{"lab": {"status": "current", "correspondence": [{"contact_email": "am9iLmRla2tlckB1bWFzc21lZC5lZHU=", "@id": "/users/83b5073a-069b-4162-9b30-6f42d5551e34/", "display_title": "Job Dekker"}], "@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "title": "Job Dekker, UMMS", "display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "tags": ["deep_data", "matrix_project"], "award": {"@type": ["Award", "Item"], "center_title": "NOFIC - Dekker", "project": "4DN", "description": "NOFIC: The spatial organization of the genome impinges on all genomic processes, including gene regulation, maintenance of genome stability and chromosome transmission to daughter cells. A detailed understanding of the spatial arrangement of the human genome, referred to as the 4D nucleome, and the biological and physical principles that drive chromosome folding requires combining approaches from the fields of molecular and cell biology, imaging, genetics and genomics with approaches from physics, computational biology, and computer simulation. We have assembled a highly interdisciplinary center with the goal of generating extensively validated maps of the 4D nucleome, its physical and dynamic properties and its role in regulating the activity of the genome. First, the center will further optimize and extensively validate a suite of genome-wide molecular methodologies, based on chromosome conformation capture (3C) that can probe the folding of chromosomes at the scale of single nucleosomes, chromatin fibers, chromosomes and the entire nucleus, across cell populations and in single cells. Given that chromosome and nuclear organization is tightly linked to biological state of the cell, the center will map the 4D nucleome for four key biological states representing different conformations during the cell cycle (interphase and mitosis), and during cell differentiation (pluripotent and differentiated states). We will obtain complementary data regarding the structure and dynamics of chromatin, at different length scales and in single cells using extensive high-throughput imaging, live cell imaging and super resolution microscopy. Data obtained with all approaches will be analyzed, integrated and modeled using a set of methods we will further develop to gain insights into the structure, physics and dynamics of chromosome folding over different length scales. Finally, a critical component of our proposal is the biological validation and further elaboration of the chromatin interaction maps that are generated from our conformational analyses. This validation will be achieved through site-specific editing of genomic sequence and epigenetic marks, the creation of new contact points within the genome, and the identification of factors (both protein and nucleic acid) that facilitat or restrict these interactions. Effects of such perturbations in the chromosome conformation on transcription will reveal relationships between specific chromosome structural features and gene expression.", "display_title": "CENTER FOR 3D STRUCTURE AND PHYSICS OF THE GENOME", "status": "current", "uuid": "ae6c618f-7a8c-441e-a886-e30bbbe591da", "@id": "/awards/1U54DK107980-01/", "name": "1U54DK107980-01", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "study": "Experimental Protocol Variations", "badges": [{"badge": {"title": "Inconsistent Replicate Info", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "display_title": "Inconsistent Replicate Info", "badge_classification": "Warning", "warning": "Inconsistent Replicate Info", "@type": ["Badge", "Item"], "status": "released", "@id": "/badges/inconsistent-replicate-info/", "description": "The experimental replicates belonging to this Experiment Set differ in some specific metadata fields", "uuid": "a4df9ff7-fe85-4672-86ac-7c38b5d9c853", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Inconsistent replicate information in average_fragment_size: 200, 350", "Inconsistent replicate information in fragment_size_range: 180-300, 250-450"]}], "status": "released", "aliases": ["dekker-lab:ExperimentSet_U54-Deep_U54-END-FA-DpnII"], "accession": "4DNESCOQ5YRS", "condition": "Formaldehyde, DpnII", "description": "Hi-C experiments on H1 derived endoderm, differentiated using the protocol from Rene Maehr lab. Cells crosslinked with FA and digested with DpnII.", "study_group": "Single Time Point and Condition", "date_created": "2020-06-24T20:17:53.239619+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "Hi-C on H1-DE cells - protocol variations", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-12-05T16:46:14.768603+00:00"}, "public_release": "2021-01-04", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "2e5dd7d1-1fbb-4dfa-bcab-70aee32cd3b2", "@id": "/experiments-hi-c/4DNEXN2ETG7Z/", "accession": "4DNEXN2ETG7Z", "display_title": "in situ Hi-C on H1-hESC differentiated to definitive endoderm with DpnII - 4DNEXN2ETG7Z", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "3b8562d5-3a09-4749-ae49-9597f4a12cf9", "@id": "/experiments-hi-c/4DNEXS6NBDQB/", "accession": "4DNEXS6NBDQB", "display_title": "in situ Hi-C on H1-hESC differentiated to definitive endoderm with DpnII - 4DNEXS6NBDQB", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"award": {"uuid": "ae6c618f-7a8c-441e-a886-e30bbbe591da", "@id": "/awards/1U54DK107980-01/", "status": "current", "@type": ["Award", "Item"], "display_title": "CENTER FOR 3D STRUCTURE AND PHYSICS OF THE GENOME", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "03f2d9e9-74bf-48cc-87d3-b67a7e5a53c5", "title": "4DNESCOQ5YRS - Processed files", "contributing_labs": [], "name": "03f2d9e9-74bf-48cc-87d3-b67a7e5a53c5", "@id": "/higlass-view-configs/03f2d9e9-74bf-48cc-87d3-b67a7e5a53c5/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "display_title": "4DNESCOQ5YRS - Processed files", "description": "4DNESCOQ5YRS (Hi-C experiments on H1 derived endoderm, differentiated using the protocol from Rene Maehr lab. Cells crosslinked with FA and digested with DpnII.): 4DNFIW8IXCX1, 4DNFIW89DNDQ, 4DNFIDM7UPM9, 4DNFI1RLNQI7", "filetype": "HiglassViewConfig", "lab": {"status": "current", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}, "location": "tab:processed-files", "description": "auto_generated_higlass_view_config"}], "static_headers": [{"lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "status": "current", "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": {"status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@type": ["Award", "Item"], "@id": "/awards/1U01CA200059-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Data Usage Guidelines", "status": "released", "aliases": [], "options": {"filetype": "md", "title_icon": "exclamation-circle", "collapsible": false, "default_open": true}, "date_created": "2018-08-06T03:09:55.543206+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-05-09T09:31:34.537494+00:00"}, "schema_version": "2", "@id": "/static-sections/621e8359-3885-40ce-965d-91894aa7b758/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "621e8359-3885-40ce-965d-91894aa7b758", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267228139"]}, "display_title": "Data Usage Guidelines", "external_references": [], "content": "\n**Data Use Guidelines:** This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) \nand the 4DN Data Portal paper \n([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p><strong>Data Use Guidelines:</strong> This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n(<a href=\"https://doi.org/10.1038/nature23884\" rel=\"noopener noreferrer\" target=\"_blank\">doi:10.1038/nature23884</a>) \nand the 4DN Data Portal paper \n(<a href=\"https://doi.org/10.1038/s41467-022-29697-4\" rel=\"noopener noreferrer\" target=\"_blank\">doi:10.1038/s41467-022-29697-4</a>), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the <a href=\"mailto:support@4dnucleome.org\">Data Coordination and Integration Center</a>.</p></div>"}, {"lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "<b>In Situ Hi-C</b>\n\n<p>\n   In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed <i>in situ</i> inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n</p>\n<p>\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n</p>\n<p>\nSee <a href=\"https://www.sciencedirect.com/science/article/pii/S0092867414014974?via%3Dihub\">Rao et al., 2014</a> for more details.\n</p>\n\n<div>\n<img style=\"width: 600px;max-width:100%;\" src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/IsHC_fig1.png\"/>\n  <br/><br/>\n  <em>Image source: Rao et al., 2014, Figure 1A</em>\n</div>", "name": "item-page-headers.ExperimentType.insituhic", "award": {"status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@type": ["Award", "Item"], "@id": "/awards/1U01CA200059-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Assay Description", "status": "released", "aliases": ["4dn-dcic-lab:experiment_infobox_hic"], "options": {"filetype": "html", "collapsible": false, "default_open": false, "convert_ext_links": true}, "date_created": "2018-09-07T18:19:43.777198+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-11-09T14:48:01.220007+00:00"}, "schema_version": "2", "@id": "/static-sections/298554ad-20e2-4449-a752-ac190123dab7/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "298554ad-20e2-4449-a752-ac190123dab7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.56c9c683-bb11-471b-b590-c656f7dc03c1"]}, "display_title": "Assay Description", "external_references": [], "content": "<b>In Situ Hi-C</b>\n\n<p>\n   In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed <i>in situ</i> inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n</p>\n<p>\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n</p>\n<p>\nSee <a href=\"https://www.sciencedirect.com/science/article/pii/S0092867414014974?via%3Dihub\">Rao et al., 2014</a> for more details.\n</p>\n\n<div>\n<img style=\"width: 600px;max-width:100%;\" src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/IsHC_fig1.png\"/>\n  <br/><br/>\n  <em>Image source: Rao et al., 2014, Figure 1A</em>\n</div>", "filetype": "html", "content_as_html": "<div class=\"html-container\"><b>In Situ Hi-C</b>\n<p>\n   In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed <i>in situ</i> inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n</p>\n<p>\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n</p>\n<p>\nSee <a href=\"https://www.sciencedirect.com/science/article/pii/S0092867414014974?via%3Dihub\" rel=\"noopener noreferrer\" target=\"_blank\">Rao et al., 2014</a> for more details.\n</p>\n<div>\n<img src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/IsHC_fig1.png\" style=\"width: 600px;max-width:100%;\"/>\n<br/><br/>\n<em>Image source: Rao et al., 2014, Figure 1A</em>\n</div></div>"}], "processed_files": [{"accession": "4DNFI3ZVW336", "@type": ["FileProcessed", "File", "Item"], "genome_assembly": "GRCh38", "file_type_detailed": "contact list-combined (pairs)", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "display_title": "pairs", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFI3ZVW336.pairs.gz", "md5sum": "0bca18c3c3b92f24dc571cad3e87d6f7", "file_type": "contact list-combined", "file_classification": "processed file", "file_size": 51873563773, "upload_key": "fd26fb44-2ee6-47fe-92ed-8df29d2c54ec/4DNFI3ZVW336.pairs.gz", "@id": "/files-processed/4DNFI3ZVW336/", "href": "/files-processed/4DNFI3ZVW336/@@download/4DNFI3ZVW336.pairs.gz", "uuid": "fd26fb44-2ee6-47fe-92ed-8df29d2c54ec", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/fd26fb44-2ee6-47fe-92ed-8df29d2c54ec/4DNFI3ZVW336.pairs.