{"lab": {"display_title": "Bas van Steensel, NKI", "correspondence": [{"contact_email": "Yi52LnN0ZWVuc2VsQG5raS5ubA==", "@id": "/users/dd8b1cd6-93cd-41e5-b184-caf1369cb39f/", "display_title": "Bas van Steensel"}], "@type": ["Lab", "Item"], "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "@id": "/labs/bas-van-steensel-lab/", "title": "Bas van Steensel, NKI", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "award": {"center_title": "NOFIC - Belmont", "display_title": "COMBINED CYTOLOGICAL, GENOMIC, AND FUNCTIONAL MAPPING OF NUCLEAR GENOME ORGANIZATION", "@type": ["Award", "Item"], "name": "1U54DK107965-01", "uuid": "91b694c3-f4d7-4ddd-8278-16f94e15c1c5", "project": "4DN", "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.", "@id": "/awards/1U54DK107965-01/", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["vanSteensel-lab:Hap1_Dam_No"], "accession": "4DNESUSK2C6C", "condition": "Dam-only control", "description": "DamID for Dam on Hap1 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": "2020-07-01T07:53:53.715843+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "DamID-seq on Hap1 cells (2020-07-01)", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-11-03T14:38:08.837656+00:00"}, "public_release": "2023-11-03", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"uuid": "bec94fc3-f0f3-4802-87da-16b58b35ae5f", "@type": ["ExperimentDamid", "Experiment", "Item"], "accession": "4DNEXEFGIYQ7", "@id": "/experiments-damid/4DNEXEFGIYQ7/", "display_title": "DamID-seq on HAP-1 (Tier 2) - 4DNEXEFGIYQ7", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"uuid": "9b1775c9-77df-48c8-af85-d07e9143252c", "@type": ["ExperimentDamid", "Experiment", "Item"], "accession": "4DNEXFXI4QYL", "@id": "/experiments-damid/4DNEXFXI4QYL/", "display_title": "DamID-seq on HAP-1 (Tier 2) - 4DNEXFXI4QYL", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 3, "tec_rep_no": 1, "replicate_exp": {"uuid": "25eeff8a-9ff2-4225-9f10-8844705fefdc", "@type": ["ExperimentDamid", "Experiment", "Item"], "accession": "4DNEXM4TOFTC", "@id": "/experiments-damid/4DNEXM4TOFTC/", "display_title": "DamID-seq on HAP-1 (Tier 2) - 4DNEXM4TOFTC", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_headers": [{"lab": {"uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "@type": ["Lab", "Item"], "status": "current", "display_title": "Bas van Steensel, NKI", "@id": "/labs/bas-van-steensel-lab/", "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/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "status": "current", "@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "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": "

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.

"}, {"lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "status": "current", "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "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/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "status": "current", "@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "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": "

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) \nand the 4DN Data Portal paper \n(doi: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.

"}], "project_release": "2020-07-14", "experiments_in_set": [{"files": [{"upload_key": "0ffae52e-83bf-4a78-8c6c-98f692a7e211/4DNFIVDH8TR2.fastq.gz", "file_type": "reads", "file_type_detailed": "reads (fastq)", "uuid": "0ffae52e-83bf-4a78-8c6c-98f692a7e211", "@id": "/files-fastq/4DNFIVDH8TR2/", "display_title": "4DNFIVDH8TR2.fastq.gz", "accession": "4DNFIVDH8TR2", "href": "/files-fastq/4DNFIVDH8TR2/@@download/4DNFIVDH8TR2.fastq.gz", "file_classification": "raw file", "file_size": 390851131, "md5sum": "c18e7224323144301dd260b56f9309e1", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/0ffae52e-83bf-4a78-8c6c-98f692a7e211/4DNFIVDH8TR2.fastq.gz", "@type": ["FileFastq", "File", "Item"], "status": "released", "lab": {"name": "bas-van-steensel-lab", "@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "display_title": "Bas van Steensel, NKI", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "quality_metric": {"display_title": "QualityMetricFastqc from 2020-07-02", "uuid": "6da13d5c-b326-485a-b5fb-a28edab42b91", "overall_quality_status": "PASS", "status": "released", "@id": "/quality-metrics-fastqc/6da13d5c-b326-485a-b5fb-a28edab42b91/", "Total Sequences": 8297089, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIVDH8TR2/fastqc_report.html", "Sequence length": "65", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "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": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"upload_key": "080517be-3137-46a3-9065-44d1f8557075/4DNFIUS6VTOH.fastq.gz", "file_type": "reads", "file_type_detailed": "reads (fastq)", "uuid": "080517be-3137-46a3-9065-44d1f8557075", "@id": "/files-fastq/4DNFIUS6VTOH/", "display_title": "4DNFIUS6VTOH.fastq.gz", "accession": "4DNFIUS6VTOH", "href": "/files-fastq/4DNFIUS6VTOH/@@download/4DNFIUS6VTOH.fastq.gz", "file_classification": "raw file", "file_size": 2107669960, "md5sum": "61abfbf32b9f2666057691d4a2cd9a23", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/080517be-3137-46a3-9065-44d1f8557075/4DNFIUS6VTOH.fastq.gz", "@type": ["FileFastq", "File", "Item"], "status": "released", "lab": {"name": "bas-van-steensel-lab", "@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "display_title": "Bas van Steensel, NKI", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "quality_metric": {"display_title": "QualityMetricFastqc from 2020-07-02", "uuid": "cb898a12-61fb-4832-83a8-2141801bae2f", "overall_quality_status": "PASS", "status": "released", "@id": "/quality-metrics-fastqc/cb898a12-61fb-4832-83a8-2141801bae2f/", "Total Sequences": 44099375, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIUS6VTOH/fastqc_report.html", "Sequence length": "65", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "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": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-damid/4DNEXEFGIYQ7/", "accession": "4DNEXEFGIYQ7", "display_title": "DamID-seq on HAP-1 (Tier 2) - 4DNEXEFGIYQ7", "@type": ["ExperimentDamid", "Experiment", "Item"], "uuid": "bec94fc3-f0f3-4802-87da-16b58b35ae5f", "status": "released", "processed_files": [{"display_title": "4DNFIQ656DWL.bam", "href": "/files-processed/4DNFIQ656DWL/@@download/4DNFIQ656DWL.bam", "uuid": "2de3336c-ff4d-43f1-a50f-34d6f34a5095", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/2de3336c-ff4d-43f1-a50f-34d6f34a5095/4DNFIQ656DWL.bam", "file_format": {"status": "released", "display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_size": 293677459, "genome_assembly": "GRCh38", "upload_key": "2de3336c-ff4d-43f1-a50f-34d6f34a5095/4DNFIQ656DWL.bam", "file_type_detailed": "alignments (bam)", "md5sum": "e0fda7a9fc271fcd1b26de4c7a21ad2a", "accession": "4DNFIQ656DWL", "file_classification": "processed file", "@id": "/files-processed/4DNFIQ656DWL/", "file_type": "alignments", "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."], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "lab": {"@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "status": "current", "@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "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": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "last_modified": {"date_modified": "2024-02-22T17:48:11.498919+00:00"}}, {"display_title": "4DNFIHKZ51DR.bam", "href": "/files-processed/4DNFIHKZ51DR/@@download/4DNFIHKZ51DR.bam", "uuid": "9abd8dd3-09ea-4cac-915c-269611619d89", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/9abd8dd3-09ea-4cac-915c-269611619d89/4DNFIHKZ51DR.bam", "file_format": {"status": "released", "display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_size": 1328936130, "genome_assembly": "GRCh38", "upload_key": "9abd8dd3-09ea-4cac-915c-269611619d89/4DNFIHKZ51DR.bam", "file_type_detailed": "alignments (bam)", "md5sum": "fb5191bdc6f7f047042159cab5daf9f0", "accession": "4DNFIHKZ51DR", "file_classification": "processed file", "@id": "/files-processed/4DNFIHKZ51DR/", "file_type": "alignments", "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."], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "lab": {"@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "status": "current", "@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "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": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "last_modified": {"date_modified": "2024-02-22T17:48:07.076992+00:00"}}], "biosample": {"biosource_summary": "HAP-1 (Tier 2)", "treatments_summary": "None", "accession": "4DNBSRHSL3C5", "@id": "/biosamples/4DNBSRHSL3C5/", "biosample_category": ["Tier 2"], "uuid": "89b6838c-4d90-4a40-827e-3b4c28370689", "modifications_summary": "None", "@type": ["Biosample", "Item"], "biosample_type": "immortalized cells", "status": "released", "display_title": "4DNBSRHSL3C5", "cell_culture_details": [{"in_vitro_differentiated": "No", "@id": "/biosample-cell-cultures/1daa0334-6954-4871-8c6a-7e22b7f04d17/", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "display_title": "BiosampleCellCulture from 2020-07-01", "uuid": "1daa0334-6954-4871-8c6a-7e22b7f04d17", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["HAP-1 biosample missing ploidy authentication"], "badge": {"display_title": "Biosample Metadata Incomplete", "warning": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "badge_classification": "Warning", "badge_icon": "/static/img/badges/biosample-icon.svg", "title": "Biosample Metadata Incomplete", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@type": ["Badge", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "biosource": [{"@type": ["Biosource", "Item"], "uuid": "187d7227-366c-4e7d-b9ae-11f27efd4918", "display_title": "HAP-1 (Tier 2) - 4DNSRCVNIBZG", "status": "released", "@id": "/biosources/4DNSRCVNIBZG/", "cell_line_tier": "Tier 2", "biosource_type": "immortalized cell line", "accession": "4DNSRCVNIBZG", "tissue": {"preferred_name": "blood cell", "display_title": "blood cell", "@type": ["OntologyTerm", "Item"], "term_id": "CL:0000081", "status": "released", "@id": "/ontology-terms/CL:0000081/", "uuid": "0d64fbe2-ed5c-43cd-a30d-d9f0320d27ed", "term_name": "blood cell", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "scientific_name": "Homo sapiens", "@id": "/organisms/9606/", "status": "released", "name": "human", "@type": ["Organism", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"@type": ["OntologyTerm", "Item"], "uuid": "57d18eec-d662-4bf7-8000-047de03ad84a", "preferred_name": "HAP-1", "synonyms": ["HAP1"], "status": "released", "term_name": "HAP-1", "term_id": "EFO:0007598", "@id": "/ontology-terms/EFO:0007598/", "display_title": "HAP-1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"tissue_source": "blood cell"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"combined": "Target: None (Control)", "field": "Target", "value": "None (Control)"}, "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 Hap1 cells (2020-07-01) Dam-only control", "title": "gatc binned files", "files": [{"file_size": 51909997, "@type": ["FileProcessed", "File", "Item"], "uuid": "bb44db80-c7a0-4f3f-ac32-56b455dc548c", "href": "/files-processed/4DNFIITVQEH1/@@download/4DNFIITVQEH1.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (compressed_txt)", "accession": "4DNFIITVQEH1", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/bb44db80-c7a0-4f3f-ac32-56b455dc548c/4DNFIITVQEH1.txt.gz", "md5sum": "f9b77193af674a958d2ca285c35760dd", "@id": "/files-processed/4DNFIITVQEH1/", "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."], "display_title": "4DNFIITVQEH1.txt.gz", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "dba26778-f40a-4561-a552-65539702ded4", "display_title": "compressed_txt", "status": "released", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:47:46.322488+00:00"}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "gatc binned files", "assay_info": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}}, {"file_size": 41875438, "@type": ["FileProcessed", "File", "Item"], "uuid": "413d8a8a-8ab2-4d85-906b-c1d46f68ee0d", "higlass_uid": "d3d8b59d-f2f0-49f1-8259-1ff141add043", "href": "/files-processed/4DNFI5R3LIZR/@@download/4DNFI5R3LIZR.bw", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (bw)", "accession": "4DNFI5R3LIZR", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/413d8a8a-8ab2-4d85-906b-c1d46f68ee0d/4DNFI5R3LIZR.bw", "md5sum": "01c4900b8ec461205db66f616a36e904", "@id": "/files-processed/4DNFI5R3LIZR/", "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."], "display_title": "4DNFI5R3LIZR.bw", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "display_title": "bw", "status": "released", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:41:36.386818+00:00"}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/66ad023b-03bf-4cbb-a145-9f2ff970c240/", "display_title": "4DNFI5R3LIZR", "status": "released", "uuid": "66ad023b-03bf-4cbb-a145-9f2ff970c240", "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": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HAP-1 (Tier 2) DamID-seq None (Control)"}}]}, {"type": "supplementary", "description": "The files associated with the 25kb bin size processing of data for DamID-seq on Hap1 cells (2020-07-01) Dam-only control", "title": "25kb binned files", "files": [{"file_size": 748125, "@type": ["FileProcessed", "File", "Item"], "uuid": "2d6e6ab1-fe7c-40fa-be69-9b4f4a553b18", "href": "/files-processed/4DNFIT3DPUEX/@@download/4DNFIT3DPUEX.