{"lab": {"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "correspondence": [{"contact_email": "am9iLmRla2tlckB1bWFzc21lZC5lZHU=", "@id": "/users/83b5073a-069b-4162-9b30-6f42d5551e34/", "display_title": "Job Dekker"}], "status": "current", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "title": "Job Dekker, UMMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}, "pi": {"error": "no view permissions"}}, "tags": ["deep_data", "matrix_project"], "award": {"project": "4DN", "name": "1U54DK107980-01", "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.", "@id": "/awards/1U54DK107980-01/", "@type": ["Award", "Item"], "display_title": "CENTER FOR 3D STRUCTURE AND PHYSICS OF THE GENOME", "uuid": "ae6c618f-7a8c-441e-a886-e30bbbe591da", "status": "current", "center_title": "NOFIC - Dekker", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "study": "Experimental Protocol Variations", "status": "released", "aliases": ["dekker-lab:ExperimentSet_U54-microC_U54-END4DN-FA-DSG-MNase"], "accession": "4DNESW1SPPTD", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "description": "Micro-C experiments on H1 derived endoderm, differentiated using the 4DN protocol.", "study_group": "Single Time Point and Condition", "date_created": "2020-06-24T20:17:55.454767+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "Micro-C on H1-DE cells - protocol variations", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-01-25T04:56:07.010539+00:00"}, "public_release": "2021-01-04", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"status": "released", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEX1JFQVNZ", "display_title": "Micro-C on H1-hESC (Tier 1) differentiated to definitive endoderm with MNase - 4DNEX1JFQVNZ", "@id": "/experiments-hi-c/4DNEX1JFQVNZ/", "uuid": "8186b39b-5ce6-48a3-97d4-0053dd10001b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 1, "tec_rep_no": 2, "replicate_exp": {"status": "released", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXOCFRELS", "display_title": "Micro-C on H1-hESC (Tier 1) differentiated to definitive endoderm with MNase - 4DNEXOCFRELS", "@id": "/experiments-hi-c/4DNEXOCFRELS/", "uuid": "f85f6c68-d38c-4599-824d-a9b6563df64d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 1, "tec_rep_no": 3, "replicate_exp": {"status": "released", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXILU11VM", "display_title": "Micro-C on H1-hESC (Tier 1) differentiated to definitive endoderm with MNase - 4DNEXILU11VM", "@id": "/experiments-hi-c/4DNEXILU11VM/", "uuid": "8bf9e611-ffb6-4890-be26-2e45fda79396", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 1, "tec_rep_no": 4, "replicate_exp": {"status": "released", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXO7YBCMP", "display_title": "Micro-C on H1-hESC (Tier 1) differentiated to definitive endoderm with MNase - 4DNEXO7YBCMP", "@id": "/experiments-hi-c/4DNEXO7YBCMP/", "uuid": "d2dc99de-19cd-4304-b7ce-eae8319d204a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"status": "released", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXHL7EHOF", "display_title": "Micro-C on H1-hESC (Tier 1) differentiated to definitive endoderm with MNase - 4DNEXHL7EHOF", "@id": "/experiments-hi-c/4DNEXHL7EHOF/", "uuid": "3e118e38-ec73-4c8a-899b-cf4b71323bd8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 2, "replicate_exp": {"status": "released", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXXSXYECB", "display_title": "Micro-C on H1-hESC (Tier 1) differentiated to definitive endoderm with MNase - 4DNEXXSXYECB", "@id": "/experiments-hi-c/4DNEXXSXYECB/", "uuid": "eed1b722-b024-4c51-bb1f-ea0ff9663fab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 3, "replicate_exp": {"status": "released", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXSCJ4HOI", "display_title": "Micro-C on H1-hESC (Tier 1) differentiated to definitive endoderm with MNase - 4DNEXSCJ4HOI", "@id": "/experiments-hi-c/4DNEXSCJ4HOI/", "uuid": "11ab026a-aceb-48cb-ba75-f03ee00d60e4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 4, "replicate_exp": {"status": "released", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEX2ZUALZI", "display_title": "Micro-C on H1-hESC (Tier 1) differentiated to definitive endoderm with MNase - 4DNEX2ZUALZI", "@id": "/experiments-hi-c/4DNEX2ZUALZI/", "uuid": "ba35dd84-26cd-4fa8-b94f-dd574d4e1da8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"status": "released", "description": "4DNESW1SPPTD (Micro-C experiments on H1 derived endoderm, differentiated using the 4DN protocol.): 4DNFINQYW56E", "contributing_labs": [{"uuid": "60479b76-821b-4c03-b0e2-c9351291b965", "status": "current", "display_title": "Oliver Rando, UMMS", "@id": "/labs/oliver-rando-lab/", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.60479b76-821b-4c03-b0e2-c9351291b965"]}}], "lab": {"@type": ["Lab", "Item"], "status": "current", "display_title": "Job Dekker, UMMS", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "title": "4DNESW1SPPTD - Processed files", "uuid": "684a8eb7-3663-43a0-9dfd-2c03b5859c13", "award": {"status": "current", "display_title": "CENTER FOR 3D STRUCTURE AND PHYSICS OF THE GENOME", "uuid": "ae6c618f-7a8c-441e-a886-e30bbbe591da", "@type": ["Award", "Item"], "@id": "/awards/1U54DK107980-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/higlass-view-configs/684a8eb7-3663-43a0-9dfd-2c03b5859c13/", "display_title": "4DNESW1SPPTD - Processed files", "filetype": "HiglassViewConfig", "name": "684a8eb7-3663-43a0-9dfd-2c03b5859c13", "@type": ["HiglassViewConfig", "UserContent", "Item"], "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": {"@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@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": {"display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "status": "current", "@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": "<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\" target=\"_blank\" rel=\"noopener noreferrer\">doi:10.1038/nature23884</a>) \nand the 4DN Data Portal paper \n(<a href=\"https://doi.org/10.1038/s41467-022-29697-4\" target=\"_blank\" rel=\"noopener noreferrer\">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>"}], "processed_files": [{"href": "/files-processed/4DNFIL84TXJ9/@@download/4DNFIL84TXJ9.pairs.gz", "file_size": 62448870527, "status": "released", "@type": ["FileProcessed", "File", "Item"], "md5sum": "fc73ad34f8c775d6555c3f1a4460aad5", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/aa6656a6-f4be-4805-b947-6f2b35626869/4DNFIL84TXJ9.pairs.gz", "file_type": "contact list-combined", "genome_assembly": "GRCh38", "file_classification": "processed file", "display_title": "4DNFIL84TXJ9.pairs.gz", "uuid": "aa6656a6-f4be-4805-b947-6f2b35626869", "accession": "4DNFIL84TXJ9", "@id": "/files-processed/4DNFIL84TXJ9/", "file_type_detailed": "contact list-combined (pairs)", "upload_key": "aa6656a6-f4be-4805-b947-6f2b35626869/4DNFIL84TXJ9.pairs.gz", "quality_metric": {"uuid": "20571a40-37b7-46ea-81e6-7039c40a76a6", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIL84TXJ9/pairsqc_report.html", "status": "released", "display_title": "QualityMetricPairsqc from 2020-07-02", "Total reads": 3400024261, "overall_quality_status": "PASS", "@id": "/quality-metrics-pairsqc/20571a40-37b7-46ea-81e6-7039c40a76a6/", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "3400024261", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "22.948", "tooltip": "Percent of filtered reads (=780.22m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "47.385", "tooltip": "Percent of filtered reads (=1611.09m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "29.668", "tooltip": "Percent of filtered reads (=1008.71m)", "numberType": "percent"}]}, "lab": {"name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "extra_files": [{"file_size": 17885569, "href": "/files-processed/4DNFIL84TXJ9/@@download/4DNFIL84TXJ9.pairs.gz.px2", "md5sum": "2d66515799111ebb08cb9068ff2f9408", "file_format": {"display_title": "pairs_px2", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "@id": "/file-formats/pairs_px2/", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "pairs_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "Micro-C", "assay_info": "MNase", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}, "contributing_labs": [{"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "external_references": [], "last_modified": {"date_modified": "2021-04-06T20:15:22.361240+00:00"}}, {"href": "/files-processed/4DNFI2WSZPG9/@@download/4DNFI2WSZPG9.hic", "file_size": 18491197022, "status": "released", "@type": ["FileProcessed", "File", "Item"], "md5sum": "384bb965d903f94157fa6e49d9232a19", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "@id": "/file-formats/hic/", "display_title": "hic", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/9e26fac7-1e30-4abb-8946-8a23b3487365/4DNFI2WSZPG9.hic", "file_type": "contact matrix", "genome_assembly": "GRCh38", "file_classification": "processed file", "display_title": "4DNFI2WSZPG9.hic", "uuid": "9e26fac7-1e30-4abb-8946-8a23b3487365", "accession": "4DNFI2WSZPG9", "@id": "/files-processed/4DNFI2WSZPG9/", "file_type_detailed": "contact matrix (hic)", "upload_key": "9e26fac7-1e30-4abb-8946-8a23b3487365/4DNFI2WSZPG9.hic", "lab": {"name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "Micro-C", "assay_info": "MNase", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}, "contributing_labs": [{"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "external_references": [], "last_modified": {"date_modified": "2021-03-28T14:24:53.029625+00:00"}}, {"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."], "href": "/files-processed/4DNFINQYW56E/@@download/4DNFINQYW56E.mcool", "file_size": 