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "extra_files": [{"href": "/files-processed/4DNFI3ZVW336/@@download/4DNFI3ZVW336.pairs.gz.px2", "file_size": 18219860, "md5sum": "6fffacf5eb8bb600a54682785dae9530", "file_format": {"@id": "/file-formats/pairs_px2/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "display_title": "pairs_px2", "file_format": "pairs_px2", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"Total reads": 2689784220, "status": "released", "display_title": "QualityMetricPairsqc from 2020-07-05", "uuid": "acb2f945-6fb8-481d-b208-a7eb8e759f1b", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "@id": "/quality-metrics-pairsqc/acb2f945-6fb8-481d-b208-a7eb8e759f1b/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI3ZVW336/pairsqc_report.html", "overall_quality_status": "PASS", "quality_metric_summary": [{"title": "Filtered Reads", "value": "2689784220", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "34.679", "tooltip": "Percent of filtered reads (=932.79m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "21.29", "tooltip": "Percent of filtered reads (=572.65m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "44.031", "tooltip": "Percent of filtered reads (=1184.35m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "name": "job-dekker-lab", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "external_references": [], "track_and_facet_info": {"dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}, "last_modified": {"date_modified": "2021-04-06T20:15:20.653237+00:00"}}, {"accession": "4DNFIJWBWE41", "@type": ["FileProcessed", "File", "Item"], "genome_assembly": "GRCh38", "file_type_detailed": "contact matrix (hic)", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/hic/", "display_title": "hic", "status": "released", "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFIJWBWE41.hic", "md5sum": "b7fffbd0432b2cb500858bae34f8d577", "file_type": "contact matrix", "file_classification": "processed file", "file_size": 20654947439, "upload_key": "f2702a45-3e8b-4980-bcd5-6bb0e291614f/4DNFIJWBWE41.hic", "@id": "/files-processed/4DNFIJWBWE41/", "href": "/files-processed/4DNFIJWBWE41/@@download/4DNFIJWBWE41.hic", "uuid": "f2702a45-3e8b-4980-bcd5-6bb0e291614f", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f2702a45-3e8b-4980-bcd5-6bb0e291614f/4DNFIJWBWE41.hic", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "lab": {"status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "name": "job-dekker-lab", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "external_references": [], "track_and_facet_info": {"dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}, "last_modified": {"date_modified": "2021-03-28T14:24:47.686813+00:00"}}, {"accession": "4DNFIW8IXCX1", "higlass_uid": "88fe6842-75a9-459e-a5cc-b2c969bd104a", "@type": ["FileProcessed", "File", "Item"], "genome_assembly": "GRCh38", "file_type_detailed": "contact matrix (mcool)", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/mcool/", "display_title": "mcool", "status": "released", "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFIW8IXCX1.mcool", "notes_to_tsv": ["WARNING - Due to a bug in the version of cooler (0.8.3) used in the current 4DN standard Hi-C processing pipeline some pixels may occur mulitple times at a single resolution with different counts being reported for each occurence.  This duplication does not affect the higlass display of these files, howevver, downstream analyses using this file may encounter issues due to this pixel duplication.  The counts from the duplicate pixels can be aggregated to determine the correct count value at that location. If this issue is problematic for your needs you should consider regenerating the matrices from the merged pairs file of the associated dataset using a more recent version of cooler.  We are working to update the pipeline but do not yet have a predicted date for when this issue will be resolved."], "md5sum": "e4c53a162bd61839810c845015159cba", "file_type": "contact matrix", "file_classification": "processed file", "file_size": 14340083604, "upload_key": "4c1a3f71-5171-483c-b472-f47e81c943ae/4DNFIW8IXCX1.mcool", "@id": "/files-processed/4DNFIW8IXCX1/", "href": "/files-processed/4DNFIW8IXCX1/@@download/4DNFIW8IXCX1.mcool", "uuid": "4c1a3f71-5171-483c-b472-f47e81c943ae", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/4c1a3f71-5171-483c-b472-f47e81c943ae/4DNFIW8IXCX1.mcool", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"status": "released", "display_title": "QualityMetricMcool from 2021-05-21", "uuid": "4b07577e-eb22-4a45-ad69-5c6934ab40c3", "@type": ["QualityMetricMcool", "QualityMetric", "Item"], "@id": "/quality-metrics-mcool/4b07577e-eb22-4a45-ad69-5c6934ab40c3/", "overall_quality_status": "PASS", "quality_metric_summary": [{"title": "Failed Balancing", "value": "None", "tooltip": "Resolutions where balancing failed", "numberType": "string"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "name": "job-dekker-lab", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "external_references": [], "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"@id": "/higlass-view-configs/b141da74-9eaf-4f63-82ab-0537983f15ad/", "status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "b141da74-9eaf-4f63-82ab-0537983f15ad", "display_title": "4DNFIW8IXCX1 - contact matrix for H1-hESC differentiated to definitive endoderm in situ Hi-C DpnII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "track_and_facet_info": {"dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS", "track_title": "contact matrix for H1-hESC differentiated to definitive endoderm in situ Hi-C DpnII"}, "last_modified": {"date_modified": "2023-08-25T17:49:23.978301+00:00"}}, {"accession": "4DNFIW89DNDQ", "higlass_uid": "K0FqoCXvRLqcz5I2XvsA0w", "@type": ["FileProcessed", "File", "Item"], "genome_assembly": "GRCh38", "file_type_detailed": "boundaries (bed)", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bed/", "display_title": "bed", "status": "released", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFIW89DNDQ.bed.gz", "md5sum": "7a13a42b4b8b4ab92fc76b1489b965ed", "file_type": "boundaries", "file_classification": "processed file", "file_size": 152264, "upload_key": "fd1c070d-12e8-40ad-9ea8-06bb10ac71d2/4DNFIW89DNDQ.bed.gz", "@id": "/files-processed/4DNFIW89DNDQ/", "href": "/files-processed/4DNFIW89DNDQ/@@download/4DNFIW89DNDQ.bed.gz", "uuid": "fd1c070d-12e8-40ad-9ea8-06bb10ac71d2", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/fd1c070d-12e8-40ad-9ea8-06bb10ac71d2/4DNFIW89DNDQ.bed.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "extra_files": [{"href": "/files-processed/4DNFIW89DNDQ/@@download/4DNFIW89DNDQ.beddb", "use_for": "visualization", "md5sum": "fad90a76c040500c3a960ec8ec2a3060", "file_format": {"@id": "/file-formats/beddb/", "uuid": "76dc8c06-67d8-487b-8fc8-d841752a0b60", "display_title": "beddb", "file_format": "beddb", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "name": "job-dekker-lab", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "external_references": [], "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"@id": "/higlass-view-configs/4fc5eb64-5690-4498-b553-8935c68ad4ba/", "status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "4fc5eb64-5690-4498-b553-8935c68ad4ba", "display_title": "4DNFIW89DNDQ - boundaries for H1-hESC differentiated to definitive endoderm in situ Hi-C DpnII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "track_and_facet_info": {"dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS", "track_title": "boundaries for H1-hESC differentiated to definitive endoderm in situ Hi-C DpnII"}, "last_modified": {"date_modified": "2021-05-10T23:48:55.583157+00:00"}}, {"accession": "4DNFIDM7UPM9", "higlass_uid": "daeaaa12-1714-4ec8-b919-2debbba3b1b0", "@type": ["FileProcessed", "File", "Item"], "genome_assembly": "GRCh38", "file_type_detailed": "insulation score-diamond (bw)", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "display_title": "bw", "status": "released", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFIDM7UPM9.bw", "md5sum": "66dfb601deb8d30c9bfbf8e37fe86c50", "file_type": "insulation score-diamond", "file_classification": "processed file", "file_size": 8507963, "upload_key": "a5c8b445-6eae-45cb-a2ed-ab387aa16482/4DNFIDM7UPM9.bw", "@id": "/files-processed/4DNFIDM7UPM9/", "href": "/files-processed/4DNFIDM7UPM9/@@download/4DNFIDM7UPM9.bw", "uuid": "a5c8b445-6eae-45cb-a2ed-ab387aa16482", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a5c8b445-6eae-45cb-a2ed-ab387aa16482/4DNFIDM7UPM9.bw", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "lab": {"status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "name": "job-dekker-lab", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "external_references": [], "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"@id": "/higlass-view-configs/c23093c9-a6c9-4ac8-9ae0-888084cd96fd/", "status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "c23093c9-a6c9-4ac8-9ae0-888084cd96fd", "display_title": "4DNFIDM7UPM9 - insulation score-diamond for H1-hESC differentiated to definitive endoderm in situ Hi-C DpnII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "track_and_facet_info": {"dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS", "track_title": "insulation score-diamond for H1-hESC differentiated to definitive endoderm in situ Hi-C DpnII"}, "last_modified": {"date_modified": "2021-03-28T14:04:30.477245+00:00"}}, {"accession": "4DNFI1RLNQI7", "higlass_uid": "5fb398e1-4c74-4c4d-b4c3-207711e7eeb2", "@type": ["FileProcessed", "File", "Item"], "genome_assembly": "GRCh38", "file_type_detailed": "compartments (bw)", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "display_title": "bw", "status": "released", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFI1RLNQI7.bw", "md5sum": "2f9e39efa2095c0e25ba8c48bbe00425", "file_type": "compartments", "file_classification": "processed file", "file_size": 212824, "upload_key": "d1af9a08-39a4-423e-be42-148fb81781cd/4DNFI1RLNQI7.bw", "@id": "/files-processed/4DNFI1RLNQI7/", "href": "/files-processed/4DNFI1RLNQI7/@@download/4DNFI1RLNQI7.bw", "uuid": "d1af9a08-39a4-423e-be42-148fb81781cd", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/d1af9a08-39a4-423e-be42-148fb81781cd/4DNFI1RLNQI7.bw", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "lab": {"status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "name": "job-dekker-lab", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "external_references": [], "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"@id": "/higlass-view-configs/bace709c-01f0-4e54-8075-37ec73ebb290/", "status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "bace709c-01f0-4e54-8075-37ec73ebb290", "display_title": "4DNFI1RLNQI7 - compartments for H1-hESC differentiated to definitive endoderm in situ Hi-C DpnII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "track_and_facet_info": {"dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS", "track_title": "compartments for H1-hESC differentiated to definitive endoderm in situ Hi-C DpnII"}, "last_modified": {"date_modified": "2021-03-28T14:51:39.637027+00:00"}}], "project_release": "2020-08-11", "experiments_in_set": [{"files": [{"accession": "4DNFIVGIOWE4", "file_size": 10807863846, "md5sum": "f64d722a9d426da85da5c5b7d727d51d", "display_title": "4DNFIVGIOWE4.