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (compressed_txt)", "accession": "4DNFIT3DPUEX", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/2d6e6ab1-fe7c-40fa-be69-9b4f4a553b18/4DNFIT3DPUEX.txt.gz", "md5sum": "f801711a04a63091642f80257b629c00", "@id": "/files-processed/4DNFIT3DPUEX/", "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."], "display_title": "4DNFIT3DPUEX.txt.gz", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "dba26778-f40a-4561-a552-65539702ded4", "display_title": "compressed_txt", "status": "released", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:42:34.043960+00:00"}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "25kb binned files", "assay_info": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}}, {"file_size": 1088333, "@type": ["FileProcessed", "File", "Item"], "uuid": "59dd808d-ea11-4f1e-b13c-7a52ebacb1d4", "higlass_uid": "8ebac403-e07b-4df2-8cec-31061e20dc3f", "href": "/files-processed/4DNFIKHJZIJ4/@@download/4DNFIKHJZIJ4.bw", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (bw)", "accession": "4DNFIKHJZIJ4", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/59dd808d-ea11-4f1e-b13c-7a52ebacb1d4/4DNFIKHJZIJ4.bw", "md5sum": "ef6890ceea40755c73182abf39710f58", "@id": "/files-processed/4DNFIKHJZIJ4/", "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."], "display_title": "4DNFIKHJZIJ4.bw", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "display_title": "bw", "status": "released", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:39:45.493717+00:00"}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/d5f30b53-b44e-4b5f-abe5-276d0a193996/", "display_title": "4DNFIKHJZIJ4", "status": "released", "uuid": "d5f30b53-b44e-4b5f-abe5-276d0a193996", "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": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HAP-1 (Tier 2) DamID-seq None (Control)"}}]}, {"type": "supplementary", "description": "Additional files associated with the 50kb bin size processing of data for DamID-seq on Hap1 cells (2020-07-01) Dam-only control", "title": "Additional 50kb binned files", "files": [{"file_size": 375640, "@type": ["FileProcessed", "File", "Item"], "uuid": "f95c75ab-3f26-48c1-9e87-37ce67b57220", "href": "/files-processed/4DNFIYDV6A8C/@@download/4DNFIYDV6A8C.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (compressed_txt)", "accession": "4DNFIYDV6A8C", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f95c75ab-3f26-48c1-9e87-37ce67b57220/4DNFIYDV6A8C.txt.gz", "md5sum": "021b5209e1c825d13c851a6a53925522", "@id": "/files-processed/4DNFIYDV6A8C/", "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."], "display_title": "4DNFIYDV6A8C.txt.gz", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "dba26778-f40a-4561-a552-65539702ded4", "display_title": "compressed_txt", "status": "released", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:41:02.570998+00:00"}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "Additional 50kb binned files", "assay_info": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}}, {"file_size": 593132, "@type": ["FileProcessed", "File", "Item"], "uuid": "2ec10407-dd04-41ab-b4e7-305523388934", "higlass_uid": "c9071bff-abb7-40e4-8c5c-a55f6c7954a9", "href": "/files-processed/4DNFITAJDFZP/@@download/4DNFITAJDFZP.bw", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (bw)", "accession": "4DNFITAJDFZP", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/2ec10407-dd04-41ab-b4e7-305523388934/4DNFITAJDFZP.bw", "md5sum": "f250140a0bd098777184a725d196dc88", "@id": "/files-processed/4DNFITAJDFZP/", "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."], "display_title": "4DNFITAJDFZP.bw", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "display_title": "bw", "status": "released", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:40:50.135348+00:00"}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/38c8e15b-c892-4fef-8cb7-ff65b2c46eef/", "display_title": "4DNFITAJDFZP", "status": "released", "uuid": "38c8e15b-c892-4fef-8cb7-ff65b2c46eef", "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": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HAP-1 (Tier 2) DamID-seq None (Control)"}}]}, {"type": "supplementary", "description": "The files associated with the 100kb bin size processing of data for DamID-seq on Hap1 cells (2020-07-01) Dam-only control", "title": "100kb binned files", "files": [{"file_size": 187195, "@type": ["FileProcessed", "File", "Item"], "uuid": "8e01a2d2-ac8f-4710-8cd1-8c7838247e94", "href": "/files-processed/4DNFITGUOMS5/@@download/4DNFITGUOMS5.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (compressed_txt)", "accession": "4DNFITGUOMS5", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8e01a2d2-ac8f-4710-8cd1-8c7838247e94/4DNFITGUOMS5.txt.gz", "md5sum": "fea6548c10e4c18d352c326c33eba47b", "@id": "/files-processed/4DNFITGUOMS5/", "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."], "display_title": "4DNFITGUOMS5.txt.gz", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "dba26778-f40a-4561-a552-65539702ded4", "display_title": "compressed_txt", "status": "released", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:42:26.790379+00:00"}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "100kb binned files", "assay_info": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}}, {"file_size": 324430, "@type": ["FileProcessed", "File", "Item"], "uuid": "cb0d7814-fce1-41f8-8f64-ec2e10ba46d8", "higlass_uid": "dae0455e-81ac-409d-8ab4-f38acb633144", "href": "/files-processed/4DNFIZG4F2FE/@@download/4DNFIZG4F2FE.bw", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (bw)", "accession": "4DNFIZG4F2FE", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/cb0d7814-fce1-41f8-8f64-ec2e10ba46d8/4DNFIZG4F2FE.bw", "md5sum": "cd889714d8c32c6dc3723b0cb0664df4", "@id": "/files-processed/4DNFIZG4F2FE/", "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."], "display_title": "4DNFIZG4F2FE.bw", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "display_title": "bw", "status": "released", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:38:18.637241+00:00"}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/f102afec-6839-4fa5-807d-cc9457b89530/", "display_title": "4DNFIZG4F2FE", "status": "released", "uuid": "f102afec-6839-4fa5-807d-cc9457b89530", "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": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HAP-1 (Tier 2) DamID-seq None (Control)"}}]}], "experiment_type": {"other_tags": ["1D"], "assay_subclassification": "Proximity to Cellular Component", "experiment_category": "Sequencing", "title": "DamID-seq", "display_title": "DamID-seq", "@type": ["ExperimentType", "Item"], "assay_classification": "Linear DNA