12685073624, "status": "released", "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "d425c6bd-4370-4321-b07b-850d706b36dc", "md5sum": "f43009ac4b78b67760992ae0247913e9", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "@id": "/file-formats/mcool/", "display_title": "mcool", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e5b24e82-a430-4a35-94ce-09a860ddf552/4DNFINQYW56E.mcool", "file_type": "contact matrix", "genome_assembly": "GRCh38", "file_classification": "processed file", "display_title": "4DNFINQYW56E.mcool", "uuid": "e5b24e82-a430-4a35-94ce-09a860ddf552", "accession": "4DNFINQYW56E", "@id": "/files-processed/4DNFINQYW56E/", "file_type_detailed": "contact matrix (mcool)", "upload_key": "e5b24e82-a430-4a35-94ce-09a860ddf552/4DNFINQYW56E.mcool", "quality_metric": {"uuid": "c25af09b-d02e-4420-853a-2d54d1c2af28", "status": "released", "display_title": "QualityMetricMcool from 2021-05-21", "overall_quality_status": "PASS", "@id": "/quality-metrics-mcool/c25af09b-d02e-4420-853a-2d54d1c2af28/", "@type": ["QualityMetricMcool", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Failed Balancing", "value": "None", "tooltip": "Resolutions where balancing failed", "numberType": "string"}]}, "lab": {"name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"status": "released", "display_title": "4DNFINQYW56E - contact matrix for H1-hESC (Tier 1) differentiated to definitive endoderm Micro-C MNase", "uuid": "8dd6592a-5c10-4462-8779-db596380e960", "@id": "/higlass-view-configs/8dd6592a-5c10-4462-8779-db596380e960/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "track_and_facet_info": {"dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "Micro-C", "assay_info": "MNase", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS", "track_title": "contact matrix for H1-hESC (Tier 1) differentiated to definitive endoderm Micro-C MNase"}, "contributing_labs": [{"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "external_references": [], "last_modified": {"date_modified": "2023-08-25T17:49:25.521137+00:00"}}, {"href": "/files-processed/4DNFIA19FZM3/@@download/4DNFIA19FZM3.bed.gz", "file_size": 188478, "status": "released", "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "N9OAJ2GASai3RfCN5m_kkQ", "md5sum": "086411e6e4e18f7906cafb9a2f52393a", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "@id": "/file-formats/bed/", "display_title": "bed", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/be3555c2-ee15-478a-9454-d96f08c43f06/4DNFIA19FZM3.bed.gz", "file_type": "boundaries", "genome_assembly": "GRCh38", "file_classification": "processed file", "display_title": "4DNFIA19FZM3.bed.gz", "uuid": "be3555c2-ee15-478a-9454-d96f08c43f06", "accession": "4DNFIA19FZM3", "@id": "/files-processed/4DNFIA19FZM3/", "file_type_detailed": "boundaries (bed)", "upload_key": "be3555c2-ee15-478a-9454-d96f08c43f06/4DNFIA19FZM3.bed.gz", "lab": {"name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"status": "released", "display_title": "4DNFIA19FZM3 - boundaries for H1-hESC (Tier 1) differentiated to definitive endoderm Micro-C MNase", "uuid": "54423695-13ad-4fcf-8a39-61574a4fb44f", "@id": "/higlass-view-configs/54423695-13ad-4fcf-8a39-61574a4fb44f/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "extra_files": [{"use_for": "visualization", "href": "/files-processed/4DNFIA19FZM3/@@download/4DNFIA19FZM3.beddb", "md5sum": "d10b257c4c9f43c4bd226795f3943fb8", "file_format": {"display_title": "beddb", "uuid": "76dc8c06-67d8-487b-8fc8-d841752a0b60", "@id": "/file-formats/beddb/", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "beddb", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "Micro-C", "assay_info": "MNase", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS", "track_title": "boundaries for H1-hESC (Tier 1) differentiated to definitive endoderm Micro-C MNase"}, "contributing_labs": [{"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "external_references": [], "last_modified": {"date_modified": "2021-05-10T23:49:05.397868+00:00"}}, {"href": "/files-processed/4DNFIXR7P794/@@download/4DNFIXR7P794.bw", "file_size": 8512905, "status": "released", "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "d9e9ee20-673c-43f5-925e-73e5adba1cae", "md5sum": "179e8328e636e94711a62da705f23262", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bw/", "display_title": "bw", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/d107b22c-288c-495b-a3fa-b3412c8664af/4DNFIXR7P794.bw", "file_type": "insulation score-diamond", "genome_assembly": "GRCh38", "file_classification": "processed file", "display_title": "4DNFIXR7P794.bw", "uuid": "d107b22c-288c-495b-a3fa-b3412c8664af", "accession": "4DNFIXR7P794", "@id": "/files-processed/4DNFIXR7P794/", "file_type_detailed": "insulation score-diamond (bw)", "upload_key": "d107b22c-288c-495b-a3fa-b3412c8664af/4DNFIXR7P794.bw", "lab": {"name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"status": "released", "display_title": "4DNFIXR7P794 - insulation score-diamond for H1-hESC (Tier 1) differentiated to definitive endoderm Micro-C MNase", "uuid": "8c032df4-6255-4b8b-b7ea-24e774ce3186", "@id": "/higlass-view-configs/8c032df4-6255-4b8b-b7ea-24e774ce3186/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "track_and_facet_info": {"dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "Micro-C", "assay_info": "MNase", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS", "track_title": "insulation score-diamond for H1-hESC (Tier 1) differentiated to definitive endoderm Micro-C MNase"}, "contributing_labs": [{"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "external_references": [], "last_modified": {"date_modified": "2021-03-28T14:04:42.941800+00:00"}}, {"href": "/files-processed/4DNFIS47UYYR/@@download/4DNFIS47UYYR.bw", "file_size": 212885, "status": "released", "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "515b2457-b9d2-48f0-a30e-5e35fb1d2687", "md5sum": "e04f2fbf01b57c6f579348f15b0a89cc", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/bw/", "display_title": "bw", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/094ff3ed-89a8-4ea6-80e2-43af9d0d1bb0/4DNFIS47UYYR.bw", "file_type": "compartments", "genome_assembly": "GRCh38", "file_classification": "processed file", "display_title": "4DNFIS47UYYR.bw", "uuid": "094ff3ed-89a8-4ea6-80e2-43af9d0d1bb0", "accession": "4DNFIS47UYYR", "@id": "/files-processed/4DNFIS47UYYR/", "file_type_detailed": "compartments (bw)", "upload_key": "094ff3ed-89a8-4ea6-80e2-43af9d0d1bb0/4DNFIS47UYYR.bw", "lab": {"name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"status": "released", "display_title": "4DNFIS47UYYR - compartments for H1-hESC (Tier 1) differentiated to definitive endoderm Micro-C MNase", "uuid": "89b5cbf4-4e01-40ed-8243-9b091b290418", "@id": "/higlass-view-configs/89b5cbf4-4e01-40ed-8243-9b091b290418/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "track_and_facet_info": {"dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "Micro-C", "assay_info": "MNase", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS", "track_title": "compartments for H1-hESC (Tier 1) differentiated to definitive endoderm Micro-C MNase"}, "contributing_labs": [{"uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "external_references": [], "last_modified": {"date_modified": "2021-03-28T14:04:25.663595+00:00"}}], "project_release": "2020-08-11", "contributing_labs": [{"@id": "/labs/oliver-rando-lab/", "uuid": "60479b76-821b-4c03-b0e2-c9351291b965", "correspondence": [{"contact_email": "b2xpdmVyLnJhbmRvQHVtYXNzbWVkLmVkdQ==", "@id": "/users/a42aa62c-9175-4dae-9319-4dc1ad6dac0a/", "display_title": "Oliver Rando"}], "status": "current", "@type": ["Lab", "Item"], "display_title": "Oliver Rando, UMMS", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.60479b76-821b-4c03-b0e2-c9351291b965"]}}], "experiments_in_set": [{"files": [{"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/32f5d20f-db0e-4518-8990-907271767f7a/4DNFIRA3BHUT.fastq.gz", "uuid": "32f5d20f-db0e-4518-8990-907271767f7a", "@id": "/files-fastq/4DNFIRA3BHUT/", "status": "released", "display_title": "4DNFIRA3BHUT.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFIRA3BHUT/@@download/4DNFIRA3BHUT.fastq.gz", "file_type": "reads", "file_size": 10964439114, "md5sum": "d7fdbc1664ee73b07fd090410720dd4d", "accession": "4DNFIRA3BHUT", "@type": ["FileFastq", "File", "Item"], "upload_key": "32f5d20f-db0e-4518-8990-907271767f7a/4DNFIRA3BHUT.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "7963c864-519b-476e-811e-2544014f7f65", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIDDSOUFG/", "file_type": "reads", "accession": "4DNFIDDSOUFG", "display_title": "4DNFIDDSOUFG.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 348419266, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIRA3BHUT/fastqc_report.html", "@id": "/quality-metrics-fastqc/b3733b93-fd6f-4238-8ba4-32c9790ee28c/", "overall_quality_status": "PASS", "uuid": "b3733b93-fd6f-4238-8ba4-32c9790ee28c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/7963c864-519b-476e-811e-2544014f7f65/4DNFIDDSOUFG.fastq.gz", "uuid": "7963c864-519b-476e-811e-2544014f7f65", "@id": "/files-fastq/4DNFIDDSOUFG/", "status": "released", "display_title": "4DNFIDDSOUFG.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFIDDSOUFG/@@download/4DNFIDDSOUFG.fastq.gz", "file_type": "reads", "file_size": 12149131642, "md5sum": "24327c13cd75c7754ec03aa074968d54", "accession": "4DNFIDDSOUFG", "@type": ["FileFastq", "File", "Item"], "upload_key": "7963c864-519b-476e-811e-2544014f7f65/4DNFIDDSOUFG.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "32f5d20f-db0e-4518-8990-907271767f7a", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIRA3BHUT/", "file_type": "reads", "accession": "4DNFIRA3BHUT", "display_title": "4DNFIRA3BHUT.