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/c75485e2-3f5a-41bc-968e-a2c5debade0c/4DNFIVGIOWE4.fastq.gz", "href": "/files-fastq/4DNFIVGIOWE4/@@download/4DNFIVGIOWE4.fastq.gz", "paired_end": "1", "uuid": "c75485e2-3f5a-41bc-968e-a2c5debade0c", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "c75485e2-3f5a-41bc-968e-a2c5debade0c/4DNFIVGIOWE4.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIVGIOWE4/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIHAPRYS5.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIHAPRYS5", "file_type": "reads", "uuid": "afd0bf99-f495-4e55-89b0-2e081921e48f", "paired_end": "2", "@id": "/files-fastq/4DNFIHAPRYS5/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 346764759, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "b9028eab-6fc2-4da2-98e7-9117a205a4db", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/b9028eab-6fc2-4da2-98e7-9117a205a4db/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIVGIOWE4/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIHAPRYS5", "file_size": 11507227589, "md5sum": "ee362ebd953e2e527e86210bdea61772", "display_title": "4DNFIHAPRYS5.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/afd0bf99-f495-4e55-89b0-2e081921e48f/4DNFIHAPRYS5.fastq.gz", "href": "/files-fastq/4DNFIHAPRYS5/@@download/4DNFIHAPRYS5.fastq.gz", "paired_end": "2", "uuid": "afd0bf99-f495-4e55-89b0-2e081921e48f", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "afd0bf99-f495-4e55-89b0-2e081921e48f/4DNFIHAPRYS5.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIHAPRYS5/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIVGIOWE4.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIVGIOWE4", "file_type": "reads", "uuid": "c75485e2-3f5a-41bc-968e-a2c5debade0c", "paired_end": "1", "@id": "/files-fastq/4DNFIVGIOWE4/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 346764759, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "bdbbbf23-d0d3-4c73-b0b8-d209df82ef40", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/bdbbbf23-d0d3-4c73-b0b8-d209df82ef40/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIHAPRYS5/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIBL1BTJY", "file_size": 10766233164, "md5sum": "bae4a5195968c35eae54757fba4be1ac", "display_title": "4DNFIBL1BTJY.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/075b27bc-c390-4f39-b857-2e8eb4f1d0e3/4DNFIBL1BTJY.fastq.gz", "href": "/files-fastq/4DNFIBL1BTJY/@@download/4DNFIBL1BTJY.fastq.gz", "paired_end": "1", "uuid": "075b27bc-c390-4f39-b857-2e8eb4f1d0e3", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "075b27bc-c390-4f39-b857-2e8eb4f1d0e3/4DNFIBL1BTJY.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIBL1BTJY/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFI6CSFBJU.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFI6CSFBJU", "file_type": "reads", "uuid": "045cebb5-b8d2-444d-8b0e-cbfd077afe37", "paired_end": "2", "@id": "/files-fastq/4DNFI6CSFBJU/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 349508033, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "f4944bf2-6104-494a-87f1-0290652da6fe", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/f4944bf2-6104-494a-87f1-0290652da6fe/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIBL1BTJY/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFI6CSFBJU", "file_size": 11552812969, "md5sum": "a8a406598f52424e7b8cd4509996b7a9", "display_title": "4DNFI6CSFBJU.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/045cebb5-b8d2-444d-8b0e-cbfd077afe37/4DNFI6CSFBJU.fastq.gz", "href": "/files-fastq/4DNFI6CSFBJU/@@download/4DNFI6CSFBJU.fastq.gz", "paired_end": "2", "uuid": "045cebb5-b8d2-444d-8b0e-cbfd077afe37", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "045cebb5-b8d2-444d-8b0e-cbfd077afe37/4DNFI6CSFBJU.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFI6CSFBJU/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIBL1BTJY.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIBL1BTJY", "file_type": "reads", "uuid": "075b27bc-c390-4f39-b857-2e8eb4f1d0e3", "paired_end": "1", "@id": "/files-fastq/4DNFIBL1BTJY/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 349508033, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "f47aed14-b5aa-45c0-bbd6-6304f0ffc5cb", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/f47aed14-b5aa-45c0-bbd6-6304f0ffc5cb/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI6CSFBJU/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIRCN4NVZ", "file_size": 10687812169, "md5sum": "ba65276322e07c6179c6030c4b195043", "display_title": "4DNFIRCN4NVZ.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/6234e60c-ad97-4414-a8e6-ddaaf5c50227/4DNFIRCN4NVZ.fastq.gz", "href": "/files-fastq/4DNFIRCN4NVZ/@@download/4DNFIRCN4NVZ.fastq.gz", "paired_end": "1", "uuid": "6234e60c-ad97-4414-a8e6-ddaaf5c50227", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "6234e60c-ad97-4414-a8e6-ddaaf5c50227/4DNFIRCN4NVZ.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIRCN4NVZ/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIX8WP8XT.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIX8WP8XT", "file_type": "reads", "uuid": "e85f2b2e-d1ae-46b4-82e8-dc88053f1c1b", "paired_end": "2", "@id": "/files-fastq/4DNFIX8WP8XT/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 343138096, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "93f16353-34f5-4553-a9c8-0a6b81584529", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/93f16353-34f5-4553-a9c8-0a6b81584529/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIRCN4NVZ/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIX8WP8XT", "file_size": 11371114934, "md5sum": "cabd1e104104bfd9d29262257b9bd243", "display_title": "4DNFIX8WP8XT.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/e85f2b2e-d1ae-46b4-82e8-dc88053f1c1b/4DNFIX8WP8XT.fastq.gz", "href": "/files-fastq/4DNFIX8WP8XT/@@download/4DNFIX8WP8XT.fastq.gz", "paired_end": "2", "uuid": "e85f2b2e-d1ae-46b4-82e8-dc88053f1c1b", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "e85f2b2e-d1ae-46b4-82e8-dc88053f1c1b/4DNFIX8WP8XT.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIX8WP8XT/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIRCN4NVZ.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIRCN4NVZ", "file_type": "reads", "uuid": "6234e60c-ad97-4414-a8e6-ddaaf5c50227", "paired_end": "1", "@id": "/files-fastq/4DNFIRCN4NVZ/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 343138096, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "e678509f-f697-497d-8e86-dd83b7065463", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/e678509f-f697-497d-8e86-dd83b7065463/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIX8WP8XT/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIO9KZE9Q", "file_size": 10681725341, "md5sum": "775f92bcdaadb315cb3912d2d832031f", "display_title": "4DNFIO9KZE9Q.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/ebc83f1e-e71e-4b84-9930-d883ce776899/4DNFIO9KZE9Q.fastq.gz", "href": "/files-fastq/4DNFIO9KZE9Q/@@download/4DNFIO9KZE9Q.fastq.gz", "paired_end": "1", "uuid": "ebc83f1e-e71e-4b84-9930-d883ce776899", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "ebc83f1e-e71e-4b84-9930-d883ce776899/4DNFIO9KZE9Q.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIO9KZE9Q/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIV4PB3YN.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIV4PB3YN", "file_type": "reads", "uuid": "96107e86-eb2c-46e3-bf02-53681fad54ce", "paired_end": "2", "@id": "/files-fastq/4DNFIV4PB3YN/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 344019707, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "7b2563f2-b0e2-47bc-bd2f-b5da4de8f38e", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/7b2563f2-b0e2-47bc-bd2f-b5da4de8f38e/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIO9KZE9Q/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIV4PB3YN", "file_size": 11369548239, "md5sum": "100cfde293a7e3e7f679deba22044438", "display_title": "4DNFIV4PB3YN.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/96107e86-eb2c-46e3-bf02-53681fad54ce/4DNFIV4PB3YN.fastq.gz", "href": "/files-fastq/4DNFIV4PB3YN/@@download/4DNFIV4PB3YN.fastq.gz", "paired_end": "2", "uuid": "96107e86-eb2c-46e3-bf02-53681fad54ce", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "96107e86-eb2c-46e3-bf02-53681fad54ce/4DNFIV4PB3YN.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIV4PB3YN/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIO9KZE9Q.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIO9KZE9Q", "file_type": "reads", "uuid": "ebc83f1e-e71e-4b84-9930-d883ce776899", "paired_end": "1", "@id": "/files-fastq/4DNFIO9KZE9Q/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 344019707, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "71a6d317-7bce-4a68-b18e-d21631ff847c", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/71a6d317-7bce-4a68-b18e-d21631ff847c/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIV4PB3YN/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIUUZ55BJ", "file_size": 10705217257, "md5sum": "bf42dc75e34f294b54eceeb2bd9f6eb2", "display_title": "4DNFIUUZ55BJ.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/8cee5915-3ee2-43c2-923f-84c86c834f4e/4DNFIUUZ55BJ.fastq.gz", "href": "/files-fastq/4DNFIUUZ55BJ/@@download/4DNFIUUZ55BJ.fastq.gz", "paired_end": "1", "uuid": "8cee5915-3ee2-43c2-923f-84c86c834f4e", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "8cee5915-3ee2-43c2-923f-84c86c834f4e/4DNFIUUZ55BJ.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIUUZ55BJ/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIEBTVUBL.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIEBTVUBL", "file_type": "reads", "uuid": "a635918a-6ed0-4549-9fb7-c0acb6d3a498", "paired_end": "2", "@id": "/files-fastq/4DNFIEBTVUBL/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 346347716, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "4b2616f7-69f4-4c65-9247-80a6acd7a186", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/4b2616f7-69f4-4c65-9247-80a6acd7a186/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIUUZ55BJ/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIEBTVUBL", "file_size": 11381814601, "md5sum": "32ae470e2a18c7bd9febea464fe67e98", "display_title": "4DNFIEBTVUBL.