Enrichment", "@id": "/experiment-types/damid-seq/", "status": "released", "assay_subclass_short": "Proximity-seq", "uuid": "b777a1da-8dc8-4473-9b8d-4f7716fb0a4a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2023-11-03T14:45:05.691570+00:00"}, "external_references": []}, {"files": [{"upload_key": "521a1ba0-d1b0-4039-b7be-dc56c1095dcc/4DNFIC2TQRJU.fastq.gz", "file_type": "reads", "file_type_detailed": "reads (fastq)", "uuid": "521a1ba0-d1b0-4039-b7be-dc56c1095dcc", "@id": "/files-fastq/4DNFIC2TQRJU/", "display_title": "4DNFIC2TQRJU.fastq.gz", "accession": "4DNFIC2TQRJU", "href": "/files-fastq/4DNFIC2TQRJU/@@download/4DNFIC2TQRJU.fastq.gz", "file_classification": "raw file", "file_size": 2041330145, "md5sum": "e9781bd88603c12f4aad9e6bb5dc5b54", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/521a1ba0-d1b0-4039-b7be-dc56c1095dcc/4DNFIC2TQRJU.fastq.gz", "@type": ["FileFastq", "File", "Item"], "status": "released", "lab": {"name": "bas-van-steensel-lab", "@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "display_title": "Bas van Steensel, NKI", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "quality_metric": {"display_title": "QualityMetricFastqc from 2020-07-02", "uuid": "49a91bb2-ff86-44b4-9050-8afb1fd699dc", "overall_quality_status": "PASS", "status": "released", "@id": "/quality-metrics-fastqc/49a91bb2-ff86-44b4-9050-8afb1fd699dc/", "Total Sequences": 42571539, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIC2TQRJU/fastqc_report.html", "Sequence length": "65", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "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": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-damid/4DNEXFXI4QYL/", "accession": "4DNEXFXI4QYL", "display_title": "DamID-seq on HAP-1 (Tier 2) - 4DNEXFXI4QYL", "@type": ["ExperimentDamid", "Experiment", "Item"], "uuid": "9b1775c9-77df-48c8-af85-d07e9143252c", "status": "released", "processed_files": [{"display_title": "4DNFITXSJMY4.bam", "href": "/files-processed/4DNFITXSJMY4/@@download/4DNFITXSJMY4.bam", "uuid": "f6fa4022-4136-4ddc-9aa1-49d94426236a", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f6fa4022-4136-4ddc-9aa1-49d94426236a/4DNFITXSJMY4.bam", "file_format": {"status": "released", "display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_size": 1178535630, "genome_assembly": "GRCh38", "upload_key": "f6fa4022-4136-4ddc-9aa1-49d94426236a/4DNFITXSJMY4.bam", "file_type_detailed": "alignments (bam)", "md5sum": "539b27fb59e38e38c358cdf30a0c5c0c", "accession": "4DNFITXSJMY4", "file_classification": "processed file", "@id": "/files-processed/4DNFITXSJMY4/", "file_type": "alignments", "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."], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "lab": {"@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "status": "current", "@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "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": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "last_modified": {"date_modified": "2024-02-22T17:47:44.021790+00:00"}}], "biosample": {"biosource_summary": "HAP-1 (Tier 2)", "treatments_summary": "None", "accession": "4DNBSAGQ5J7C", "@id": "/biosamples/4DNBSAGQ5J7C/", "biosample_category": ["Tier 2"], "uuid": "d0046e55-9cbe-4bf8-a426-ac7909df06f1", "modifications_summary": "None", "@type": ["Biosample", "Item"], "biosample_type": "immortalized cells", "status": "released", "display_title": "4DNBSAGQ5J7C", "cell_culture_details": [{"in_vitro_differentiated": "No", "@id": "/biosample-cell-cultures/c84331a8-56c4-4087-8cbb-a73b8f3d7c8b/", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "display_title": "BiosampleCellCulture from 2020-07-01", "uuid": "c84331a8-56c4-4087-8cbb-a73b8f3d7c8b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["HAP-1 biosample missing ploidy authentication"], "badge": {"display_title": "Biosample Metadata Incomplete", "warning": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "badge_classification": "Warning", "badge_icon": "/static/img/badges/biosample-icon.svg", "title": "Biosample Metadata Incomplete", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@type": ["Badge", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "biosource": [{"@type": ["Biosource", "Item"], "uuid": "187d7227-366c-4e7d-b9ae-11f27efd4918", "display_title": "HAP-1 (Tier 2) - 4DNSRCVNIBZG", "status": "released", "@id": "/biosources/4DNSRCVNIBZG/", "cell_line_tier": "Tier 2", "biosource_type": "immortalized cell line", "accession": "4DNSRCVNIBZG", "tissue": {"preferred_name": "blood cell", "display_title": "blood cell", "@type": ["OntologyTerm", "Item"], "term_id": "CL:0000081", "status": "released", "@id": "/ontology-terms/CL:0000081/", "uuid": "0d64fbe2-ed5c-43cd-a30d-d9f0320d27ed", "term_name": "blood cell", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "scientific_name": "Homo sapiens", "@id": "/organisms/9606/", "status": "released", "name": "human", "@type": ["Organism", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"@type": ["OntologyTerm", "Item"], "uuid": "57d18eec-d662-4bf7-8000-047de03ad84a", "preferred_name": "HAP-1", "synonyms": ["HAP1"], "status": "released", "term_name": "HAP-1", "term_id": "EFO:0007598", "@id": "/ontology-terms/EFO:0007598/", "display_title": "HAP-1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"tissue_source": "blood cell"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"combined": "Target: None (Control)", "field": "Target", "value": "None (Control)"}, "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 Hap1 cells (2020-07-01) Dam-only control", "title": "gatc binned files", "files": [{"file_size": 51413556, "@type": ["FileProcessed", "File", "Item"], "uuid": "a42258b8-ce12-4d2f-9e57-32dac73af7f8", "href": "/files-processed/4DNFIQNLLS17/@@download/4DNFIQNLLS17.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (compressed_txt)", "accession": "4DNFIQNLLS17", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a42258b8-ce12-4d2f-9e57-32dac73af7f8/4DNFIQNLLS17.txt.gz", "md5sum": "9c137f80f0e9c5e4a4ef66d5b02fd002", "@id": "/files-processed/4DNFIQNLLS17/", "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."], "display_title": "4DNFIQNLLS17.txt.gz", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "dba26778-f40a-4561-a552-65539702ded4", "display_title": "compressed_txt", "status": "released", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:47:40.438379+00:00"}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "gatc binned files", "assay_info": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}}, {"file_size": 