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 348419266, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIDDSOUFG/fastqc_report.html", "@id": "/quality-metrics-fastqc/5e8bd220-6ef0-4a24-80ca-b9b2a960dd22/", "overall_quality_status": "PASS", "uuid": "5e8bd220-6ef0-4a24-80ca-b9b2a960dd22", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/18c16f22-cd71-48da-8f6f-5ccce7ca6ae5/4DNFINO9Y18W.fastq.gz", "uuid": "18c16f22-cd71-48da-8f6f-5ccce7ca6ae5", "@id": "/files-fastq/4DNFINO9Y18W/", "status": "released", "display_title": "4DNFINO9Y18W.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFINO9Y18W/@@download/4DNFINO9Y18W.fastq.gz", "file_type": "reads", "file_size": 11031684846, "md5sum": "c5e69315cdc9b86d84713cd613d36b76", "accession": "4DNFINO9Y18W", "@type": ["FileFastq", "File", "Item"], "upload_key": "18c16f22-cd71-48da-8f6f-5ccce7ca6ae5/4DNFINO9Y18W.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "a017c9df-ae53-4b67-90c8-d8a21ebd5cd4", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFI6UQAHXC/", "file_type": "reads", "accession": "4DNFI6UQAHXC", "display_title": "4DNFI6UQAHXC.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 350721136, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFINO9Y18W/fastqc_report.html", "@id": "/quality-metrics-fastqc/21542027-cf54-46ef-8127-48f311cd41a2/", "overall_quality_status": "PASS", "uuid": "21542027-cf54-46ef-8127-48f311cd41a2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/a017c9df-ae53-4b67-90c8-d8a21ebd5cd4/4DNFI6UQAHXC.fastq.gz", "uuid": "a017c9df-ae53-4b67-90c8-d8a21ebd5cd4", "@id": "/files-fastq/4DNFI6UQAHXC/", "status": "released", "display_title": "4DNFI6UQAHXC.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFI6UQAHXC/@@download/4DNFI6UQAHXC.fastq.gz", "file_type": "reads", "file_size": 12143282808, "md5sum": "a2c3192d7dfa9351ff7303962cfe3084", "accession": "4DNFI6UQAHXC", "@type": ["FileFastq", "File", "Item"], "upload_key": "a017c9df-ae53-4b67-90c8-d8a21ebd5cd4/4DNFI6UQAHXC.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "18c16f22-cd71-48da-8f6f-5ccce7ca6ae5", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFINO9Y18W/", "file_type": "reads", "accession": "4DNFINO9Y18W", "display_title": "4DNFINO9Y18W.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 350721136, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI6UQAHXC/fastqc_report.html", "@id": "/quality-metrics-fastqc/fa5b6950-cc89-4c43-823d-a9b3b17b0e30/", "overall_quality_status": "PASS", "uuid": "fa5b6950-cc89-4c43-823d-a9b3b17b0e30", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}], "display_title": "Micro-C on H1-hESC (Tier 1) differentiated to definitive endoderm with MNase - 4DNEX1JFQVNZ", "@type": ["ExperimentHiC", "Experiment", "Item"], "status": "released", "@id": "/experiments-hi-c/4DNEX1JFQVNZ/", "crosslinking_method": "1% Formaldehyde and 3mM DSG", "uuid": "8186b39b-5ce6-48a3-97d4-0053dd10001b", "accession": "4DNEX1JFQVNZ", "processed_files": [{"href": "/files-processed/4DNFIW2YO3FQ/@@download/4DNFIW2YO3FQ.bam", "file_classification": "processed file", "file_type": "alignments", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "47c38460-c9f5-4b5f-b870-5829a49c0dde", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "alignments (bam)", "md5sum": "5557eb7b61074d56e33dbe348f69732b", "accession": "4DNFIW2YO3FQ", "display_title": "4DNFIW2YO3FQ.bam", "status": "released", "genome_assembly": "GRCh38", "file_size": 66331685269, "@id": "/files-processed/4DNFIW2YO3FQ/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/47c38460-c9f5-4b5f-b870-5829a49c0dde/4DNFIW2YO3FQ.bam", "upload_key": "47c38460-c9f5-4b5f-b870-5829a49c0dde/4DNFIW2YO3FQ.bam", "quality_metric": {"@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-bamqc/dd6017ea-8527-4da4-823b-61114733117c/", "overall_quality_status": "PASS", "display_title": "QualityMetricBamqc from 2020-07-01", "uuid": "dd6017ea-8527-4da4-823b-61114733117c", "quality_metric_summary": [{"title": "Total Reads", "value": "699140402", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "3.97", "tooltip": "Percent of total reads (=27.75m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "20.268", "tooltip": "Percent of total reads (=141.7m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "9.526", "tooltip": "Percent of total reads (=66.6m)", "numberType": "percent"}, {"title": "Walks", "value": "0.004", "tooltip": "Percent of total reads (=0.03m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.141", "tooltip": "Percent of total reads (=0.99m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "status": "current", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-03-28T14:28:54.518759+00:00"}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "processed file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}}, {"href": "/files-processed/4DNFIOBB3FJV/@@download/4DNFIOBB3FJV.pairs.gz", "file_classification": "processed file", "file_type": "contact list-replicate", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "fe734ab2-b05a-46b4-9ca3-833429822877", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "contact list-replicate (pairs)", "md5sum": "4dddaa9cb5858ad34695e0495a3d19ce", "accession": "4DNFIOBB3FJV", "display_title": "4DNFIOBB3FJV.pairs.gz", "status": "released", "genome_assembly": "GRCh38", "file_size": 8913158455, "@id": "/files-processed/4DNFIOBB3FJV/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/fe734ab2-b05a-46b4-9ca3-833429822877/4DNFIOBB3FJV.pairs.gz", "upload_key": "fe734ab2-b05a-46b4-9ca3-833429822877/4DNFIOBB3FJV.pairs.gz", "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIOBB3FJV/pairsqc_report.html", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Total reads": 463054749, "status": "released", "@id": "/quality-metrics-pairsqc/8cf88b86-e43f-4d0b-aec3-b7d1cbda5339/", "overall_quality_status": "PASS", "display_title": "QualityMetricPairsqc from 2020-07-01", "uuid": "8cf88b86-e43f-4d0b-aec3-b7d1cbda5339", "quality_metric_summary": [{"title": "Filtered Reads", "value": "463054749", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "24.977", "tooltip": "Percent of filtered reads (=115.66m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "50.667", "tooltip": "Percent of filtered reads (=234.62m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "24.356", "tooltip": "Percent of filtered reads (=112.78m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "extra_files": [{"href": "/files-processed/4DNFIOBB3FJV/@@download/4DNFIOBB3FJV.pairs.gz.px2", "file_size": 30409463, "md5sum": "81933a96f96044e83828a84c39a15732", "file_format": {"display_title": "pairs_px2", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs_px2/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "file_format": "pairs_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "status": "current", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-04-06T20:16:58.080691+00:00"}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "processed file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}}], "biosample": {"biosample_type": "in vitro differentiated cells", "display_title": "4DNBSMW55C3H", "@id": "/biosamples/4DNBSMW55C3H/", "biosource_summary": "H1-hESC (Tier 1) differentiated to definitive endoderm", "accession": "4DNBSMW55C3H", "biosample_category": ["H1-hESC", "In vitro Differentiation"], "@type": ["Biosample", "Item"], "status": "released", "treatments_summary": "None", "modifications_summary": "None", "uuid": "3af6c45d-a937-49f1-ae40-dac0f56498b4", "cell_culture_details": [{"display_title": "BiosampleCellCulture from 2020-06-24", "uuid": "782af389-598d-4d8a-8681-2bd3309675cd", "@id": "/biosample-cell-cultures/782af389-598d-4d8a-8681-2bd3309675cd/", "in_vitro_differentiated": "Yes", "@type": ["BiosampleCellCulture", "Item"], "status": "released", "tissue": {"@id": "/ontology-terms/UBERON:0005439/", "term_id": "UBERON:0005439", "display_title": "definitive endoderm", "@type": ["OntologyTerm", "Item"], "term_name": "definitive endoderm", "preferred_name": "definitive endoderm", "status": "released", "synonyms": ["embryonic endoderm"], "uuid": "52e444bc-62c2-4524-a29c-4aa4d1d96f26", "slim_terms": [{"status": "released", "@id": "/ontology-terms/UBERON:0000925/", "@type": ["OntologyTerm", "Item"], "display_title": "endoderm", "uuid": "111121bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosource": [{"@type": ["Biosource", "Item"], "@id": "/biosources/4DNSRV3SKQ8M/", "accession": "4DNSRV3SKQ8M", "uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "status": "released", "cell_line_tier": "Tier 1", "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "biosource_type": "stem cell derived cell line", "tissue": {"term_name": "stem cell", "term_id": "CL:0000034", "preferred_name": "stem cell", "display_title": "stem cell", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000034/", "synonyms": ["animal stem cell"], "status": "released", "slim_terms": [{"status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"term_id": "EFO:0003042", "status": "released", "term_name": "H1-hESC", "display_title": "H1-hESC", "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "@id": "/ontology-terms/EFO:0003042/", "preferred_name": "H1-hESC", "synonyms": ["H1"], "@type": ["OntologyTerm", "Item"], "slim_terms": [{"status": "current", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"display_title": "H. sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@type": ["Organism", "Item"], "status": "released", "scientific_name": "Homo sapiens", "@id": "/organisms/9606/", "name": "human", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing doubling_number"], "badge": {"warning": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "badge_icon": "/static/img/badges/biosample-icon.svg", "status": "released", "@type": ["Badge", "Item"], "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "badge_classification": "Warning", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"organ_system": ["endoderm"], "tissue_source": "definitive endoderm"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"display_title": "MNase", "status": "released", "@type": ["Enzyme", "Item"], "uuid": "e781b59c-ef3d-4ae4-9a94-4a34190bc6d2", "@id": "/enzymes/MNase/", "name": "MNase", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"field": "Enzyme", "value": "MNase", "combined": "Enzyme: MNase"}, "experiment_type": {"assay_classification": "3C via Ligation", "assay_subclassification": "DNA-DNA Pairwise Interactions", "status": "released", "@type": ["ExperimentType", "Item"], "assay_subclass_short": "Hi-C", "@id": "/experiment-types/micro-c/", "experiment_category": "Sequencing", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "uuid": "bc7899cf-8352-4360-b9be-efc3c7e3a574", "title": "Micro-C", "display_title": "Micro-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-01-04T14:57:10.452604+00:00"}, "external_references": []}, {"files": [{"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/8dbdc78e-acea-4733-a0fe-16e00f99fadb/4DNFIFL5NLDP.fastq.gz", "uuid": "8dbdc78e-acea-4733-a0fe-16e00f99fadb", "@id": "/files-fastq/4DNFIFL5NLDP/", "status": "released", "display_title": "4DNFIFL5NLDP.