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/a635918a-6ed0-4549-9fb7-c0acb6d3a498/4DNFIEBTVUBL.fastq.gz", "href": "/files-fastq/4DNFIEBTVUBL/@@download/4DNFIEBTVUBL.fastq.gz", "paired_end": "2", "uuid": "a635918a-6ed0-4549-9fb7-c0acb6d3a498", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "a635918a-6ed0-4549-9fb7-c0acb6d3a498/4DNFIEBTVUBL.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIEBTVUBL/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIUUZ55BJ.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIUUZ55BJ", "file_type": "reads", "uuid": "8cee5915-3ee2-43c2-923f-84c86c834f4e", "paired_end": "1", "@id": "/files-fastq/4DNFIUUZ55BJ/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 346347716, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "1190d68f-fbf7-4122-bd52-c27485b8aa12", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/1190d68f-fbf7-4122-bd52-c27485b8aa12/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIEBTVUBL/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIIFDO2YT", "file_size": 10686212644, "md5sum": "f2835881a335047a4d50e16298bc8504", "display_title": "4DNFIIFDO2YT.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/3aaa640b-894d-4979-8331-17bc94de4a4f/4DNFIIFDO2YT.fastq.gz", "href": "/files-fastq/4DNFIIFDO2YT/@@download/4DNFIIFDO2YT.fastq.gz", "paired_end": "1", "uuid": "3aaa640b-894d-4979-8331-17bc94de4a4f", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "3aaa640b-894d-4979-8331-17bc94de4a4f/4DNFIIFDO2YT.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIIFDO2YT/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFI35OF1DT.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFI35OF1DT", "file_type": "reads", "uuid": "2117c392-0c5b-4fa0-b0e8-778ff6f7ed49", "paired_end": "2", "@id": "/files-fastq/4DNFI35OF1DT/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 342915777, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "02861108-7207-4d18-82fa-470d26db5003", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/02861108-7207-4d18-82fa-470d26db5003/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIIFDO2YT/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFI35OF1DT", "file_size": 11349264046, "md5sum": "546ae997a0cc60cac26cd800681f4cda", "display_title": "4DNFI35OF1DT.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/2117c392-0c5b-4fa0-b0e8-778ff6f7ed49/4DNFI35OF1DT.fastq.gz", "href": "/files-fastq/4DNFI35OF1DT/@@download/4DNFI35OF1DT.fastq.gz", "paired_end": "2", "uuid": "2117c392-0c5b-4fa0-b0e8-778ff6f7ed49", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "2117c392-0c5b-4fa0-b0e8-778ff6f7ed49/4DNFI35OF1DT.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFI35OF1DT/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIIFDO2YT.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIIFDO2YT", "file_type": "reads", "uuid": "3aaa640b-894d-4979-8331-17bc94de4a4f", "paired_end": "1", "@id": "/files-fastq/4DNFIIFDO2YT/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 342915777, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "6ae0b20d-c16c-4199-a138-10659099ad96", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/6ae0b20d-c16c-4199-a138-10659099ad96/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI35OF1DT/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFI4C5PW55", "file_size": 10615554602, "md5sum": "2bd62a8084d485818959c76a10276fa0", "display_title": "4DNFI4C5PW55.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/a273d4fc-6708-42a4-8aef-b53ca5ccdb8b/4DNFI4C5PW55.fastq.gz", "href": "/files-fastq/4DNFI4C5PW55/@@download/4DNFI4C5PW55.fastq.gz", "paired_end": "1", "uuid": "a273d4fc-6708-42a4-8aef-b53ca5ccdb8b", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "a273d4fc-6708-42a4-8aef-b53ca5ccdb8b/4DNFI4C5PW55.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFI4C5PW55/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIMY54334.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIMY54334", "file_type": "reads", "uuid": "ef46f133-088d-4c87-9a78-4e3947abc166", "paired_end": "2", "@id": "/files-fastq/4DNFIMY54334/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 341206974, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "85d7070b-cade-4095-8c76-e631e86844ca", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/85d7070b-cade-4095-8c76-e631e86844ca/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI4C5PW55/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIMY54334", "file_size": 11350708999, "md5sum": "d699c628c10d1025860c12dc3acc5d21", "display_title": "4DNFIMY54334.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/ef46f133-088d-4c87-9a78-4e3947abc166/4DNFIMY54334.fastq.gz", "href": "/files-fastq/4DNFIMY54334/@@download/4DNFIMY54334.fastq.gz", "paired_end": "2", "uuid": "ef46f133-088d-4c87-9a78-4e3947abc166", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "ef46f133-088d-4c87-9a78-4e3947abc166/4DNFIMY54334.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIMY54334/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFI4C5PW55.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFI4C5PW55", "file_type": "reads", "uuid": "a273d4fc-6708-42a4-8aef-b53ca5ccdb8b", "paired_end": "1", "@id": "/files-fastq/4DNFI4C5PW55/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 341206974, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "748bd2ca-6a03-407c-84ae-278275eba34b", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/748bd2ca-6a03-407c-84ae-278275eba34b/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIMY54334/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFISK6PTSJ", "file_size": 10644069710, "md5sum": "b510b6fc869198484e02443c4c53deed", "display_title": "4DNFISK6PTSJ.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/c9382772-90a9-445c-9d10-bcf4fa3783b3/4DNFISK6PTSJ.fastq.gz", "href": "/files-fastq/4DNFISK6PTSJ/@@download/4DNFISK6PTSJ.fastq.gz", "paired_end": "1", "uuid": "c9382772-90a9-445c-9d10-bcf4fa3783b3", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "c9382772-90a9-445c-9d10-bcf4fa3783b3/4DNFISK6PTSJ.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFISK6PTSJ/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIM3K5AFS.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIM3K5AFS", "file_type": "reads", "uuid": "f9e1654a-4161-4664-9b1d-f42f57d6303f", "paired_end": "2", "@id": "/files-fastq/4DNFIM3K5AFS/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 339243099, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "804727d5-dc08-4e86-8427-41d190df0a97", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/804727d5-dc08-4e86-8427-41d190df0a97/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFISK6PTSJ/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIM3K5AFS", "file_size": 11317426715, "md5sum": "2116559a1df692fdb49180cf256557af", "display_title": "4DNFIM3K5AFS.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/f9e1654a-4161-4664-9b1d-f42f57d6303f/4DNFIM3K5AFS.fastq.gz", "href": "/files-fastq/4DNFIM3K5AFS/@@download/4DNFIM3K5AFS.fastq.gz", "paired_end": "2", "uuid": "f9e1654a-4161-4664-9b1d-f42f57d6303f", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "f9e1654a-4161-4664-9b1d-f42f57d6303f/4DNFIM3K5AFS.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIM3K5AFS/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFISK6PTSJ.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFISK6PTSJ", "file_type": "reads", "uuid": "c9382772-90a9-445c-9d10-bcf4fa3783b3", "paired_end": "1", "@id": "/files-fastq/4DNFISK6PTSJ/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 339243099, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "c2a16ceb-3234-4475-a456-fa1a73432ce9", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/c2a16ceb-3234-4475-a456-fa1a73432ce9/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIM3K5AFS/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFI1L78MJG", "file_size": 10894868046, "md5sum": "8138b5ab7b8f4ac8f78851c672fe5274", "display_title": "4DNFI1L78MJG.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/969c00a9-e3dd-415f-9d66-53fde2272b3b/4DNFI1L78MJG.fastq.gz", "href": "/files-fastq/4DNFI1L78MJG/@@download/4DNFI1L78MJG.fastq.gz", "paired_end": "1", "uuid": "969c00a9-e3dd-415f-9d66-53fde2272b3b", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "969c00a9-e3dd-415f-9d66-53fde2272b3b/4DNFI1L78MJG.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFI1L78MJG/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIHOFSBZM.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIHOFSBZM", "file_type": "reads", "uuid": "05a8873e-5576-4ee2-ac64-40ba69aace42", "paired_end": "2", "@id": "/files-fastq/4DNFIHOFSBZM/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 354844450, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "387a6e18-cc3c-4d13-be0f-c82610c57413", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/387a6e18-cc3c-4d13-be0f-c82610c57413/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI1L78MJG/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIHOFSBZM", "file_size": 11665958009, "md5sum": "ad5677a892924c684cd0608d6e50c812", "display_title": "4DNFIHOFSBZM.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/05a8873e-5576-4ee2-ac64-40ba69aace42/4DNFIHOFSBZM.fastq.gz", "href": "/files-fastq/4DNFIHOFSBZM/@@download/4DNFIHOFSBZM.fastq.gz", "paired_end": "2", "uuid": "05a8873e-5576-4ee2-ac64-40ba69aace42", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "05a8873e-5576-4ee2-ac64-40ba69aace42/4DNFIHOFSBZM.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIHOFSBZM/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFI1L78MJG.