41189598, "@type": ["FileProcessed", "File", "Item"], "uuid": "29133914-9c09-4dbe-8fc9-2217869d0f6f", "higlass_uid": "16fe357b-6128-477e-bdae-351e01b9aa5a", "href": "/files-processed/4DNFIG8TP1KG/@@download/4DNFIG8TP1KG.bw", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (bw)", "accession": "4DNFIG8TP1KG", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/29133914-9c09-4dbe-8fc9-2217869d0f6f/4DNFIG8TP1KG.bw", "md5sum": "67f382c231849e913f2776305f354629", "@id": "/files-processed/4DNFIG8TP1KG/", "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."], "display_title": "4DNFIG8TP1KG.bw", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "display_title": "bw", "status": "released", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:41:29.582455+00:00"}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/a2e7e1dd-8021-46bb-b180-74296acab082/", "display_title": "4DNFIG8TP1KG", "status": "released", "uuid": "a2e7e1dd-8021-46bb-b180-74296acab082", "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": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HAP-1 (Tier 2) DamID-seq None (Control)"}}]}, {"type": "supplementary", "description": "The files associated with the 25kb bin size processing of data for DamID-seq on Hap1 cells (2020-07-01) Dam-only control", "title": "25kb binned files", "files": [{"file_size": 739328, "@type": ["FileProcessed", "File", "Item"], "uuid": "e5670e4a-77c5-4cd3-b1de-1a85ceda5ce3", "href": "/files-processed/4DNFIJRMQ7TJ/@@download/4DNFIJRMQ7TJ.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (compressed_txt)", "accession": "4DNFIJRMQ7TJ", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e5670e4a-77c5-4cd3-b1de-1a85ceda5ce3/4DNFIJRMQ7TJ.txt.gz", "md5sum": "90d47551b8364d3ce643d5b24c059f0e", "@id": "/files-processed/4DNFIJRMQ7TJ/", "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."], "display_title": "4DNFIJRMQ7TJ.txt.gz", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "dba26778-f40a-4561-a552-65539702ded4", "display_title": "compressed_txt", "status": "released", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:42:29.524429+00:00"}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "25kb binned files", "assay_info": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}}, {"file_size": 1066769, "@type": ["FileProcessed", "File", "Item"], "uuid": "ec3ef06f-8986-4060-888c-2242ba0d4fd9", "higlass_uid": "131430e5-c9a4-48e8-8a3e-f8bf67e28e4d", "href": "/files-processed/4DNFINME2KCX/@@download/4DNFINME2KCX.bw", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (bw)", "accession": "4DNFINME2KCX", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ec3ef06f-8986-4060-888c-2242ba0d4fd9/4DNFINME2KCX.bw", "md5sum": "3f3ebad192202b18809d67301af420fd", "@id": "/files-processed/4DNFINME2KCX/", "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."], "display_title": "4DNFINME2KCX.bw", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "display_title": "bw", "status": "released", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:39:41.103478+00:00"}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/17934d35-9860-4721-9077-bad95b996916/", "display_title": "4DNFINME2KCX", "status": "released", "uuid": "17934d35-9860-4721-9077-bad95b996916", "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": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HAP-1 (Tier 2) DamID-seq None (Control)"}}]}, {"type": "supplementary", "description": "Additional files associated with the 50kb bin size processing of data for DamID-seq on Hap1 cells (2020-07-01) Dam-only control", "title": "Additional 50kb binned files", "files": [{"file_size": 371495, "@type": ["FileProcessed", "File", "Item"], "uuid": "0251fe38-489d-4c15-9a92-9c10678015e5", "href": "/files-processed/4DNFIIPCMOIS/@@download/4DNFIIPCMOIS.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (compressed_txt)", "accession": "4DNFIIPCMOIS", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/0251fe38-489d-4c15-9a92-9c10678015e5/4DNFIIPCMOIS.txt.gz", "md5sum": "7519c6d879c37c56be67641e640cd45a", "@id": "/files-processed/4DNFIIPCMOIS/", "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."], "display_title": "4DNFIIPCMOIS.txt.gz", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "dba26778-f40a-4561-a552-65539702ded4", "display_title": "compressed_txt", "status": "released", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:40:57.480810+00:00"}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "Additional 50kb binned files", "assay_info": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}}, {"file_size": 583776, "@type": ["FileProcessed", "File", "Item"], "uuid": "4f3c45eb-af07-4fd6-90c9-50774225ea53", "higlass_uid": "be61b71e-dd82-4706-ad16-e33959d0a840", "href": "/files-processed/4DNFI9XYJLPF/@@download/4DNFI9XYJLPF.bw", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (bw)", "accession": "4DNFI9XYJLPF", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/4f3c45eb-af07-4fd6-90c9-50774225ea53/4DNFI9XYJLPF.bw", "md5sum": "b1a81c959f6be2fdc09c17cadfa9fbf8", "@id": "/files-processed/4DNFI9XYJLPF/", "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."], "display_title": "4DNFI9XYJLPF.bw", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "display_title": "bw", "status": "released", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:40:45.092149+00:00"}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/c5424b99-d384-4d15-b1b1-ab06949cc9d5/", "display_title": "4DNFI9XYJLPF", "status": "released", "uuid": "c5424b99-d384-4d15-b1b1-ab06949cc9d5", "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": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HAP-1 (Tier 2) DamID-seq None (Control)"}}]}, {"type": "supplementary", "description": "The files associated with the 100kb bin size processing of data for DamID-seq on Hap1 cells (2020-07-01) Dam-only control", "title": "100kb binned files", "files": [{"file_size": 185187, "@type": ["FileProcessed", "File", "Item"], "uuid": "911d2048-cd13-4752-a1d1-6cf59473218c", "href": "/files-processed/4DNFI612GKM5/@@download/4DNFI612GKM5.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (compressed_txt)", "accession": "4DNFI612GKM5", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/911d2048-cd13-4752-a1d1-6cf59473218c/4DNFI612GKM5.txt.gz", "md5sum": "c8a11774542e2b14ebcbebc0ee43f0e4", "@id": "/files-processed/4DNFI612GKM5/", "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."], "display_title": "4DNFI612GKM5.txt.gz", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "dba26778-f40a-4561-a552-65539702ded4", "display_title": "compressed_txt", "status": "released", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:42:22.411922+00:00"}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "100kb binned files", "assay_info": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}}, {"file_size": 