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFIFL5NLDP/@@download/4DNFIFL5NLDP.fastq.gz", "file_type": "reads", "file_size": 11124011362, "md5sum": "f953beec7ff992fb81d9dbac15210f50", "accession": "4DNFIFL5NLDP", "@type": ["FileFastq", "File", "Item"], "upload_key": "8dbdc78e-acea-4733-a0fe-16e00f99fadb/4DNFIFL5NLDP.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "c6234fe1-4f43-4be7-9db7-da57edf2a5fa", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFI71VGMKQ/", "file_type": "reads", "accession": "4DNFI71VGMKQ", "display_title": "4DNFI71VGMKQ.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 361029849, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIFL5NLDP/fastqc_report.html", "@id": "/quality-metrics-fastqc/7f19102e-f4a1-4b14-9b0c-40042a28f22c/", "overall_quality_status": "PASS", "uuid": "7f19102e-f4a1-4b14-9b0c-40042a28f22c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 2", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/c6234fe1-4f43-4be7-9db7-da57edf2a5fa/4DNFI71VGMKQ.fastq.gz", "uuid": "c6234fe1-4f43-4be7-9db7-da57edf2a5fa", "@id": "/files-fastq/4DNFI71VGMKQ/", "status": "released", "display_title": "4DNFI71VGMKQ.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFI71VGMKQ/@@download/4DNFI71VGMKQ.fastq.gz", "file_type": "reads", "file_size": 12220623810, "md5sum": "c93a23293bc11f39ae5f40e9a7e6ddea", "accession": "4DNFI71VGMKQ", "@type": ["FileFastq", "File", "Item"], "upload_key": "c6234fe1-4f43-4be7-9db7-da57edf2a5fa/4DNFI71VGMKQ.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "8dbdc78e-acea-4733-a0fe-16e00f99fadb", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIFL5NLDP/", "file_type": "reads", "accession": "4DNFIFL5NLDP", "display_title": "4DNFIFL5NLDP.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 361029849, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI71VGMKQ/fastqc_report.html", "@id": "/quality-metrics-fastqc/a53b0db1-bc64-4383-9197-9466b9905b8c/", "overall_quality_status": "PASS", "uuid": "a53b0db1-bc64-4383-9197-9466b9905b8c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 2", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/dfda4715-9026-4493-8f0c-1bffaffee1fc/4DNFID884RIZ.fastq.gz", "uuid": "dfda4715-9026-4493-8f0c-1bffaffee1fc", "@id": "/files-fastq/4DNFID884RIZ/", "status": "released", "display_title": "4DNFID884RIZ.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFID884RIZ/@@download/4DNFID884RIZ.fastq.gz", "file_type": "reads", "file_size": 11326234083, "md5sum": "61ae42a7fe14ceeb948eb4a9f882a351", "accession": "4DNFID884RIZ", "@type": ["FileFastq", "File", "Item"], "upload_key": "dfda4715-9026-4493-8f0c-1bffaffee1fc/4DNFID884RIZ.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "97fb2134-28d9-4b3e-b90b-b97a832ac78c", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFICOXOXXJ/", "file_type": "reads", "accession": "4DNFICOXOXXJ", "display_title": "4DNFICOXOXXJ.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 368057782, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFID884RIZ/fastqc_report.html", "@id": "/quality-metrics-fastqc/85e7c86a-4792-4931-8530-35a03a1d4fde/", "overall_quality_status": "PASS", "uuid": "85e7c86a-4792-4931-8530-35a03a1d4fde", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 2", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/97fb2134-28d9-4b3e-b90b-b97a832ac78c/4DNFICOXOXXJ.fastq.gz", "uuid": "97fb2134-28d9-4b3e-b90b-b97a832ac78c", "@id": "/files-fastq/4DNFICOXOXXJ/", "status": "released", "display_title": "4DNFICOXOXXJ.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFICOXOXXJ/@@download/4DNFICOXOXXJ.fastq.gz", "file_type": "reads", "file_size": 12530592234, "md5sum": "d21434789dc62456de5b1c743f03f2fa", "accession": "4DNFICOXOXXJ", "@type": ["FileFastq", "File", "Item"], "upload_key": "97fb2134-28d9-4b3e-b90b-b97a832ac78c/4DNFICOXOXXJ.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "dfda4715-9026-4493-8f0c-1bffaffee1fc", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFID884RIZ/", "file_type": "reads", "accession": "4DNFID884RIZ", "display_title": "4DNFID884RIZ.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 368057782, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFICOXOXXJ/fastqc_report.html", "@id": "/quality-metrics-fastqc/769a7ac1-6eb9-499a-ae9c-cd778ea96f29/", "overall_quality_status": "PASS", "uuid": "769a7ac1-6eb9-499a-ae9c-cd778ea96f29", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 2", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}], "display_title": "Micro-C on H1-hESC (Tier 1) differentiated to definitive endoderm with MNase - 4DNEXOCFRELS", "@type": ["ExperimentHiC", "Experiment", "Item"], "status": "released", "@id": "/experiments-hi-c/4DNEXOCFRELS/", "crosslinking_method": "1% Formaldehyde and 3mM DSG", "uuid": "f85f6c68-d38c-4599-824d-a9b6563df64d", "accession": "4DNEXOCFRELS", "processed_files": [{"href": "/files-processed/4DNFINAFVEJR/@@download/4DNFINAFVEJR.bam", "file_classification": "processed file", "file_type": "alignments", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "c19249e3-433b-40f2-b5a1-8382216aa3f1", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "alignments (bam)", "md5sum": "51c8e5484186ebaed89f9c3d1037b30e", "accession": "4DNFINAFVEJR", "display_title": "4DNFINAFVEJR.bam", "status": "released", "genome_assembly": "GRCh38", "file_size": 66866801998, "@id": "/files-processed/4DNFINAFVEJR/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c19249e3-433b-40f2-b5a1-8382216aa3f1/4DNFINAFVEJR.bam", "upload_key": "c19249e3-433b-40f2-b5a1-8382216aa3f1/4DNFINAFVEJR.bam", "quality_metric": {"@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-bamqc/a1624fc8-e976-4b75-9cbf-79a056e6c87a/", "overall_quality_status": "PASS", "display_title": "QualityMetricBamqc from 2020-07-01", "uuid": "a1624fc8-e976-4b75-9cbf-79a056e6c87a", "quality_metric_summary": [{"title": "Total Reads", "value": "729087631", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "3.94", "tooltip": "Percent of total reads (=28.72m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "20.129", "tooltip": "Percent of total reads (=146.76m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "12.038", "tooltip": "Percent of total reads (=87.77m)", "numberType": "percent"}, {"title": "Walks", "value": "0.005", "tooltip": "Percent of total reads (=0.04m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.129", "tooltip": "Percent of total reads (=0.94m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "status": "current", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-03-28T14:28:52.972249+00:00"}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "processed file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 2", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}}, {"href": "/files-processed/4DNFINVTGV2T/@@download/4DNFINVTGV2T.pairs.gz", "file_classification": "processed file", "file_type": "contact list-replicate", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "975abee3-b033-4946-9152-26fa22ab2490", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "contact list-replicate (pairs)", "md5sum": "2099f754c251c0f42c66850aa68a090e", "accession": "4DNFINVTGV2T", "display_title": "4DNFINVTGV2T.pairs.gz", "status": "released", "genome_assembly": "GRCh38", "file_size": 8947462405, "@id": "/files-processed/4DNFINVTGV2T/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/975abee3-b033-4946-9152-26fa22ab2490/4DNFINVTGV2T.pairs.gz", "upload_key": "975abee3-b033-4946-9152-26fa22ab2490/4DNFINVTGV2T.pairs.gz", "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFINVTGV2T/pairsqc_report.html", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Total reads": 465804948, "status": "released", "@id": "/quality-metrics-pairsqc/2ae76867-6343-48f9-bf9d-478860477482/", "overall_quality_status": "PASS", "display_title": "QualityMetricPairsqc from 2020-07-01", "uuid": "2ae76867-6343-48f9-bf9d-478860477482", "quality_metric_summary": [{"title": "Filtered Reads", "value": "465804948", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "25.491", "tooltip": "Percent of filtered reads (=118.74m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "51.21", "tooltip": "Percent of filtered reads (=238.54m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "23.299", "tooltip": "Percent of filtered reads (=108.53m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "extra_files": [{"href": "/files-processed/4DNFINVTGV2T/@@download/4DNFINVTGV2T.pairs.gz.px2", "file_size": 30207515, "md5sum": "18779d92344607f675b3f23777e50b98", "file_format": {"display_title": "pairs_px2", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs_px2/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "file_format": "pairs_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "status": "current", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-04-06T20:16:57.170588+00:00"}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "processed file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 2", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}}], "biosample": {"biosample_type": "in vitro differentiated cells", "display_title": "4DNBSMW55C3H", "@id": "/biosamples/4DNBSMW55C3H/", "biosource_summary": "H1-hESC (Tier 1) differentiated to definitive endoderm", "accession": "4DNBSMW55C3H", "biosample_category": ["H1-hESC", "In vitro Differentiation"], "@type": ["Biosample", "Item"], "status": "released", "treatments_summary": "None", "modifications_summary": "None", "uuid": "3af6c45d-a937-49f1-ae40-dac0f56498b4", "cell_culture_details": [{"display_title": "BiosampleCellCulture from 2020-06-24", "uuid": "782af389-598d-4d8a-8681-2bd3309675cd", "@id": "/biosample-cell-cultures/782af389-598d-4d8a-8681-2bd3309675cd/", "in_vitro_differentiated": "Yes", "@type": ["BiosampleCellCulture", "Item"], "status": "released", "tissue": {"@id": "/ontology-terms/UBERON:0005439/", "term_id": "UBERON:0005439", "display_title": "definitive endoderm", "@type": ["OntologyTerm", "Item"], "term_name": "definitive endoderm", "preferred_name": "definitive endoderm", "status": "released", "synonyms": ["embryonic endoderm"], "uuid": "52e444bc-62c2-4524-a29c-4aa4d1d96f26", "slim_terms": [{"status": "released", "@id": "/ontology-terms/UBERON:0000925/", "@type": ["OntologyTerm", "Item"], "display_title": "endoderm", "uuid": "111121bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosource": [{"@type": ["Biosource", "Item"], "@id": "/biosources/4DNSRV3SKQ8M/", "accession": "4DNSRV3SKQ8M", "uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "status": "released", "cell_line_tier": "Tier 1", "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "biosource_type": "stem cell derived cell line", "tissue": {"term_name": "stem cell", "term_id": "CL:0000034", "preferred_name": "stem cell", "display_title": "stem cell", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000034/", "synonyms": ["animal stem cell"], "status": "released", "slim_terms": [{"status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"term_id": "EFO:0003042", "status": "released", "term_name": "H1-hESC", "display_title": "H1-hESC", "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "@id": "/ontology-terms/EFO:0003042/", "preferred_name": "H1-hESC", "synonyms": ["H1"], "@type": ["OntologyTerm", "Item"], "slim_terms": [{"status": "current", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"display_title": "H. sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@type": ["Organism", "Item"], "status": "released", "scientific_name": "Homo sapiens", "@id": "/organisms/9606/", "name": "human", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing doubling_number"], "badge": {"warning": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "badge_icon": "/static/img/badges/biosample-icon.svg", "status": "released", "@type": ["Badge", "Item"], "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "badge_classification": "Warning", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"organ_system": ["endoderm"], "tissue_source": "definitive endoderm"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"display_title": "MNase", "status": "released", "@type": ["Enzyme", "Item"], "uuid": "e781b59c-ef3d-4ae4-9a94-4a34190bc6d2", "@id": "/enzymes/MNase/", "name": "MNase", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"field": "Enzyme", "value": "MNase", "combined": "Enzyme: MNase"}, "experiment_type": {"assay_classification": "3C via Ligation", "assay_subclassification": "DNA-DNA Pairwise Interactions", "status": "released", "@type": ["ExperimentType", "Item"], "assay_subclass_short": "Hi-C", "@id": "/experiment-types/micro-c/", "experiment_category": "Sequencing", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "uuid": "bc7899cf-8352-4360-b9be-efc3c7e3a574", "title": "Micro-C", "display_title": "Micro-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-01-04T14:57:21.276603+00:00"}, "external_references": []}, {"files": [{"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/7b13b3c6-d0ff-49c7-9eea-d093a8e1d67d/4DNFIGFB4DFR.fastq.gz", "uuid": "7b13b3c6-d0ff-49c7-9eea-d093a8e1d67d", "@id": "/files-fastq/4DNFIGFB4DFR/", "status": "released", "display_title": "4DNFIGFB4DFR.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFIGFB4DFR/@@download/4DNFIGFB4DFR.fastq.gz", "file_type": "reads", "file_size": 10876994909, "md5sum": "1ef08393362df0eb91e019ec1895da69", "accession": "4DNFIGFB4DFR", "@type": ["FileFastq", "File", "Item"], "upload_key": "7b13b3c6-d0ff-49c7-9eea-d093a8e1d67d/4DNFIGFB4DFR.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "65603c3c-4d70-45a1-8cd7-4e33c9f0f64a", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIDSOYXXS/", "file_type": "reads", "accession": "4DNFIDSOYXXS", "display_title": "4DNFIDSOYXXS.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 352829833, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIGFB4DFR/fastqc_report.html", "@id": "/quality-metrics-fastqc/37dfd422-8232-498f-abf1-5570ea696866/", "overall_quality_status": "PASS", "uuid": "37dfd422-8232-498f-abf1-5570ea696866", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 3", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/65603c3c-4d70-45a1-8cd7-4e33c9f0f64a/4DNFIDSOYXXS.fastq.gz", "uuid": "65603c3c-4d70-45a1-8cd7-4e33c9f0f64a", "@id": "/files-fastq/4DNFIDSOYXXS/", "status": "released", "display_title": "4DNFIDSOYXXS.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFIDSOYXXS/@@download/4DNFIDSOYXXS.fastq.gz", "file_type": "reads", "file_size": 12218354319, "md5sum": "f2efe038355fee233d939e627dba38b8", "accession": "4DNFIDSOYXXS", "@type": ["FileFastq", "File", "Item"], "upload_key": "65603c3c-4d70-45a1-8cd7-4e33c9f0f64a/4DNFIDSOYXXS.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "7b13b3c6-d0ff-49c7-9eea-d093a8e1d67d", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIGFB4DFR/", "file_type": "reads", "accession": "4DNFIGFB4DFR", "display_title": "4DNFIGFB4DFR.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 352829833, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIDSOYXXS/fastqc_report.html", "@id": "/quality-metrics-fastqc/deb0e7f4-802f-45f0-b3fd-8e56a4e01b10/", "overall_quality_status": "PASS", "uuid": "deb0e7f4-802f-45f0-b3fd-8e56a4e01b10", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 3", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/559552ea-364c-43b7-9f92-25b25016eb3c/4DNFI3ONUDCF.fastq.gz", "uuid": "559552ea-364c-43b7-9f92-25b25016eb3c", "@id": "/files-fastq/4DNFI3ONUDCF/", "status": "released", "display_title": "4DNFI3ONUDCF.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFI3ONUDCF/@@download/4DNFI3ONUDCF.fastq.gz", "file_type": "reads", "file_size": 10728450104, "md5sum": "92a6e987cb3756ffba479c8e9abe7684", "accession": "4DNFI3ONUDCF", "@type": ["FileFastq", "File", "Item"], "upload_key": "559552ea-364c-43b7-9f92-25b25016eb3c/4DNFI3ONUDCF.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "3d3b0dc3-53a6-42c9-a2db-0d7078449095", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIVON2BXT/", "file_type": "reads", "accession": "4DNFIVON2BXT", "display_title": "4DNFIVON2BXT.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 340210164, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI3ONUDCF/fastqc_report.html", "@id": "/quality-metrics-fastqc/d9481539-5884-4159-8337-a43cce7aebb3/", "overall_quality_status": "PASS", "uuid": "d9481539-5884-4159-8337-a43cce7aebb3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 3", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/3d3b0dc3-53a6-42c9-a2db-0d7078449095/4DNFIVON2BXT.fastq.gz", "uuid": "3d3b0dc3-53a6-42c9-a2db-0d7078449095", "@id": "/files-fastq/4DNFIVON2BXT/", "status": "released", "display_title": "4DNFIVON2BXT.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFIVON2BXT/@@download/4DNFIVON2BXT.fastq.gz", "file_type": "reads", "file_size": 11927055416, "md5sum": "06157848f6a9dd22fc7f266ed797ea8e", "accession": "4DNFIVON2BXT", "@type": ["FileFastq", "File", "Item"], "upload_key": "3d3b0dc3-53a6-42c9-a2db-0d7078449095/4DNFIVON2BXT.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "559552ea-364c-43b7-9f92-25b25016eb3c", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFI3ONUDCF/", "file_type": "reads", "accession": "4DNFI3ONUDCF", "display_title": "4DNFI3ONUDCF.