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFI1L78MJG", "file_type": "reads", "uuid": "969c00a9-e3dd-415f-9d66-53fde2272b3b", "paired_end": "1", "@id": "/files-fastq/4DNFI1L78MJG/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 354844450, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "6ec6fe39-ca33-4652-abfb-b08057796cca", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/6ec6fe39-ca33-4652-abfb-b08057796cca/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIHOFSBZM/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "status": "released", "@id": "/experiments-hi-c/4DNEXN2ETG7Z/", "uuid": "2e5dd7d1-1fbb-4dfa-bcab-70aee32cd3b2", "display_title": "in situ Hi-C on H1-hESC differentiated to definitive endoderm with DpnII - 4DNEXN2ETG7Z", "accession": "4DNEXN2ETG7Z", "crosslinking_method": "1% Formaldehyde", "processed_files": [{"display_title": "4DNFIV6EETGG.bam", "md5sum": "830acb67561af87cfc78596e053e969e", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@type": ["FileFormat", "Item"], "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "abd9b864-f57e-40a8-83b6-6e9a7a112e38", "file_classification": "processed file", "upload_key": "abd9b864-f57e-40a8-83b6-6e9a7a112e38/4DNFIV6EETGG.bam", "file_type_detailed": "alignments (bam)", "@id": "/files-processed/4DNFIV6EETGG/", "file_type": "alignments", "@type": ["FileProcessed", "File", "Item"], "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/abd9b864-f57e-40a8-83b6-6e9a7a112e38/4DNFIV6EETGG.bam", "file_size": 277505335309, "accession": "4DNFIV6EETGG", "genome_assembly": "GRCh38", "href": "/files-processed/4DNFIV6EETGG/@@download/4DNFIV6EETGG.bam", "last_modified": {"date_modified": "2021-03-28T14:27:31.877877+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "display_title": "Job Dekker, UMMS", "status": "current", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "quality_metric": {"display_title": "QualityMetricBamqc from 2020-07-03", "@id": "/quality-metrics-bamqc/03d00d5e-73e8-4e12-a358-58443253eb46/", "overall_quality_status": "PASS", "uuid": "03d00d5e-73e8-4e12-a358-58443253eb46", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Reads", "value": "3107988611", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "18.373", "tooltip": "Percent of total reads (=571.04m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "23.514", "tooltip": "Percent of total reads (=730.82m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "14.312", "tooltip": "Percent of total reads (=444.8m)", "numberType": "percent"}, {"title": "Walks", "value": "0.005", "tooltip": "Percent of total reads (=0.16m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.198", "tooltip": "Percent of total reads (=6.14m)", "numberType": "percent"}]}, "lab": {"@type": ["Lab", "Item"], "status": "current", "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}}, {"display_title": "4DNFI8ZY3RGN.pairs.gz", "md5sum": "fb1a5fc8c841c125b9a67bd92ef88e2b", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "pairs", "@id": "/file-formats/pairs/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "45ca14da-c098-4063-a248-11a7221ba36f", "file_classification": "processed file", "upload_key": "45ca14da-c098-4063-a248-11a7221ba36f/4DNFI8ZY3RGN.pairs.gz", "file_type_detailed": "contact list-replicate (pairs)", "@id": "/files-processed/4DNFI8ZY3RGN/", "file_type": "contact list-replicate", "@type": ["FileProcessed", "File", "Item"], "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/45ca14da-c098-4063-a248-11a7221ba36f/4DNFI8ZY3RGN.pairs.gz", "file_size": 28011284502, "accession": "4DNFI8ZY3RGN", "genome_assembly": "GRCh38", "href": "/files-processed/4DNFI8ZY3RGN/@@download/4DNFI8ZY3RGN.pairs.gz", "extra_files": [{"file_size": 36453223, "md5sum": "25fb948a81d1c72fcdb7cc5b6ac18381", "href": "/files-processed/4DNFI8ZY3RGN/@@download/4DNFI8ZY3RGN.pairs.gz.px2", "file_format": {"status": "released", "display_title": "pairs_px2", "@type": ["FileFormat", "Item"], "file_format": "pairs_px2", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "@id": "/file-formats/pairs_px2/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "last_modified": {"date_modified": "2021-04-06T20:16:16.136688+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "display_title": "Job Dekker, UMMS", "status": "current", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "quality_metric": {"display_title": "QualityMetricPairsqc from 2020-07-03", "@id": "/quality-metrics-pairsqc/7a7945dd-c0d5-4f0a-80a0-b0ca1e4b952b/", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI8ZY3RGN/pairsqc_report.html", "uuid": "7a7945dd-c0d5-4f0a-80a0-b0ca1e4b952b", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "status": "released", "Total reads": 1361177676, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "1361177676", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "34.031", "tooltip": "Percent of filtered reads (=463.22m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "17.945", "tooltip": "Percent of filtered reads (=244.26m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "48.025", "tooltip": "Percent of filtered reads (=653.7m)", "numberType": "percent"}]}, "lab": {"@type": ["Lab", "Item"], "status": "current", "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}}], "biosample": {"status": "released", "uuid": "ed2a60d8-08ca-4157-aba8-3ffff7dd4222", "display_title": "4DNBSRA5OL4G", "treatments_summary": "None", "modifications_summary": "None", "@id": "/biosamples/4DNBSRA5OL4G/", "biosource_summary": "H1-hESC differentiated to definitive endoderm", "accession": "4DNBSRA5OL4G", "biosample_type": "in vitro differentiated cells", "@type": ["Biosample", "Item"], "biosample_category": ["H1-hESC", "In vitro Differentiation"], "biosource": [{"biosource_type": "stem cell derived cell line", "status": "released", "accession": "4DNSRHNAF6M6", "display_title": "H1-hESC - 4DNSRHNAF6M6", "@id": "/biosources/4DNSRHNAF6M6/", "cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "uuid": "44b0b763-065f-40f3-8432-8bd66d9f1be3", "tissue": {"preferred_name": "stem cell", "term_name": "stem cell", "term_id": "CL:0000034", "display_title": "stem cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000034/", "synonyms": ["animal stem cell"], "status": "released", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "slim_terms": [{"display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "name": "human", "display_title": "H. sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"preferred_name": "H1-hESC", "synonyms": ["H1"], "term_name": "H1-hESC", "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "term_id": "EFO:0003042", "display_title": "H1-hESC", "status": "released", "@id": "/ontology-terms/EFO:0003042/", "@type": ["OntologyTerm", "Item"], "slim_terms": [{"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "badges": [{"messages": ["Biosample missing doubling_number", "Biosample missing morphology_image"], "badge": {"title": "Biosample Metadata Incomplete", "status": "released", "badge_icon": "/static/img/badges/biosample-icon.svg", "warning": "Biosample Metadata Incomplete", "@type": ["Badge", "Item"], "badge_classification": "Warning", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "@id": "/badges/biosample-metadata-incomplete/", "display_title": "Biosample Metadata Incomplete", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "cell_culture_details": [{"display_title": "BiosampleCellCulture from 2020-06-24", "in_vitro_differentiated": "Yes", "@id": "/biosample-cell-cultures/2a57a856-2390-42f2-9b0f-92c922982b27/", "uuid": "2a57a856-2390-42f2-9b0f-92c922982b27", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "tissue": {"display_title": "definitive endoderm", "uuid": "52e444bc-62c2-4524-a29c-4aa4d1d96f26", "term_name": "definitive endoderm", "synonyms": ["embryonic endoderm"], "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0005439/", "preferred_name": "definitive endoderm", "term_id": "UBERON:0005439", "slim_terms": [{"uuid": "111121bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "display_title": "endoderm", "@id": "/ontology-terms/UBERON:0000925/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"tissue_source": "definitive endoderm", "organ_system": ["endoderm"]}}, "digestion_enzyme": {"display_title": "DpnII", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "name": "DpnII", "@type": ["Enzyme", "Item"], "status": "released", "@id": "/enzymes/DpnII/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "experiment_type": {"experiment_category": "Sequencing", "assay_classification": "3C via Ligation", "status": "released", "assay_subclassification": "DNA-DNA Pairwise Interactions", "assay_subclass_short": "Hi-C", "display_title": "in situ Hi-C", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "title": "in situ Hi-C", "@type": ["ExperimentType", "Item"], "@id": "/experiment-types/in-situ-hi-c/", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "field": "Enzyme", "value": "DpnII"}, "last_modified": {"date_modified": "2021-01-04T14:57:16.955632+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"files": [{"accession": "4DNFIX7B63QD", "file_size": 10623138015, "md5sum": "2a4233f18052742ec7c3794236375f8e", "display_title": "4DNFIX7B63QD.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/6a9f36e2-7e55-4cb8-bd92-b00a8a1941ee/4DNFIX7B63QD.fastq.gz", "href": "/files-fastq/4DNFIX7B63QD/@@download/4DNFIX7B63QD.fastq.gz", "paired_end": "1", "uuid": "6a9f36e2-7e55-4cb8-bd92-b00a8a1941ee", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "6a9f36e2-7e55-4cb8-bd92-b00a8a1941ee/4DNFIX7B63QD.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIX7B63QD/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIQWN2DCC.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIQWN2DCC", "file_type": "reads", "uuid": "b378f75c-498f-48ee-aa71-946054c234c3", "paired_end": "2", "@id": "/files-fastq/4DNFIQWN2DCC/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 341124406, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "45838c6a-2935-4256-a3e9-6d6e19aee429", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/45838c6a-2935-4256-a3e9-6d6e19aee429/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIX7B63QD/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIQWN2DCC", "file_size": 11356423726, "md5sum": "ea7a65b5937c6553e37d8be46b519492", "display_title": "4DNFIQWN2DCC.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/b378f75c-498f-48ee-aa71-946054c234c3/4DNFIQWN2DCC.fastq.gz", "href": "/files-fastq/4DNFIQWN2DCC/@@download/4DNFIQWN2DCC.fastq.gz", "paired_end": "2", "uuid": "b378f75c-498f-48ee-aa71-946054c234c3", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "b378f75c-498f-48ee-aa71-946054c234c3/4DNFIQWN2DCC.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIQWN2DCC/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIX7B63QD.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIX7B63QD", "file_type": "reads", "uuid": "6a9f36e2-7e55-4cb8-bd92-b00a8a1941ee", "paired_end": "1", "@id": "/files-fastq/4DNFIX7B63QD/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 341124406, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "18852f33-8656-4961-8a47-f5dfaad139f1", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/18852f33-8656-4961-8a47-f5dfaad139f1/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIQWN2DCC/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIV21KXK4", "file_size": 10914720999, "md5sum": "9c0edbae40c1199d58292edd5a4656d7", "display_title": "4DNFIV21KXK4.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/b240a49f-ce01-4788-86ba-68aa57b2565f/4DNFIV21KXK4.fastq.gz", "href": "/files-fastq/4DNFIV21KXK4/@@download/4DNFIV21KXK4.fastq.gz", "paired_end": "1", "uuid": "b240a49f-ce01-4788-86ba-68aa57b2565f", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "b240a49f-ce01-4788-86ba-68aa57b2565f/4DNFIV21KXK4.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIV21KXK4/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIRKN7652.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIRKN7652", "file_type": "reads", "uuid": "f1524068-3924-4f80-83ca-1a00066fe0b2", "paired_end": "2", "@id": "/files-fastq/4DNFIRKN7652/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 357851084, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "839b83bf-1017-4c83-b1f1-bc6ca5af0652", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/839b83bf-1017-4c83-b1f1-bc6ca5af0652/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIV21KXK4/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIRKN7652", "file_size": 11670810717, "md5sum": "0c4289763d1537979edb7db43ada8450", "display_title": "4DNFIRKN7652.