321485, "@type": ["FileProcessed", "File", "Item"], "uuid": "fad11567-9f04-4074-8d75-245ca9bd39dc", "higlass_uid": "dc2127cc-7d00-4870-88ad-1159411438ae", "href": "/files-processed/4DNFI33QJ52F/@@download/4DNFI33QJ52F.bw", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (bw)", "accession": "4DNFI33QJ52F", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/fad11567-9f04-4074-8d75-245ca9bd39dc/4DNFI33QJ52F.bw", "md5sum": "9d40b6fce8851af14695a8f5345f25c8", "@id": "/files-processed/4DNFI33QJ52F/", "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."], "display_title": "4DNFI33QJ52F.bw", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "display_title": "bw", "status": "released", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:38:13.968780+00:00"}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/4eb8adeb-e8c2-413f-96b1-9009fea5677c/", "display_title": "4DNFI33QJ52F", "status": "released", "uuid": "4eb8adeb-e8c2-413f-96b1-9009fea5677c", "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": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HAP-1 (Tier 2) DamID-seq None (Control)"}}]}], "experiment_type": {"other_tags": ["1D"], "assay_subclassification": "Proximity to Cellular Component", "experiment_category": "Sequencing", "title": "DamID-seq", "display_title": "DamID-seq", "@type": ["ExperimentType", "Item"], "assay_classification": "Linear DNA Enrichment", "@id": "/experiment-types/damid-seq/", "status": "released", "assay_subclass_short": "Proximity-seq", "uuid": "b777a1da-8dc8-4473-9b8d-4f7716fb0a4a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2023-11-03T14:45:12.181060+00:00"}, "external_references": []}, {"files": [{"upload_key": "933f182d-433e-4ea8-8adb-0502d4dc94f6/4DNFI9OP7C75.fastq.gz", "file_type": "reads", "file_type_detailed": "reads (fastq)", "uuid": "933f182d-433e-4ea8-8adb-0502d4dc94f6", "@id": "/files-fastq/4DNFI9OP7C75/", "display_title": "4DNFI9OP7C75.fastq.gz", "accession": "4DNFI9OP7C75", "href": "/files-fastq/4DNFI9OP7C75/@@download/4DNFI9OP7C75.fastq.gz", "file_classification": "raw file", "file_size": 1276870782, "md5sum": "bae41d3abbf9af97925cf0c7247eda6d", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/933f182d-433e-4ea8-8adb-0502d4dc94f6/4DNFI9OP7C75.fastq.gz", "@type": ["FileFastq", "File", "Item"], "status": "released", "lab": {"name": "bas-van-steensel-lab", "@id": "/labs/bas-van-steensel-lab/", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "display_title": "Bas van Steensel, NKI", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "quality_metric": {"display_title": "QualityMetricFastqc from 2020-07-02", "uuid": "37636ac6-9696-4802-8705-3b2d4e9f5aa1", "overall_quality_status": "PASS", "status": "released", "@id": "/quality-metrics-fastqc/37636ac6-9696-4802-8705-3b2d4e9f5aa1/", "Total Sequences": 25076883, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI9OP7C75/fastqc_report.html", "Sequence length": "65", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "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": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-damid/4DNEXM4TOFTC/", "accession": "4DNEXM4TOFTC", "display_title": "DamID-seq on HAP-1 (Tier 2) - 4DNEXM4TOFTC", "@type": ["ExperimentDamid", "Experiment", "Item"], "uuid": "25eeff8a-9ff2-4225-9f10-8844705fefdc", "status": "released", "processed_files": [{"display_title": "4DNFIU2EH9PJ.bam", "href": "/files-processed/4DNFIU2EH9PJ/@@download/4DNFIU2EH9PJ.bam", "uuid": "51af630f-0a57-407d-9b5e-209a39e87247", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/51af630f-0a57-407d-9b5e-209a39e87247/4DNFIU2EH9PJ.bam", "file_format": {"status": "released", "display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_size": 780503268, "genome_assembly": "GRCh38", "upload_key": "51af630f-0a57-407d-9b5e-209a39e87247/4DNFIU2EH9PJ.bam", "file_type_detailed": "alignments (bam)", "md5sum": "7720aada86e905b0e594f5fdc3dc546f", "accession": "4DNFIU2EH9PJ", "file_classification": "processed file", "@id": "/files-processed/4DNFIU2EH9PJ/", "file_type": "alignments", "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."], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [], "lab": {"@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "status": "current", "@id": "/labs/bas-van-steensel-lab/", "name": "bas-van-steensel-lab", "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": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}, "last_modified": {"date_modified": "2024-02-22T17:47:26.082941+00:00"}}], "biosample": {"biosource_summary": "HAP-1 (Tier 2)", "treatments_summary": "None", "accession": "4DNBSS67P22E", "@id": "/biosamples/4DNBSS67P22E/", "biosample_category": ["Tier 2"], "uuid": "9b337ee7-08ad-439e-9470-bc47b57f24f0", "modifications_summary": "None", "@type": ["Biosample", "Item"], "biosample_type": "immortalized cells", "status": "released", "display_title": "4DNBSS67P22E", "cell_culture_details": [{"in_vitro_differentiated": "No", "@id": "/biosample-cell-cultures/fe61b845-e21c-4674-8cbb-77a212b3280c/", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "display_title": "BiosampleCellCulture from 2020-07-01", "uuid": "fe61b845-e21c-4674-8cbb-77a212b3280c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["HAP-1 biosample missing ploidy authentication"], "badge": {"display_title": "Biosample Metadata Incomplete", "warning": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "badge_classification": "Warning", "badge_icon": "/static/img/badges/biosample-icon.svg", "title": "Biosample Metadata Incomplete", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@type": ["Badge", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "biosource": [{"@type": ["Biosource", "Item"], "uuid": "187d7227-366c-4e7d-b9ae-11f27efd4918", "display_title": "HAP-1 (Tier 2) - 4DNSRCVNIBZG", "status": "released", "@id": "/biosources/4DNSRCVNIBZG/", "cell_line_tier": "Tier 2", "biosource_type": "immortalized cell line", "accession": "4DNSRCVNIBZG", "tissue": {"preferred_name": "blood cell", "display_title": "blood cell", "@type": ["OntologyTerm", "Item"], "term_id": "CL:0000081", "status": "released", "@id": "/ontology-terms/CL:0000081/", "uuid": "0d64fbe2-ed5c-43cd-a30d-d9f0320d27ed", "term_name": "blood cell", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "scientific_name": "Homo sapiens", "@id": "/organisms/9606/", "status": "released", "name": "human", "@type": ["Organism", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"@type": ["OntologyTerm", "Item"], "uuid": "57d18eec-d662-4bf7-8000-047de03ad84a", "preferred_name": "HAP-1", "synonyms": ["HAP1"], "status": "released", "term_name": "HAP-1", "term_id": "EFO:0007598", "@id": "/ontology-terms/EFO:0007598/", "display_title": "HAP-1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"tissue_source": "blood cell"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"combined": "Target: None (Control)", "field": "Target", "value": "None (Control)"}, "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 Hap1 cells (2020-07-01) Dam-only control", "title": "gatc binned files", "files": [{"file_size": 50422470, "@type": ["FileProcessed", "File", "Item"], "uuid": "0a8c8409-ad9b-4c61-aee1-60b1c1b3ea71", "href": "/files-processed/4DNFIH4RU9QP/@@download/4DNFIH4RU9QP.