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 340210164, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIVON2BXT/fastqc_report.html", "@id": "/quality-metrics-fastqc/6ed74249-9dc2-475e-ae86-95f7b96a201b/", "overall_quality_status": "PASS", "uuid": "6ed74249-9dc2-475e-ae86-95f7b96a201b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 3", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}], "display_title": "Micro-C on H1-hESC (Tier 1) differentiated to definitive endoderm with MNase - 4DNEXILU11VM", "@type": ["ExperimentHiC", "Experiment", "Item"], "status": "released", "@id": "/experiments-hi-c/4DNEXILU11VM/", "crosslinking_method": "1% Formaldehyde and 3mM DSG", "uuid": "8bf9e611-ffb6-4890-be26-2e45fda79396", "accession": "4DNEXILU11VM", "processed_files": [{"href": "/files-processed/4DNFI6IZCIGL/@@download/4DNFI6IZCIGL.bam", "file_classification": "processed file", "file_type": "alignments", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "78cb6fd9-0e10-45b5-98c8-9b62f5a5139e", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "alignments (bam)", "md5sum": "8eaec736acaeb7e08c0e274623eadc45", "accession": "4DNFI6IZCIGL", "display_title": "4DNFI6IZCIGL.bam", "status": "released", "genome_assembly": "GRCh38", "file_size": 64112048401, "@id": "/files-processed/4DNFI6IZCIGL/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/78cb6fd9-0e10-45b5-98c8-9b62f5a5139e/4DNFI6IZCIGL.bam", "upload_key": "78cb6fd9-0e10-45b5-98c8-9b62f5a5139e/4DNFI6IZCIGL.bam", "quality_metric": {"@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-bamqc/967a1166-b4f1-4d3d-bb34-69278014d61a/", "overall_quality_status": "PASS", "display_title": "QualityMetricBamqc from 2020-07-01", "uuid": "967a1166-b4f1-4d3d-bb34-69278014d61a", "quality_metric_summary": [{"title": "Total Reads", "value": "693039997", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "4.248", "tooltip": "Percent of total reads (=29.44m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "20.949", "tooltip": "Percent of total reads (=145.19m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "12.643", "tooltip": "Percent of total reads (=87.62m)", "numberType": "percent"}, {"title": "Walks", "value": "0.004", "tooltip": "Percent of total reads (=0.03m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.139", "tooltip": "Percent of total reads (=0.96m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "status": "current", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-03-28T14:28:51.209840+00:00"}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "processed file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 3", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}}, {"href": "/files-processed/4DNFIFUTHP4Q/@@download/4DNFIFUTHP4Q.pairs.gz", "file_classification": "processed file", "file_type": "contact list-replicate", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "f7765647-9f6a-49ef-ac41-a2b0a56eac51", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "contact list-replicate (pairs)", "md5sum": "37655c381062a6bc45a1fd915002bca5", "accession": "4DNFIFUTHP4Q", "display_title": "4DNFIFUTHP4Q.pairs.gz", "status": "released", "genome_assembly": "GRCh38", "file_size": 8297930743, "@id": "/files-processed/4DNFIFUTHP4Q/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f7765647-9f6a-49ef-ac41-a2b0a56eac51/4DNFIFUTHP4Q.pairs.gz", "upload_key": "f7765647-9f6a-49ef-ac41-a2b0a56eac51/4DNFIFUTHP4Q.pairs.gz", "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIFUTHP4Q/pairsqc_report.html", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Total reads": 430764299, "status": "released", "@id": "/quality-metrics-pairsqc/e1780653-cc93-4340-b77f-f11d6859bd0e/", "overall_quality_status": "PASS", "display_title": "QualityMetricPairsqc from 2020-07-01", "uuid": "e1780653-cc93-4340-b77f-f11d6859bd0e", "quality_metric_summary": [{"title": "Filtered Reads", "value": "430764299", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "23.723", "tooltip": "Percent of filtered reads (=102.19m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "50.37", "tooltip": "Percent of filtered reads (=216.97m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "25.907", "tooltip": "Percent of filtered reads (=111.6m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "extra_files": [{"href": "/files-processed/4DNFIFUTHP4Q/@@download/4DNFIFUTHP4Q.pairs.gz.px2", "file_size": 30213357, "md5sum": "fa7c40f6afdde7fec8a0d2625e76a0a7", "file_format": {"display_title": "pairs_px2", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs_px2/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "file_format": "pairs_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "status": "current", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-04-06T20:16:56.474848+00:00"}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "processed file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 3", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}}], "biosample": {"biosample_type": "in vitro differentiated cells", "display_title": "4DNBSMW55C3H", "@id": "/biosamples/4DNBSMW55C3H/", "biosource_summary": "H1-hESC (Tier 1) differentiated to definitive endoderm", "accession": "4DNBSMW55C3H", "biosample_category": ["H1-hESC", "In vitro Differentiation"], "@type": ["Biosample", "Item"], "status": "released", "treatments_summary": "None", "modifications_summary": "None", "uuid": "3af6c45d-a937-49f1-ae40-dac0f56498b4", "cell_culture_details": [{"display_title": "BiosampleCellCulture from 2020-06-24", "uuid": "782af389-598d-4d8a-8681-2bd3309675cd", "@id": "/biosample-cell-cultures/782af389-598d-4d8a-8681-2bd3309675cd/", "in_vitro_differentiated": "Yes", "@type": ["BiosampleCellCulture", "Item"], "status": "released", "tissue": {"@id": "/ontology-terms/UBERON:0005439/", "term_id": "UBERON:0005439", "display_title": "definitive endoderm", "@type": ["OntologyTerm", "Item"], "term_name": "definitive endoderm", "preferred_name": "definitive endoderm", "status": "released", "synonyms": ["embryonic endoderm"], "uuid": "52e444bc-62c2-4524-a29c-4aa4d1d96f26", "slim_terms": [{"status": "released", "@id": "/ontology-terms/UBERON:0000925/", "@type": ["OntologyTerm", "Item"], "display_title": "endoderm", "uuid": "111121bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosource": [{"@type": ["Biosource", "Item"], "@id": "/biosources/4DNSRV3SKQ8M/", "accession": "4DNSRV3SKQ8M", "uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "status": "released", "cell_line_tier": "Tier 1", "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "biosource_type": "stem cell derived cell line", "tissue": {"term_name": "stem cell", "term_id": "CL:0000034", "preferred_name": "stem cell", "display_title": "stem cell", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000034/", "synonyms": ["animal stem cell"], "status": "released", "slim_terms": [{"status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"term_id": "EFO:0003042", "status": "released", "term_name": "H1-hESC", "display_title": "H1-hESC", "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "@id": "/ontology-terms/EFO:0003042/", "preferred_name": "H1-hESC", "synonyms": ["H1"], "@type": ["OntologyTerm", "Item"], "slim_terms": [{"status": "current", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"display_title": "H. sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@type": ["Organism", "Item"], "status": "released", "scientific_name": "Homo sapiens", "@id": "/organisms/9606/", "name": "human", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing doubling_number"], "badge": {"warning": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "badge_icon": "/static/img/badges/biosample-icon.svg", "status": "released", "@type": ["Badge", "Item"], "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "badge_classification": "Warning", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"organ_system": ["endoderm"], "tissue_source": "definitive endoderm"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"display_title": "MNase", "status": "released", "@type": ["Enzyme", "Item"], "uuid": "e781b59c-ef3d-4ae4-9a94-4a34190bc6d2", "@id": "/enzymes/MNase/", "name": "MNase", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"field": "Enzyme", "value": "MNase", "combined": "Enzyme: MNase"}, "experiment_type": {"assay_classification": "3C via Ligation", "assay_subclassification": "DNA-DNA Pairwise Interactions", "status": "released", "@type": ["ExperimentType", "Item"], "assay_subclass_short": "Hi-C", "@id": "/experiment-types/micro-c/", "experiment_category": "Sequencing", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "uuid": "bc7899cf-8352-4360-b9be-efc3c7e3a574", "title": "Micro-C", "display_title": "Micro-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-01-04T14:57:25.147994+00:00"}, "external_references": []}, {"files": [{"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/0c8365c9-0e47-467a-b9e6-81f828c47661/4DNFIR35LDEC.fastq.gz", "uuid": "0c8365c9-0e47-467a-b9e6-81f828c47661", "@id": "/files-fastq/4DNFIR35LDEC/", "status": "released", "display_title": "4DNFIR35LDEC.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFIR35LDEC/@@download/4DNFIR35LDEC.fastq.gz", "file_type": "reads", "file_size": 10747510075, "md5sum": "134d8ccad8cea1e758e3acbac06dbd78", "accession": "4DNFIR35LDEC", "@type": ["FileFastq", "File", "Item"], "upload_key": "0c8365c9-0e47-467a-b9e6-81f828c47661/4DNFIR35LDEC.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "f1b50388-3f65-4e07-8278-771801ac92f7", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFITGG93RZ/", "file_type": "reads", "accession": "4DNFITGG93RZ", "display_title": "4DNFITGG93RZ.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 341103558, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIR35LDEC/fastqc_report.html", "@id": "/quality-metrics-fastqc/08dd263e-fe45-441b-88e7-ea3d7bee7f9a/", "overall_quality_status": "PASS", "uuid": "08dd263e-fe45-441b-88e7-ea3d7bee7f9a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 4", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/f1b50388-3f65-4e07-8278-771801ac92f7/4DNFITGG93RZ.fastq.gz", "uuid": "f1b50388-3f65-4e07-8278-771801ac92f7", "@id": "/files-fastq/4DNFITGG93RZ/", "status": "released", "display_title": "4DNFITGG93RZ.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFITGG93RZ/@@download/4DNFITGG93RZ.fastq.gz", "file_type": "reads", "file_size": 11778654931, "md5sum": "6c38cfd6dc2910b1f327d298aaec940f", "accession": "4DNFITGG93RZ", "@type": ["FileFastq", "File", "Item"], "upload_key": "f1b50388-3f65-4e07-8278-771801ac92f7/4DNFITGG93RZ.