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/f1524068-3924-4f80-83ca-1a00066fe0b2/4DNFIRKN7652.fastq.gz", "href": "/files-fastq/4DNFIRKN7652/@@download/4DNFIRKN7652.fastq.gz", "paired_end": "2", "uuid": "f1524068-3924-4f80-83ca-1a00066fe0b2", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "f1524068-3924-4f80-83ca-1a00066fe0b2/4DNFIRKN7652.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIRKN7652/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIV21KXK4.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIV21KXK4", "file_type": "reads", "uuid": "b240a49f-ce01-4788-86ba-68aa57b2565f", "paired_end": "1", "@id": "/files-fastq/4DNFIV21KXK4/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 357851084, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "1a114d5f-ad15-4e90-8f19-be5fdf60da65", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/1a114d5f-ad15-4e90-8f19-be5fdf60da65/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIRKN7652/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFI9665N2K", "file_size": 10844128709, "md5sum": "91918863074422ac8e09a0fc8efe3aba", "display_title": "4DNFI9665N2K.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/a0578f2d-c186-4740-8200-d689cfd49645/4DNFI9665N2K.fastq.gz", "href": "/files-fastq/4DNFI9665N2K/@@download/4DNFI9665N2K.fastq.gz", "paired_end": "1", "uuid": "a0578f2d-c186-4740-8200-d689cfd49645", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "a0578f2d-c186-4740-8200-d689cfd49645/4DNFI9665N2K.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFI9665N2K/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFI5ABOFRP.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFI5ABOFRP", "file_type": "reads", "uuid": "1eac0270-49a0-4ad8-bf83-3b037f6f92ba", "paired_end": "2", "@id": "/files-fastq/4DNFI5ABOFRP/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 353023432, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "39ed2214-8e4f-4f73-afa4-b488b67d0982", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/39ed2214-8e4f-4f73-afa4-b488b67d0982/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI9665N2K/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFI5ABOFRP", "file_size": 11609607525, "md5sum": "4b1db58814d70a60586f0803b1baf0e0", "display_title": "4DNFI5ABOFRP.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/1eac0270-49a0-4ad8-bf83-3b037f6f92ba/4DNFI5ABOFRP.fastq.gz", "href": "/files-fastq/4DNFI5ABOFRP/@@download/4DNFI5ABOFRP.fastq.gz", "paired_end": "2", "uuid": "1eac0270-49a0-4ad8-bf83-3b037f6f92ba", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "1eac0270-49a0-4ad8-bf83-3b037f6f92ba/4DNFI5ABOFRP.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFI5ABOFRP/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFI9665N2K.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFI9665N2K", "file_type": "reads", "uuid": "a0578f2d-c186-4740-8200-d689cfd49645", "paired_end": "1", "@id": "/files-fastq/4DNFI9665N2K/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 353023432, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "03d435df-3cd9-43ff-99e0-58e5bb5db671", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/03d435df-3cd9-43ff-99e0-58e5bb5db671/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI5ABOFRP/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFI3TMZ76R", "file_size": 10592487544, "md5sum": "2c4adfbdd3f4a93f3a8a269c72659c3e", "display_title": "4DNFI3TMZ76R.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/94ab1388-33a7-44a2-8a1a-b336808e3e18/4DNFI3TMZ76R.fastq.gz", "href": "/files-fastq/4DNFI3TMZ76R/@@download/4DNFI3TMZ76R.fastq.gz", "paired_end": "1", "uuid": "94ab1388-33a7-44a2-8a1a-b336808e3e18", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "94ab1388-33a7-44a2-8a1a-b336808e3e18/4DNFI3TMZ76R.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFI3TMZ76R/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIV6E8QK6.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIV6E8QK6", "file_type": "reads", "uuid": "1261c05b-51d1-400c-8819-48eff045d920", "paired_end": "2", "@id": "/files-fastq/4DNFIV6E8QK6/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 344122444, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "04cc40c1-2501-4394-a473-890d37de7a7a", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/04cc40c1-2501-4394-a473-890d37de7a7a/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI3TMZ76R/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIV6E8QK6", "file_size": 11228799061, "md5sum": "d1cfa5e00d24c632896f89082e2679f4", "display_title": "4DNFIV6E8QK6.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/1261c05b-51d1-400c-8819-48eff045d920/4DNFIV6E8QK6.fastq.gz", "href": "/files-fastq/4DNFIV6E8QK6/@@download/4DNFIV6E8QK6.fastq.gz", "paired_end": "2", "uuid": "1261c05b-51d1-400c-8819-48eff045d920", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "1261c05b-51d1-400c-8819-48eff045d920/4DNFIV6E8QK6.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIV6E8QK6/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFI3TMZ76R.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFI3TMZ76R", "file_type": "reads", "uuid": "94ab1388-33a7-44a2-8a1a-b336808e3e18", "paired_end": "1", "@id": "/files-fastq/4DNFI3TMZ76R/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 344122444, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "c6542651-a6c1-4ae8-a35c-cf25543bee95", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/c6542651-a6c1-4ae8-a35c-cf25543bee95/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIV6E8QK6/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIIENXMC7", "file_size": 10834649568, "md5sum": "846272bdd7122fa03676878de58991e9", "display_title": "4DNFIIENXMC7.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/64c2050a-bb37-4ff7-b71f-75f1b04905f4/4DNFIIENXMC7.fastq.gz", "href": "/files-fastq/4DNFIIENXMC7/@@download/4DNFIIENXMC7.fastq.gz", "paired_end": "1", "uuid": "64c2050a-bb37-4ff7-b71f-75f1b04905f4", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "64c2050a-bb37-4ff7-b71f-75f1b04905f4/4DNFIIENXMC7.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIIENXMC7/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIQUAFLV2.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIQUAFLV2", "file_type": "reads", "uuid": "99a89633-e752-47d2-b20f-da2dab73f5ed", "paired_end": "2", "@id": "/files-fastq/4DNFIQUAFLV2/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 345571204, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "2923c6b9-37d7-4472-a51e-8a6167808ae7", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/2923c6b9-37d7-4472-a51e-8a6167808ae7/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIIENXMC7/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIQUAFLV2", "file_size": 11469014230, "md5sum": "a56869e8c255e8396d9209273f1bdf93", "display_title": "4DNFIQUAFLV2.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/99a89633-e752-47d2-b20f-da2dab73f5ed/4DNFIQUAFLV2.fastq.gz", "href": "/files-fastq/4DNFIQUAFLV2/@@download/4DNFIQUAFLV2.fastq.gz", "paired_end": "2", "uuid": "99a89633-e752-47d2-b20f-da2dab73f5ed", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "99a89633-e752-47d2-b20f-da2dab73f5ed/4DNFIQUAFLV2.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIQUAFLV2/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIIENXMC7.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIIENXMC7", "file_type": "reads", "uuid": "64c2050a-bb37-4ff7-b71f-75f1b04905f4", "paired_end": "1", "@id": "/files-fastq/4DNFIIENXMC7/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 345571204, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "142462c4-e285-4cf4-9c44-1e11edbdc606", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/142462c4-e285-4cf4-9c44-1e11edbdc606/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIQUAFLV2/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIPHND66U", "file_size": 10823607757, "md5sum": "ca0c38dc84ff9acabd4428da1f66c819", "display_title": "4DNFIPHND66U.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/bd3ea52d-6449-4407-9f4e-6a63aea5c2bb/4DNFIPHND66U.fastq.gz", "href": "/files-fastq/4DNFIPHND66U/@@download/4DNFIPHND66U.fastq.gz", "paired_end": "1", "uuid": "bd3ea52d-6449-4407-9f4e-6a63aea5c2bb", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "bd3ea52d-6449-4407-9f4e-6a63aea5c2bb/4DNFIPHND66U.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIPHND66U/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIEGL7SK2.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIEGL7SK2", "file_type": "reads", "uuid": "430e94a3-fa80-4ff4-ad0f-927df9c8e137", "paired_end": "2", "@id": "/files-fastq/4DNFIEGL7SK2/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 343840729, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "923bd411-fa02-42f2-9f1f-58109d7df2c0", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/923bd411-fa02-42f2-9f1f-58109d7df2c0/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIPHND66U/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIEGL7SK2", "file_size": 11404224697, "md5sum": "a1f41efdb9b491f293dbc756d4178156", "display_title": "4DNFIEGL7SK2.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/430e94a3-fa80-4ff4-ad0f-927df9c8e137/4DNFIEGL7SK2.fastq.gz", "href": "/files-fastq/4DNFIEGL7SK2/@@download/4DNFIEGL7SK2.fastq.gz", "paired_end": "2", "uuid": "430e94a3-fa80-4ff4-ad0f-927df9c8e137", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "430e94a3-fa80-4ff4-ad0f-927df9c8e137/4DNFIEGL7SK2.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIEGL7SK2/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIPHND66U.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIPHND66U", "file_type": "reads", "uuid": "bd3ea52d-6449-4407-9f4e-6a63aea5c2bb", "paired_end": "1", "@id": "/files-fastq/4DNFIPHND66U/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 343840729, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "16416de7-7368-4503-b846-6b6184dccfe0", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/16416de7-7368-4503-b846-6b6184dccfe0/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIEGL7SK2/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIRRUA29Q", "file_size": 10620984619, "md5sum": "444ac62392b4e1f909912bb0a3fe86e8", "display_title": "4DNFIRRUA29Q.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/ea9e91a4-236f-4bf5-bfa3-813c0f288f63/4DNFIRRUA29Q.fastq.gz", "href": "/files-fastq/4DNFIRRUA29Q/@@download/4DNFIRRUA29Q.fastq.gz", "paired_end": "1", "uuid": "ea9e91a4-236f-4bf5-bfa3-813c0f288f63", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "ea9e91a4-236f-4bf5-bfa3-813c0f288f63/4DNFIRRUA29Q.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIRRUA29Q/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIZ8C8L7H.