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (compressed_txt)", "accession": "4DNFIH4RU9QP", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/0a8c8409-ad9b-4c61-aee1-60b1c1b3ea71/4DNFIH4RU9QP.txt.gz", "md5sum": "9ed3b01983a53aa628ff976b9e737038", "@id": "/files-processed/4DNFIH4RU9QP/", "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."], "display_title": "4DNFIH4RU9QP.txt.gz", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "dba26778-f40a-4561-a552-65539702ded4", "display_title": "compressed_txt", "status": "released", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:47:34.570476+00:00"}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "gatc binned files", "assay_info": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}}, {"file_size": 39861230, "@type": ["FileProcessed", "File", "Item"], "uuid": "c871eee8-7b80-4296-9f5f-0f95894c6fc8", "higlass_uid": "96aed730-55f5-4f60-8d39-6ce07380f984", "href": "/files-processed/4DNFI3QFCPIE/@@download/4DNFI3QFCPIE.bw", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (bw)", "accession": "4DNFI3QFCPIE", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c871eee8-7b80-4296-9f5f-0f95894c6fc8/4DNFI3QFCPIE.bw", "md5sum": "703d8a55c1bf7535333fc6acad5224ff", "@id": "/files-processed/4DNFI3QFCPIE/", "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."], "display_title": "4DNFI3QFCPIE.bw", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "display_title": "bw", "status": "released", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:41:23.562390+00:00"}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/4552d59a-38e8-4108-a6af-fe2332f9bf72/", "display_title": "4DNFI3QFCPIE", "status": "released", "uuid": "4552d59a-38e8-4108-a6af-fe2332f9bf72", "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": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HAP-1 (Tier 2) DamID-seq None (Control)"}}]}, {"type": "supplementary", "description": "The files associated with the 25kb bin size processing of data for DamID-seq on Hap1 cells (2020-07-01) Dam-only control", "title": "25kb binned files", "files": [{"file_size": 718596, "@type": ["FileProcessed", "File", "Item"], "uuid": "8461bcd2-b51e-4df4-906e-fbcce058da0f", "href": "/files-processed/4DNFIJPABV3J/@@download/4DNFIJPABV3J.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (compressed_txt)", "accession": "4DNFIJPABV3J", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8461bcd2-b51e-4df4-906e-fbcce058da0f/4DNFIJPABV3J.txt.gz", "md5sum": "cc19cfa3b0a25cc171c26659082967f6", "@id": "/files-processed/4DNFIJPABV3J/", "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."], "display_title": "4DNFIJPABV3J.txt.gz", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "dba26778-f40a-4561-a552-65539702ded4", "display_title": "compressed_txt", "status": "released", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:42:25.212948+00:00"}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "25kb binned files", "assay_info": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}}, {"file_size": 1026051, "@type": ["FileProcessed", "File", "Item"], "uuid": "9b0c23a4-ce2b-406b-8994-f38bac45f383", "higlass_uid": "36bb68a1-a5f7-4a63-bf58-3a753ca9e46a", "href": "/files-processed/4DNFIX7VUYVN/@@download/4DNFIX7VUYVN.bw", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (bw)", "accession": "4DNFIX7VUYVN", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/9b0c23a4-ce2b-406b-8994-f38bac45f383/4DNFIX7VUYVN.bw", "md5sum": "5247e4f467ab9f3bf449de1a673b6e10", "@id": "/files-processed/4DNFIX7VUYVN/", "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."], "display_title": "4DNFIX7VUYVN.bw", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "display_title": "bw", "status": "released", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:39:36.726422+00:00"}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/a996ad60-4c02-4184-9b50-74437ce5609c/", "display_title": "4DNFIX7VUYVN", "status": "released", "uuid": "a996ad60-4c02-4184-9b50-74437ce5609c", "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": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HAP-1 (Tier 2) DamID-seq None (Control)"}}]}, {"type": "supplementary", "description": "Additional files associated with the 50kb bin size processing of data for DamID-seq on Hap1 cells (2020-07-01) Dam-only control", "title": "Additional 50kb binned files", "files": [{"file_size": 361343, "@type": ["FileProcessed", "File", "Item"], "uuid": "e19327c7-33bb-4bce-96ed-8c341ab440ed", "href": "/files-processed/4DNFIEIPU1KN/@@download/4DNFIEIPU1KN.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (compressed_txt)", "accession": "4DNFIEIPU1KN", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e19327c7-33bb-4bce-96ed-8c341ab440ed/4DNFIEIPU1KN.txt.gz", "md5sum": "94d2710a5a7e4eb2f9870c10b5278ad7", "@id": "/files-processed/4DNFIEIPU1KN/", "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."], "display_title": "4DNFIEIPU1KN.txt.gz", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "dba26778-f40a-4561-a552-65539702ded4", "display_title": "compressed_txt", "status": "released", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:40:52.469964+00:00"}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "Additional 50kb binned files", "assay_info": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}}, {"file_size": 562597, "@type": ["FileProcessed", "File", "Item"], "uuid": "1d074bc2-a2d7-4298-8f1f-6dc40216bd47", "higlass_uid": "7d684bc5-cdf7-402f-a879-fd4fd24960c2", "href": "/files-processed/4DNFIK7ZD3Y4/@@download/4DNFIK7ZD3Y4.bw", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (bw)", "accession": "4DNFIK7ZD3Y4", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/1d074bc2-a2d7-4298-8f1f-6dc40216bd47/4DNFIK7ZD3Y4.bw", "md5sum": "360e0792f7a66e34ce2bedc032105a2c", "@id": "/files-processed/4DNFIK7ZD3Y4/", "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."], "display_title": "4DNFIK7ZD3Y4.bw", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "display_title": "bw", "status": "released", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:40:40.530153+00:00"}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/cdcaeede-1f0c-46c1-b213-9f1e91628c3a/", "display_title": "4DNFIK7ZD3Y4", "status": "released", "uuid": "cdcaeede-1f0c-46c1-b213-9f1e91628c3a", "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": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HAP-1 (Tier 2) DamID-seq None (Control)"}}]}, {"type": "supplementary", "description": "The files associated with the 100kb bin size processing of data for DamID-seq on Hap1 cells (2020-07-01) Dam-only control", "title": "100kb binned files", "files": [{"file_size": 181223, "@type": ["FileProcessed", "File", "Item"], "uuid": "afa3ce95-76cd-47da-b866-03e28d1bf2da", "href": "/files-processed/4DNFI4CFRF9K/@@download/4DNFI4CFRF9K.txt.gz", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (compressed_txt)", "accession": "4DNFI4CFRF9K", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/afa3ce95-76cd-47da-b866-03e28d1bf2da/4DNFI4CFRF9K.txt.gz", "md5sum": "fc71557b478152d53b43e2e80830e657", "@id": "/files-processed/4DNFI4CFRF9K/", "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."], "display_title": "4DNFI4CFRF9K.txt.gz", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "dba26778-f40a-4561-a552-65539702ded4", "display_title": "compressed_txt", "status": "released", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:42:17.674856+00:00"}, "track_and_facet_info": {"experimental_lab": "Bas van Steensel, NKI", "experiment_type": "DamID-seq", "experiment_bucket": "100kb binned files", "assay_info": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI"}}, {"file_size": 313471, "@type": ["FileProcessed", "File", "Item"], "uuid": "50c044b7-fffb-4571-8173-37502b7c72f4", "higlass_uid": "bee2d206-1942-4d23-bcd3-7ed01f1f8151", "href": "/files-processed/4DNFIN9GE3RD/@@download/4DNFIN9GE3RD.bw", "genome_assembly": "GRCh38", "file_type": "counts", "status": "released", "file_type_detailed": "counts (bw)", "accession": "4DNFIN9GE3RD", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/50c044b7-fffb-4571-8173-37502b7c72f4/4DNFIN9GE3RD.bw", "md5sum": "8d30cbb1511a8c34e5b42ebddc28543a", "@id": "/files-processed/4DNFIN9GE3RD/", "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."], "display_title": "4DNFIN9GE3RD.bw", "lab": {"status": "current", "@id": "/labs/bas-van-steensel-lab/", "@type": ["Lab", "Item"], "display_title": "Bas van Steensel, NKI", "uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "name": "bas-van-steensel-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "display_title": "bw", "status": "released", "file_format": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-02-22T17:38:09.601051+00:00"}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/78772582-6b17-453f-95ab-be20bdb81621/", "display_title": "4DNFIN9GE3RD", "status": "released", "uuid": "78772582-6b17-453f-95ab-be20bdb81621", "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": "None (Control)", "dataset": "DamID-seq on Hap1 cells (2020-07-01)", "condition": "Dam-only control", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "HAP-1 (Tier 2)", "lab_name": "Bas van Steensel, NKI", "track_title": "counts for HAP-1 (Tier 2) DamID-seq None (Control)"}}]}], "experiment_type": {"other_tags": ["1D"], "assay_subclassification": "Proximity to Cellular Component", "experiment_category": "Sequencing", "title": "DamID-seq", "display_title": "DamID-seq", "@type": ["ExperimentType", "Item"], "assay_classification": "Linear DNA Enrichment", "@id": "/experiment-types/damid-seq/", "status": "released", "assay_subclass_short": "Proximity-seq", "uuid": "b777a1da-8dc8-4473-9b8d-4f7716fb0a4a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2023-11-03T14:45:16.154682+00:00"}, "external_references": []}], "experimentset_type": "replicate", "other_processed_files": [{"type": "supplementary", "files": [], "title": "gatc binned files", "higlass_item_uuid": null, "higlass_view_config": {"uuid": "ad77a6c2-9a38-4a8a-9f09-d4e8da018877", "@id": "/higlass-view-configs/ad77a6c2-9a38-4a8a-9f09-d4e8da018877/", "status": "released", "display_title": "4DNESUSK2C6C - gatc binned files", "description": "Supplementary Files (gatc binned files) for 4DNESUSK2C6C (DamID for Dam on Hap1 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): 4DNFI5R3LIZR, 4DNFIG8TP1KG, 4DNFI3QFCPIE", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}, "last_modified": {"date_modified": "2023-11-03T14:44:36.101220+00:00"}}}, {"type": "supplementary", "files": [], "title": "25kb binned files", "higlass_item_uuid": null, "higlass_view_config": {"uuid": "b68dcd40-c868-4c0e-bb22-60f48e1a534e", "@id": "/higlass-view-configs/b68dcd40-c868-4c0e-bb22-60f48e1a534e/", "status": "released", "display_title": "4DNESUSK2C6C - 25kb binned files", "description": "Supplementary Files (25kb binned files) for 4DNESUSK2C6C (DamID for Dam on Hap1 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): 4DNFIKHJZIJ4, 4DNFINME2KCX, 4DNFIX7VUYVN", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}, "last_modified": {"date_modified": "2023-11-03T14:44:36.029859+00:00"}}}, {"type": "supplementary", "files": [], "title": "Additional 50kb binned files", "higlass_item_uuid": null, "higlass_view_config": {"uuid": "f9810944-746a-49cd-8ac3-b048304295e1", "@id": "/higlass-view-configs/f9810944-746a-49cd-8ac3-b048304295e1/", "status": "released", "display_title": "4DNESUSK2C6C - Additional 50kb binned files", "description": "Supplementary Files (Additional 50kb binned files) for 4DNESUSK2C6C (DamID for Dam on Hap1 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): 4DNFITAJDFZP, 4DNFI9XYJLPF, 4DNFIK7ZD3Y4", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}, "last_modified": {"date_modified": "2023-11-03T14:44:35.346065+00:00"}}}, {"type": "supplementary", "files": [], "title": "100kb binned files", "higlass_item_uuid": null, "higlass_view_config": {"uuid": "c22ebd56-f284-4214-a3b2-f4d05d88fb1a", "@id": "/higlass-view-configs/c22ebd56-f284-4214-a3b2-f4d05d88fb1a/", "status": "released", "display_title": "4DNESUSK2C6C - 100kb binned files", "description": "Supplementary Files (100kb binned files) for 4DNESUSK2C6C (DamID for Dam on Hap1 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): 4DNFIZG4F2FE, 4DNFI33QJ52F, 4DNFIN9GE3RD", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}, "last_modified": {"date_modified": "2023-11-03T14:44:38.219712+00:00"}}}], "@id": "/experiment-set-replicates/4DNESUSK2C6C/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "e6162a0b-af7d-443c-bfca-c599ba8f8d79", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESUSK2C6C", "external_references": [], "pubs_using": [], "publications_of_set": [], "number_of_experiments": 3, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSRHSL3C5/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["HAP-1 biosample missing ploidy authentication"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}, {"parent": "/biosamples/4DNBSAGQ5J7C/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["HAP-1 biosample missing ploidy authentication"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}, {"parent": "/biosamples/4DNBSS67P22E/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["HAP-1 biosample missing ploidy authentication"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}]}, "validation-errors": []}