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "0c8365c9-0e47-467a-b9e6-81f828c47661", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIR35LDEC/", "file_type": "reads", "accession": "4DNFIR35LDEC", "display_title": "4DNFIR35LDEC.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 341103558, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFITGG93RZ/fastqc_report.html", "@id": "/quality-metrics-fastqc/220dc1f4-293d-4b4d-b16c-5231abf60746/", "overall_quality_status": "PASS", "uuid": "220dc1f4-293d-4b4d-b16c-5231abf60746", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 4", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/4e6acb7d-b222-434b-a250-0098302701ce/4DNFIEZ97SVM.fastq.gz", "uuid": "4e6acb7d-b222-434b-a250-0098302701ce", "@id": "/files-fastq/4DNFIEZ97SVM/", "status": "released", "display_title": "4DNFIEZ97SVM.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFIEZ97SVM/@@download/4DNFIEZ97SVM.fastq.gz", "file_type": "reads", "file_size": 10668665380, "md5sum": "471d3668d24780ded1544dadf7278ac8", "accession": "4DNFIEZ97SVM", "@type": ["FileFastq", "File", "Item"], "upload_key": "4e6acb7d-b222-434b-a250-0098302701ce/4DNFIEZ97SVM.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "09fee941-0a37-4802-8a9a-564300817a80", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIFNKSKIP/", "file_type": "reads", "accession": "4DNFIFNKSKIP", "display_title": "4DNFIFNKSKIP.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 332466326, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIEZ97SVM/fastqc_report.html", "@id": "/quality-metrics-fastqc/57776764-be13-4520-a39d-a13f2c358280/", "overall_quality_status": "PASS", "uuid": "57776764-be13-4520-a39d-a13f2c358280", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 4", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/09fee941-0a37-4802-8a9a-564300817a80/4DNFIFNKSKIP.fastq.gz", "uuid": "09fee941-0a37-4802-8a9a-564300817a80", "@id": "/files-fastq/4DNFIFNKSKIP/", "status": "released", "display_title": "4DNFIFNKSKIP.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFIFNKSKIP/@@download/4DNFIFNKSKIP.fastq.gz", "file_type": "reads", "file_size": 11777912524, "md5sum": "b601f7aeeb51c8a04f3ae03bcba2baf5", "accession": "4DNFIFNKSKIP", "@type": ["FileFastq", "File", "Item"], "upload_key": "09fee941-0a37-4802-8a9a-564300817a80/4DNFIFNKSKIP.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "4e6acb7d-b222-434b-a250-0098302701ce", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIEZ97SVM/", "file_type": "reads", "accession": "4DNFIEZ97SVM", "display_title": "4DNFIEZ97SVM.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 332466326, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIFNKSKIP/fastqc_report.html", "@id": "/quality-metrics-fastqc/1871404d-2973-477c-b450-de4ca22f4d25/", "overall_quality_status": "PASS", "uuid": "1871404d-2973-477c-b450-de4ca22f4d25", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 4", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}], "display_title": "Micro-C on H1-hESC (Tier 1) differentiated to definitive endoderm with MNase - 4DNEXO7YBCMP", "@type": ["ExperimentHiC", "Experiment", "Item"], "status": "released", "@id": "/experiments-hi-c/4DNEXO7YBCMP/", "crosslinking_method": "1% Formaldehyde and 3mM DSG", "uuid": "d2dc99de-19cd-4304-b7ce-eae8319d204a", "accession": "4DNEXO7YBCMP", "processed_files": [{"href": "/files-processed/4DNFIEZBPTSB/@@download/4DNFIEZBPTSB.bam", "file_classification": "processed file", "file_type": "alignments", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "f5dff738-bed4-42e5-b10b-17b786d8e2d2", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "alignments (bam)", "md5sum": "c6f0abc6cd3446b5e68d569d41e7e3cb", "accession": "4DNFIEZBPTSB", "display_title": "4DNFIEZBPTSB.bam", "status": "released", "genome_assembly": "GRCh38", "file_size": 64052349667, "@id": "/files-processed/4DNFIEZBPTSB/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f5dff738-bed4-42e5-b10b-17b786d8e2d2/4DNFIEZBPTSB.bam", "upload_key": "f5dff738-bed4-42e5-b10b-17b786d8e2d2/4DNFIEZBPTSB.bam", "quality_metric": {"@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-bamqc/0d38ac50-0bc4-4dbf-a6cd-4edca23015b3/", "overall_quality_status": "PASS", "display_title": "QualityMetricBamqc from 2020-07-01", "uuid": "0d38ac50-0bc4-4dbf-a6cd-4edca23015b3", "quality_metric_summary": [{"title": "Total Reads", "value": "673569884", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "4.436", "tooltip": "Percent of total reads (=29.88m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "20.985", "tooltip": "Percent of total reads (=141.35m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "9.918", "tooltip": "Percent of total reads (=66.81m)", "numberType": "percent"}, {"title": "Walks", "value": "0.004", "tooltip": "Percent of total reads (=0.03m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.147", "tooltip": "Percent of total reads (=0.99m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "status": "current", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-03-28T14:28:49.609360+00:00"}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "processed file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 4", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}}, {"href": "/files-processed/4DNFIET7BS77/@@download/4DNFIET7BS77.pairs.gz", "file_classification": "processed file", "file_type": "contact list-replicate", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "0c9b8b8d-1416-423a-9731-be194aad3a3d", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "contact list-replicate (pairs)", "md5sum": "d9c51642067560e2c2b4ae05aa1de991", "accession": "4DNFIET7BS77", "display_title": "4DNFIET7BS77.pairs.gz", "status": "released", "genome_assembly": "GRCh38", "file_size": 8418917298, "@id": "/files-processed/4DNFIET7BS77/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/0c9b8b8d-1416-423a-9731-be194aad3a3d/4DNFIET7BS77.pairs.gz", "upload_key": "0c9b8b8d-1416-423a-9731-be194aad3a3d/4DNFIET7BS77.pairs.gz", "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIET7BS77/pairsqc_report.html", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Total reads": 435510575, "status": "released", "@id": "/quality-metrics-pairsqc/1f43a6d9-56ed-4f91-a9c5-440535ec3c7c/", "overall_quality_status": "PASS", "display_title": "QualityMetricPairsqc from 2020-07-01", "uuid": "1f43a6d9-56ed-4f91-a9c5-440535ec3c7c", "quality_metric_summary": [{"title": "Filtered Reads", "value": "435510575", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "23.793", "tooltip": "Percent of filtered reads (=103.62m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "49.365", "tooltip": "Percent of filtered reads (=214.99m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "26.842", "tooltip": "Percent of filtered reads (=116.9m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "extra_files": [{"href": "/files-processed/4DNFIET7BS77/@@download/4DNFIET7BS77.pairs.gz.px2", "file_size": 30517608, "md5sum": "0264e42356751bb63e2ec14511d297de", "file_format": {"display_title": "pairs_px2", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs_px2/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "file_format": "pairs_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "status": "current", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-04-06T20:16:55.712433+00:00"}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "processed file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 1, Techrep 4", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}}], "biosample": {"biosample_type": "in vitro differentiated cells", "display_title": "4DNBSMW55C3H", "@id": "/biosamples/4DNBSMW55C3H/", "biosource_summary": "H1-hESC (Tier 1) differentiated to definitive endoderm", "accession": "4DNBSMW55C3H", "biosample_category": ["H1-hESC", "In vitro Differentiation"], "@type": ["Biosample", "Item"], "status": "released", "treatments_summary": "None", "modifications_summary": "None", "uuid": "3af6c45d-a937-49f1-ae40-dac0f56498b4", "cell_culture_details": [{"display_title": "BiosampleCellCulture from 2020-06-24", "uuid": "782af389-598d-4d8a-8681-2bd3309675cd", "@id": "/biosample-cell-cultures/782af389-598d-4d8a-8681-2bd3309675cd/", "in_vitro_differentiated": "Yes", "@type": ["BiosampleCellCulture", "Item"], "status": "released", "tissue": {"@id": "/ontology-terms/UBERON:0005439/", "term_id": "UBERON:0005439", "display_title": "definitive endoderm", "@type": ["OntologyTerm", "Item"], "term_name": "definitive endoderm", "preferred_name": "definitive endoderm", "status": "released", "synonyms": ["embryonic endoderm"], "uuid": "52e444bc-62c2-4524-a29c-4aa4d1d96f26", "slim_terms": [{"status": "released", "@id": "/ontology-terms/UBERON:0000925/", "@type": ["OntologyTerm", "Item"], "display_title": "endoderm", "uuid": "111121bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosource": [{"@type": ["Biosource", "Item"], "@id": "/biosources/4DNSRV3SKQ8M/", "accession": "4DNSRV3SKQ8M", "uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "status": "released", "cell_line_tier": "Tier 1", "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "biosource_type": "stem cell derived cell line", "tissue": {"term_name": "stem cell", "term_id": "CL:0000034", "preferred_name": "stem cell", "display_title": "stem cell", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000034/", "synonyms": ["animal stem cell"], "status": "released", "slim_terms": [{"status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"term_id": "EFO:0003042", "status": "released", "term_name": "H1-hESC", "display_title": "H1-hESC", "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "@id": "/ontology-terms/EFO:0003042/", "preferred_name": "H1-hESC", "synonyms": ["H1"], "@type": ["OntologyTerm", "Item"], "slim_terms": [{"status": "current", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"display_title": "H. sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@type": ["Organism", "Item"], "status": "released", "scientific_name": "Homo