", "file_type": "NADs", "file_size": 128241, "file_type_detailed": "NADs (compressed_txt)", "lab": {"display_title": "Bas van Steensel, NKI", "@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "status": "current", "@type": ["Lab", "Item"], "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:37:25.105398+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "DamID-seq on HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "experimental_lab": "Bas van Steensel, NKI", "replicate_info": "merged replicates", "experiment_bucket": "100kb binned files", "experiment_type": "DamID-seq", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}}, {"@id": "/files-processed/4DNFI3CIFYU9/", "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."], "accession": "4DNFI3CIFYU9", "md5sum": "92b844fbf3cffb1a20c7d66c2d1186c8", "display_title": "4DNFI3CIFYU9.bed.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/5aedd03a-4c7f-482d-8617-78d7349dcb7f/4DNFI3CIFYU9.bed.gz", "file_format": {"display_title": "bed", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bed/", "status": "released", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFI3CIFYU9/@@download/4DNFI3CIFYU9.bed.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "5aedd03a-4c7f-482d-8617-78d7349dcb7f", "higlass_uid": "PZrVg4N0Svi2iuM7wmSAOw", "status": "released", "genome_assembly": "GRCh38", "file_type": "NADs", "file_size": 2286, "file_type_detailed": "NADs (bed)", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"status": "released", "@id": "/higlass-view-configs/a587a695-2b94-430a-844d-d4bff901d600/", "uuid": "a587a695-2b94-430a-844d-d4bff901d600", "display_title": "4DNFI3CIFYU9 - NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "lab": {"display_title": "Bas van Steensel, NKI", "@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "status": "current", "@type": ["Lab", "Item"], "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:49:45.148045+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "DamID-seq on HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "experimental_lab": "Bas van Steensel, NKI", "replicate_info": "merged replicates", "experiment_bucket": "100kb binned files", "experiment_type": "DamID-seq", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "NADs for HCT116 (Tier 2) DamID-seq Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)"}}], "title": "100kb binned files", "description": "The files associated with the 100kb bin size processing of data for DamID-seq on HCT116 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam", "higlass_view_config": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "0a528028-7b8d-4b64-b273-28c85ff12392", "description": "Supplementary Files (100kb binned files) for 4DNES3PG7E7F (DamID for Nucleolus (4X-AP3) on HCT116 wildtype cells - cells were transduced with virus expressing a Dam fusion protein, gDNA was harvested after 3 or 4 days and processed for DamID-seq): 4DNFIRTSEB3U, 4DNFI3CIFYU9", "@id": "/higlass-view-configs/0a528028-7b8d-4b64-b273-28c85ff12392/", "status": "released", "display_title": "4DNES3PG7E7F - 100kb binned files", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}, "last_modified": {"date_modified": "2024-02-23T06:04:00.998198+00:00"}}}, {"type": "supplementary", "files": [{"@id": "/files-processed/4DNFIA4X7K21/", "accession": "4DNFIA4X7K21", "md5sum": "02e5367bdc5dcc38844df470e9d8465e", "display_title": "4DNFIA4X7K21.html", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/b166f91d-4ce4-4efe-99d1-590baa4b82f5/4DNFIA4X7K21.html", "file_format": {"display_title": "html", "@type": ["FileFormat", "Item"], "@id": "/file-formats/html/", "status": "released", "uuid": "8bd6fe41-6af8-43c9-b24a-d74241898f09", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFIA4X7K21/@@download/4DNFIA4X7K21.html", "@type": ["FileProcessed", "File", "Item"], "uuid": "b166f91d-4ce4-4efe-99d1-590baa4b82f5", "status": "released", "genome_assembly": "GRCh38", "file_type": "other", "file_size": 6512973, "file_type_detailed": "other (html)", "lab": {"display_title": "Bas van Steensel, NKI", "@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "status": "current", "@type": ["Lab", "Item"], "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "last_modified": {"date_modified": "2024-02-22T17:31:35.745181+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "DamID-seq on HCT116 cells (2020-07-01)", "condition": "Nucleolar Targeting Signal (4X-AP3)-Dam", "experimental_lab": "Bas van Steensel, NKI", "replicate_info": "merged replicates", "experiment_bucket": "Other files - non-binned", "experiment_type": "DamID-seq", "assay_info": "Nucleolus Localization Sequence (4X-AP3D1) (engineered reagent)", "biosource_name": "HCT116 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}}], "title": "Other files - non-binned", "description": "Non-bin specific files for DamID-seq on HCT116 cells (2020-07-01) Nucleolar Targeting Signal (4X-AP3)-Dam"}], "@id": "/experiment-set-replicates/4DNES3PG7E7F/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "1ea2308b-7f90-42a5-8d00-c4c33f88af9f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNES3PG7E7F", "external_references": [], "pubs_using": [], "publications_of_set": [], "number_of_experiments": 3, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSAH3ZFBQ/", "embedded_path": "experiments_in_set.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"}}}, {"parent": "/biosamples/4DNBSA3GV3KY/", "embedded_path": "experiments_in_set.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"}}}, {"parent": "/biosamples/4DNBS54371JN/", "embedded_path": "experiments_in_set.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": []}