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIZ8C8L7H", "file_type": "reads", "uuid": "d75756ce-901e-4974-a95a-c4f07fddd5b5", "paired_end": "2", "@id": "/files-fastq/4DNFIZ8C8L7H/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 340495633, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "8ebc4316-ac52-4797-bfd4-19d8312a5d72", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/8ebc4316-ac52-4797-bfd4-19d8312a5d72/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIRRUA29Q/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIZ8C8L7H", "file_size": 11155967747, "md5sum": "5ee854f3735516fc6972a2e670382ffd", "display_title": "4DNFIZ8C8L7H.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/d75756ce-901e-4974-a95a-c4f07fddd5b5/4DNFIZ8C8L7H.fastq.gz", "href": "/files-fastq/4DNFIZ8C8L7H/@@download/4DNFIZ8C8L7H.fastq.gz", "paired_end": "2", "uuid": "d75756ce-901e-4974-a95a-c4f07fddd5b5", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "d75756ce-901e-4974-a95a-c4f07fddd5b5/4DNFIZ8C8L7H.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIZ8C8L7H/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIRRUA29Q.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIRRUA29Q", "file_type": "reads", "uuid": "ea9e91a4-236f-4bf5-bfa3-813c0f288f63", "paired_end": "1", "@id": "/files-fastq/4DNFIRRUA29Q/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 340495633, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "c60bfef3-e9b2-4d19-86c6-f39bdd034278", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/c60bfef3-e9b2-4d19-86c6-f39bdd034278/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIZ8C8L7H/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFITGZKF48", "file_size": 10648714001, "md5sum": "7f09ac2bf6af1fa3a715e784e7ada7b1", "display_title": "4DNFITGZKF48.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/45e2d7be-c026-49f4-aaf1-d407e3c6373b/4DNFITGZKF48.fastq.gz", "href": "/files-fastq/4DNFITGZKF48/@@download/4DNFITGZKF48.fastq.gz", "paired_end": "1", "uuid": "45e2d7be-c026-49f4-aaf1-d407e3c6373b", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "45e2d7be-c026-49f4-aaf1-d407e3c6373b/4DNFITGZKF48.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFITGZKF48/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIWNOIQGQ.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIWNOIQGQ", "file_type": "reads", "uuid": "f4abe495-0013-4cf8-bcc0-a677018730e2", "paired_end": "2", "@id": "/files-fastq/4DNFIWNOIQGQ/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 348669316, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "bcfbe929-d650-454c-abe7-c85943847224", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/bcfbe929-d650-454c-abe7-c85943847224/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFITGZKF48/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIWNOIQGQ", "file_size": 11357209300, "md5sum": "e79932db655eb423a4a206bc62888a27", "display_title": "4DNFIWNOIQGQ.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/f4abe495-0013-4cf8-bcc0-a677018730e2/4DNFIWNOIQGQ.fastq.gz", "href": "/files-fastq/4DNFIWNOIQGQ/@@download/4DNFIWNOIQGQ.fastq.gz", "paired_end": "2", "uuid": "f4abe495-0013-4cf8-bcc0-a677018730e2", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "f4abe495-0013-4cf8-bcc0-a677018730e2/4DNFIWNOIQGQ.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIWNOIQGQ/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFITGZKF48.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFITGZKF48", "file_type": "reads", "uuid": "45e2d7be-c026-49f4-aaf1-d407e3c6373b", "paired_end": "1", "@id": "/files-fastq/4DNFITGZKF48/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 348669316, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "18ae79eb-ba6e-4868-8a22-db688e7fd659", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/18ae79eb-ba6e-4868-8a22-db688e7fd659/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIWNOIQGQ/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIKT1VHL2", "file_size": 8963333743, "md5sum": "d875a36ce1989a09b7508ce6c8b30feb", "display_title": "4DNFIKT1VHL2.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/ddbec6b8-a926-4bc8-9356-6146ce9e6c60/4DNFIKT1VHL2.fastq.gz", "href": "/files-fastq/4DNFIKT1VHL2/@@download/4DNFIKT1VHL2.fastq.gz", "paired_end": "1", "uuid": "ddbec6b8-a926-4bc8-9356-6146ce9e6c60", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "ddbec6b8-a926-4bc8-9356-6146ce9e6c60/4DNFIKT1VHL2.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIKT1VHL2/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIH1AHOXG.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIH1AHOXG", "file_type": "reads", "uuid": "302b4bce-ab68-4507-85c5-be9fd9795998", "paired_end": "2", "@id": "/files-fastq/4DNFIH1AHOXG/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 291663692, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "bbce7b6e-c2de-410f-9976-79a284f4b0c9", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/bbce7b6e-c2de-410f-9976-79a284f4b0c9/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIKT1VHL2/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIH1AHOXG", "file_size": 9248818484, "md5sum": "9fc92609981f46cabe12e1f8d7a3f738", "display_title": "4DNFIH1AHOXG.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/302b4bce-ab68-4507-85c5-be9fd9795998/4DNFIH1AHOXG.fastq.gz", "href": "/files-fastq/4DNFIH1AHOXG/@@download/4DNFIH1AHOXG.fastq.gz", "paired_end": "2", "uuid": "302b4bce-ab68-4507-85c5-be9fd9795998", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "upload_key": "302b4bce-ab68-4507-85c5-be9fd9795998/4DNFIH1AHOXG.fastq.gz", "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIH1AHOXG/", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIKT1VHL2.fastq.gz", "status": "released", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIKT1VHL2", "file_type": "reads", "uuid": "ddbec6b8-a926-4bc8-9356-6146ce9e6c60", "paired_end": "1", "@id": "/files-fastq/4DNFIKT1VHL2/", "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"Total Sequences": 291663692, "Sequence length": "50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2020-06-26", "uuid": "24e894b7-fe94-4fc4-b646-ae1c1517a8d8", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/24e894b7-fe94-4fc4-b646-ae1c1517a8d8/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIH1AHOXG/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "status": "released", "@id": "/experiments-hi-c/4DNEXS6NBDQB/", "uuid": "3b8562d5-3a09-4749-ae49-9597f4a12cf9", "display_title": "in situ Hi-C on H1-hESC differentiated to definitive endoderm with DpnII - 4DNEXS6NBDQB", "accession": "4DNEXS6NBDQB", "crosslinking_method": "1% Formaldehyde", "processed_files": [{"display_title": "4DNFICP57SBD.bam", "md5sum": "9c1167b1e7805053ff6712c396f5f0b1", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@type": ["FileFormat", "Item"], "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "cf8c55c1-bdef-4fdc-bd55-d8c2a8fae708", "file_classification": "processed file", "upload_key": "cf8c55c1-bdef-4fdc-bd55-d8c2a8fae708/4DNFICP57SBD.bam", "file_type_detailed": "alignments (bam)", "@id": "/files-processed/4DNFICP57SBD/", "file_type": "alignments", "@type": ["FileProcessed", "File", "Item"], "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/cf8c55c1-bdef-4fdc-bd55-d8c2a8fae708/4DNFICP57SBD.bam", "file_size": 263645573733, "accession": "4DNFICP57SBD", "genome_assembly": "GRCh38", "href": "/files-processed/4DNFICP57SBD/@@download/4DNFICP57SBD.bam", "last_modified": {"date_modified": "2021-03-28T14:27:30.118558+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "display_title": "Job Dekker, UMMS", "status": "current", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "quality_metric": {"display_title": "QualityMetricBamqc from 2020-07-03", "@id": "/quality-metrics-bamqc/096b6c53-4f65-47c2-8088-0cd2d86d83b7/", "overall_quality_status": "PASS", "uuid": "096b6c53-4f65-47c2-8088-0cd2d86d83b7", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Reads", "value": "3066361940", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "15.146", "tooltip": "Percent of total reads (=464.44m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "22.792", "tooltip": "Percent of total reads (=698.89m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "18.724", "tooltip": "Percent of total reads (=574.15m)", "numberType": "percent"}, {"title": "Walks", "value": "0.009", "tooltip": "Percent of total reads (=0.28m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.154", "tooltip": "Percent of total reads (=4.73m)", "numberType": "percent"}]}, "lab": {"@type": ["Lab", "Item"], "status": "current", "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}}, {"display_title": "4DNFI2LE5JIJ.pairs.gz", "md5sum": "14d79292a5b04eaad82b67826009d336", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "pairs", "@id": "/file-formats/pairs/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "1e0358c9-0c7f-469c-99f9-0ec05be9223e", "file_classification": "processed file", "upload_key": "1e0358c9-0c7f-469c-99f9-0ec05be9223e/4DNFI2LE5JIJ.pairs.gz", "file_type_detailed": "contact list-replicate (pairs)", "@id": "/files-processed/4DNFI2LE5JIJ/", "file_type": "contact list-replicate", "@type": ["FileProcessed", "File", "Item"], "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/1e0358c9-0c7f-469c-99f9-0ec05be9223e/4DNFI2LE5JIJ.pairs.gz", "file_size": 26982505323, "accession": "4DNFI2LE5JIJ", "genome_assembly": "GRCh38", "href": "/files-processed/4DNFI2LE5JIJ/@@download/4DNFI2LE5JIJ.pairs.gz", "extra_files": [{"file_size": 36176849, "md5sum": "12192dc87b4e08985a4c30dd96f02bc5", "href": "/files-processed/4DNFI2LE5JIJ/@@download/4DNFI2LE5JIJ.pairs.gz.px2", "file_format": {"status": "released", "display_title": "pairs_px2", "@type": ["FileFormat", "Item"], "file_format": "pairs_px2", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "@id": "/file-formats/pairs_px2/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "last_modified": {"date_modified": "2021-04-06T20:16:15.389615+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "display_title": "Job Dekker, UMMS", "status": "current", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "quality_metric": {"display_title": "QualityMetricPairsqc from 2020-07-07", "@id": "/quality-metrics-pairsqc/e2d0411f-4bb6-472a-a6c0-4884d2f182e6/", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI2LE5JIJ/pairsqc_report.html", "uuid": "e2d0411f-4bb6-472a-a6c0-4884d2f182e6", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "status": "released", "Total reads": 1328606544, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "1328606544", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "35.343", "tooltip": "Percent of filtered reads (=469.57m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "24.717", "tooltip": "Percent of filtered reads (=328.39m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "39.94", "tooltip": "Percent of filtered reads (=530.65m)", "numberType": "percent"}]}, "lab": {"@type": ["Lab", "Item"], "status": "current", "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "DpnII", "dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}}], "biosample": {"status": "released", "uuid": "1661d75f-69a7-4f62-a2f6-47fbbe98efa1", "display_title": "4DNBSGC8M4B7", "treatments_summary": "None", "modifications_summary": "None", "@id": "/biosamples/4DNBSGC8M4B7/", "biosource_summary": "H1-hESC differentiated to definitive endoderm", "accession": "4DNBSGC8M4B7", "biosample_type": "in vitro differentiated cells", "@type": ["Biosample", "Item"], "biosample_category": ["H1-hESC", "In vitro Differentiation"], "biosource": [{"biosource_type": "stem cell derived cell line", "status": "released", "accession": "4DNSRHNAF6M6", "display_title": "H1-hESC - 4DNSRHNAF6M6", "@id": "/biosources/4DNSRHNAF6M6/", "cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "uuid": "44b0b763-065f-40f3-8432-8bd66d9f1be3", "tissue": {"preferred_name": "stem cell", "term_name": "stem cell", "term_id": "CL:0000034", "display_title": "stem cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000034/", "synonyms": ["animal stem cell"], "status": "released", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "slim_terms": [{"display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "name": "human", "display_title": "H. sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"preferred_name": "H1-hESC", "synonyms": ["H1"], "term_name": "H1-hESC", "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "term_id": "EFO:0003042", "display_title": "H1-hESC", "status": "released", "@id": "/ontology-terms/EFO:0003042/", "@type": ["OntologyTerm", "Item"], "slim_terms": [{"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "badges": [{"messages": ["Biosample missing doubling_number"], "badge": {"title": "Biosample Metadata Incomplete", "status": "released", "badge_icon": "/static/img/badges/biosample-icon.svg", "warning": "Biosample Metadata Incomplete", "@type": ["Badge", "Item"], "badge_classification": "Warning", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "@id": "/badges/biosample-metadata-incomplete/", "display_title": "Biosample Metadata Incomplete", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "cell_culture_details": [{"display_title": "BiosampleCellCulture from 2020-06-24", "in_vitro_differentiated": "Yes", "@id": "/biosample-cell-cultures/1127ef20-8d74-4c09-9903-bedca8baa013/", "uuid": "1127ef20-8d74-4c09-9903-bedca8baa013", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "tissue": {"display_title": "definitive endoderm", "uuid": "52e444bc-62c2-4524-a29c-4aa4d1d96f26", "term_name": "definitive endoderm", "synonyms": ["embryonic endoderm"], "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/UBERON:0005439/", "preferred_name": "definitive endoderm", "term_id": "UBERON:0005439", "slim_terms": [{"uuid": "111121bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "display_title": "endoderm", "@id": "/ontology-terms/UBERON:0000925/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"tissue_source": "definitive endoderm", "organ_system": ["endoderm"]}}, "digestion_enzyme": {"display_title": "DpnII", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "name": "DpnII", "@type": ["Enzyme", "Item"], "status": "released", "@id": "/enzymes/DpnII/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "experiment_type": {"experiment_category": "Sequencing", "assay_classification": "3C via Ligation", "status": "released", "assay_subclassification": "DNA-DNA Pairwise Interactions", "assay_subclass_short": "Hi-C", "display_title": "in situ Hi-C", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "title": "in situ Hi-C", "@type": ["ExperimentType", "Item"], "@id": "/experiment-types/in-situ-hi-c/", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "field": "Enzyme", "value": "DpnII"}, "last_modified": {"date_modified": "2021-01-04T14:56:34.346744+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experimentset_type": "replicate", "completed_processes": ["insulation_scores_and_boundaries_v1", "HiC_Pipeline_0.2.7", "compartments_v1.2"], "other_processed_files": [{"type": "supplementary", "files": [{"file_size": 1051226, "uuid": "dac1e5c2-7c90-406b-9f5d-dfb14a78a490", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "accession": "4DNFIFU6KTSG", "genome_assembly": "GRCh38", "file_type": "compartments", "md5sum": "ad728667f2b83ff8b0d811e9d03d9622", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dac1e5c2-7c90-406b-9f5d-dfb14a78a490/4DNFIFU6KTSG.txt.gz", "file_type_detailed": "compartments (compressed_txt)", "@id": "/files-processed/4DNFIFU6KTSG/", "display_title": "4DNFIFU6KTSG.txt.gz", "href": "/files-processed/4DNFIFU6KTSG/@@download/4DNFIFU6KTSG.txt.gz", "status": "released", "file_format": {"@id": "/file-formats/compressed_txt/", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "status": "released", "display_title": "compressed_txt", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "last_modified": {"date_modified": "2021-12-16T07:02:19.310034+00:00"}, "track_and_facet_info": {"dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "Compartment, insulation and loop calls - Dekker Lab", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"higlass_uid": "24c6768a-35e0-4077-9c9d-f053148cd756", "file_size": 322371, "uuid": "d9c51daa-e7a3-4b20-8db1-bbd8e9849822", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "accession": "4DNFIEB8OCEM", "genome_assembly": "GRCh38", "file_type": "compartments", "md5sum": "5d342a8f3d5a585283b2f6ae77f93809", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/d9c51daa-e7a3-4b20-8db1-bbd8e9849822/4DNFIEB8OCEM.bw", "file_type_detailed": "compartments (bw)", "@id": "/files-processed/4DNFIEB8OCEM/", "display_title": "4DNFIEB8OCEM.bw", "href": "/files-processed/4DNFIEB8OCEM/@@download/4DNFIEB8OCEM.bw", "status": "released", "file_format": {"@id": "/file-formats/bw/", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "bw", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "last_modified": {"date_modified": "2021-12-16T07:02:09.811636+00:00"}, "track_and_facet_info": {"dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "Compartment, insulation and loop calls - Dekker Lab", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS", "track_title": "compartments for H1-hESC differentiated to definitive endoderm in situ Hi-C DpnII"}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "27f516b8-0c43-4180-a6b2-60f2a7fc42ef", "@id": "/higlass-view-configs/27f516b8-0c43-4180-a6b2-60f2a7fc42ef/", "display_title": "4DNFIEB8OCEM - compartments for H1-hESC differentiated to definitive endoderm in situ Hi-C DpnII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 4875251, "uuid": "3ceba342-b7ad-45a6-8d59-6fdb6e26bd8e", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "accession": "4DNFIU5WDUE5", "genome_assembly": "GRCh38", "file_type": "insulation score", "md5sum": "e0859621010947f4930fb9d34b44c1a3", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/3ceba342-b7ad-45a6-8d59-6fdb6e26bd8e/4DNFIU5WDUE5.txt.gz", "file_type_detailed": "insulation score (compressed_txt)", "@id": "/files-processed/4DNFIU5WDUE5/", "display_title": "4DNFIU5WDUE5.txt.gz", "href": "/files-processed/4DNFIU5WDUE5/@@download/4DNFIU5WDUE5.txt.gz", "status": "released", "file_format": {"@id": "/file-formats/compressed_txt/", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "status": "released", "display_title": "compressed_txt", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "last_modified": {"date_modified": "2021-12-16T07:02:00.704620+00:00"}, "track_and_facet_info": {"dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "Compartment, insulation and loop calls - Dekker Lab", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 715995, "uuid": "9cde8d17-20db-4155-8a10-ce478cc342cc", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "accession": "4DNFIW5Z7XD3", "genome_assembly": "GRCh38", "file_type": "dot calls", "md5sum": "c5fe46390bfa1897fa82a67826dd4906", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/9cde8d17-20db-4155-8a10-ce478cc342cc/4DNFIW5Z7XD3.bedpe.gz", "file_type_detailed": "dot calls (bedpe)", "@id": "/files-processed/4DNFIW5Z7XD3/", "display_title": "4DNFIW5Z7XD3.bedpe.gz", "href": "/files-processed/4DNFIW5Z7XD3/@@download/4DNFIW5Z7XD3.bedpe.gz", "status": "released", "file_format": {"@id": "/file-formats/bedpe/", "uuid": "d13d06cf-218e-4f61-55f0-94f556118b2c", "status": "released", "display_title": "bedpe", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "last_modified": {"date_modified": "2021-12-16T07:01:52.531741+00:00"}, "track_and_facet_info": {"dataset": "Hi-C on H1-DE cells - protocol variations", "condition": "Formaldehyde, DpnII", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "Compartment, insulation and loop calls - Dekker Lab", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "H1-hESC differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "title": "Compartment, insulation and loop calls - Dekker Lab", "description": "These files are provided by the Dekker Lab. Note that they are derived from lab-generated processed files and not from the files in the 'Processed Files' tab that were generated by the standardized 4DN-DCIC pipeline.", "higlass_view_config": {"display_title": "4DNESCOQ5YRS - Compartment, insulation and loop calls - Dekker Lab", "status": "released", "@id": "/higlass-view-configs/e51b8025-121e-41c6-9651-ad0bfd71263c/", "description": "Supplementary Files (Compartment, insulation and loop calls - Dekker Lab) for 4DNESCOQ5YRS (Hi-C experiments on H1 derived endoderm, differentiated using the protocol from Rene Maehr lab. Cells crosslinked with FA and digested with DpnII.): 4DNFIEB8OCEM", "uuid": "e51b8025-121e-41c6-9651-ad0bfd71263c", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}, "last_modified": {"date_modified": "2022-12-06T06:02:28.518066+00:00"}}}], "@id": "/experiment-set-replicates/4DNESCOQ5YRS/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "2a68c55a-b02f-4679-8f20-890e014d718c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESCOQ5YRS", "external_references": [], "pubs_using": [], "publications_of_set": [], "number_of_experiments": 2, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSRA5OL4G/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing doubling_number", "Biosample missing morphology_image"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}, {"parent": "/biosamples/4DNBSGC8M4B7/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing doubling_number"], "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": "/experiment-set-replicates/4DNESCOQ5YRS/", "embedded_path": "badges", "item": {"messages": ["Inconsistent replicate information in average_fragment_size: 200, 350", "Inconsistent replicate information in fragment_size_range: 180-300, 250-450"], "badge": {"commendation": null, "warning": "Inconsistent Replicate Info", "uuid": "a4df9ff7-fe85-4672-86ac-7c38b5d9c853", "@id": "/badges/inconsistent-replicate-info/", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "description": "The experimental replicates belonging to this Experiment Set differ in some specific metadata fields"}}}]}, "validation-errors": []}