sapiens", "@id": "/organisms/9606/", "name": "human", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing doubling_number"], "badge": {"warning": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "badge_icon": "/static/img/badges/biosample-icon.svg", "status": "released", "@type": ["Badge", "Item"], "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "badge_classification": "Warning", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"organ_system": ["endoderm"], "tissue_source": "definitive endoderm"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"display_title": "MNase", "status": "released", "@type": ["Enzyme", "Item"], "uuid": "e781b59c-ef3d-4ae4-9a94-4a34190bc6d2", "@id": "/enzymes/MNase/", "name": "MNase", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"field": "Enzyme", "value": "MNase", "combined": "Enzyme: MNase"}, "experiment_type": {"assay_classification": "3C via Ligation", "assay_subclassification": "DNA-DNA Pairwise Interactions", "status": "released", "@type": ["ExperimentType", "Item"], "assay_subclass_short": "Hi-C", "@id": "/experiment-types/micro-c/", "experiment_category": "Sequencing", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "uuid": "bc7899cf-8352-4360-b9be-efc3c7e3a574", "title": "Micro-C", "display_title": "Micro-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-01-04T14:56:20.216939+00:00"}, "external_references": []}, {"files": [{"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/e3a0f39e-befa-481c-8ed2-136f5cf62de9/4DNFISOWJW5Z.fastq.gz", "uuid": "e3a0f39e-befa-481c-8ed2-136f5cf62de9", "@id": "/files-fastq/4DNFISOWJW5Z/", "status": "released", "display_title": "4DNFISOWJW5Z.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFISOWJW5Z/@@download/4DNFISOWJW5Z.fastq.gz", "file_type": "reads", "file_size": 11456918355, "md5sum": "0dff55d3be238ceefb25afa3d177110a", "accession": "4DNFISOWJW5Z", "@type": ["FileFastq", "File", "Item"], "upload_key": "e3a0f39e-befa-481c-8ed2-136f5cf62de9/4DNFISOWJW5Z.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "e861e34e-d56b-40af-8c8f-7da081db6d73", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIM8DHDRG/", "file_type": "reads", "accession": "4DNFIM8DHDRG", "display_title": "4DNFIM8DHDRG.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 385275403, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFISOWJW5Z/fastqc_report.html", "@id": "/quality-metrics-fastqc/b39a32a9-b881-4796-ace7-eaf0b0ed4da5/", "overall_quality_status": "PASS", "uuid": "b39a32a9-b881-4796-ace7-eaf0b0ed4da5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/e861e34e-d56b-40af-8c8f-7da081db6d73/4DNFIM8DHDRG.fastq.gz", "uuid": "e861e34e-d56b-40af-8c8f-7da081db6d73", "@id": "/files-fastq/4DNFIM8DHDRG/", "status": "released", "display_title": "4DNFIM8DHDRG.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFIM8DHDRG/@@download/4DNFIM8DHDRG.fastq.gz", "file_type": "reads", "file_size": 13536588971, "md5sum": "ccdad5ced10b4496395ae78fcb0cbf51", "accession": "4DNFIM8DHDRG", "@type": ["FileFastq", "File", "Item"], "upload_key": "e861e34e-d56b-40af-8c8f-7da081db6d73/4DNFIM8DHDRG.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "e3a0f39e-befa-481c-8ed2-136f5cf62de9", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFISOWJW5Z/", "file_type": "reads", "accession": "4DNFISOWJW5Z", "display_title": "4DNFISOWJW5Z.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 385275403, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIM8DHDRG/fastqc_report.html", "@id": "/quality-metrics-fastqc/a6994c78-99f2-4f9c-9506-0ef6232e387c/", "overall_quality_status": "PASS", "uuid": "a6994c78-99f2-4f9c-9506-0ef6232e387c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/f0590e79-2437-42ab-be75-67f241114bcf/4DNFI1OZ8CQ4.fastq.gz", "uuid": "f0590e79-2437-42ab-be75-67f241114bcf", "@id": "/files-fastq/4DNFI1OZ8CQ4/", "status": "released", "display_title": "4DNFI1OZ8CQ4.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFI1OZ8CQ4/@@download/4DNFI1OZ8CQ4.fastq.gz", "file_type": "reads", "file_size": 11573689171, "md5sum": "d1cac250d9ca1c4ab3210e1824d24b49", "accession": "4DNFI1OZ8CQ4", "@type": ["FileFastq", "File", "Item"], "upload_key": "f0590e79-2437-42ab-be75-67f241114bcf/4DNFI1OZ8CQ4.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "db3138b7-a4ae-4519-a3ee-6994d716fcbb", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIV4WKGF9/", "file_type": "reads", "accession": "4DNFIV4WKGF9", "display_title": "4DNFIV4WKGF9.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 388779331, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI1OZ8CQ4/fastqc_report.html", "@id": "/quality-metrics-fastqc/9b571a71-85a4-48e0-a2ba-9bf6dccb77b1/", "overall_quality_status": "PASS", "uuid": "9b571a71-85a4-48e0-a2ba-9bf6dccb77b1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/db3138b7-a4ae-4519-a3ee-6994d716fcbb/4DNFIV4WKGF9.fastq.gz", "uuid": "db3138b7-a4ae-4519-a3ee-6994d716fcbb", "@id": "/files-fastq/4DNFIV4WKGF9/", "status": "released", "display_title": "4DNFIV4WKGF9.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFIV4WKGF9/@@download/4DNFIV4WKGF9.fastq.gz", "file_type": "reads", "file_size": 13594496725, "md5sum": "2f39474e0a6b8008ae31cc6fbb355c75", "accession": "4DNFIV4WKGF9", "@type": ["FileFastq", "File", "Item"], "upload_key": "db3138b7-a4ae-4519-a3ee-6994d716fcbb/4DNFIV4WKGF9.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "f0590e79-2437-42ab-be75-67f241114bcf", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFI1OZ8CQ4/", "file_type": "reads", "accession": "4DNFI1OZ8CQ4", "display_title": "4DNFI1OZ8CQ4.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 388779331, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIV4WKGF9/fastqc_report.html", "@id": "/quality-metrics-fastqc/eebc2ec3-59d5-425b-b1b5-058246689db3/", "overall_quality_status": "PASS", "uuid": "eebc2ec3-59d5-425b-b1b5-058246689db3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}], "display_title": "Micro-C on H1-hESC (Tier 1) differentiated to definitive endoderm with MNase - 4DNEXHL7EHOF", "@type": ["ExperimentHiC", "Experiment", "Item"], "status": "released", "@id": "/experiments-hi-c/4DNEXHL7EHOF/", "crosslinking_method": "1% Formaldehyde and 3mM DSG", "uuid": "3e118e38-ec73-4c8a-899b-cf4b71323bd8", "accession": "4DNEXHL7EHOF", "processed_files": [{"href": "/files-processed/4DNFI8Z2LSG4/@@download/4DNFI8Z2LSG4.bam", "file_classification": "processed file", "file_type": "alignments", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "3fe25777-b88f-4257-8a57-d61658cd7dd0", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "alignments (bam)", "md5sum": "a68d46913220cb44bccc64cf63be2c93", "accession": "4DNFI8Z2LSG4", "display_title": "4DNFI8Z2LSG4.bam", "status": "released", "genome_assembly": "GRCh38", "file_size": 62312934885, "@id": "/files-processed/4DNFI8Z2LSG4/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/3fe25777-b88f-4257-8a57-d61658cd7dd0/4DNFI8Z2LSG4.bam", "upload_key": "3fe25777-b88f-4257-8a57-d61658cd7dd0/4DNFI8Z2LSG4.bam", "quality_metric": {"@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-bamqc/dfc2d87a-5872-4820-8fed-cddc2e66abef/", "overall_quality_status": "PASS", "display_title": "QualityMetricBamqc from 2020-07-01", "uuid": "dfc2d87a-5872-4820-8fed-cddc2e66abef", "quality_metric_summary": [{"title": "Total Reads", "value": "774054734", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "4.236", "tooltip": "Percent of total reads (=32.79m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "20.329", "tooltip": "Percent of total reads (=157.36m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "33.118", "tooltip": "Percent of total reads (=256.35m)", "numberType": "percent"}, {"title": "Walks", "value": "0.005", "tooltip": "Percent of total reads (=0.04m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.106", "tooltip": "Percent of total reads (=0.82m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "status": "current", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-03-28T14:28:39.510917+00:00"}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "processed file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}}, {"href": "/files-processed/4DNFIC6HA2QF/@@download/4DNFIC6HA2QF.pairs.gz", "file_classification": "processed file", "file_type": "contact list-replicate", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "258a0f6d-4caf-46d8-9eef-a86205dc193b", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "contact list-replicate (pairs)", "md5sum": "40dcaf6c4074d6265b80c9b25ef90d65", "accession": "4DNFIC6HA2QF", "display_title": "4DNFIC6HA2QF.pairs.gz", "status": "released", "genome_assembly": "GRCh38", "file_size": 6455692695, "@id": "/files-processed/4DNFIC6HA2QF/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/258a0f6d-4caf-46d8-9eef-a86205dc193b/4DNFIC6HA2QF.pairs.gz", "upload_key": "258a0f6d-4caf-46d8-9eef-a86205dc193b/4DNFIC6HA2QF.pairs.gz", "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIC6HA2QF/pairsqc_report.html", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Total reads": 327525157, "status": "released", "@id": "/quality-metrics-pairsqc/5496c21e-469b-430c-821f-6afd9de8792d/", "overall_quality_status": "PASS", "display_title": "QualityMetricPairsqc from 2020-07-01", "uuid": "5496c21e-469b-430c-821f-6afd9de8792d", "quality_metric_summary": [{"title": "Filtered Reads", "value": "327525157", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "22.433", "tooltip": "Percent of filtered reads (=73.48m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "42.998", "tooltip": "Percent of filtered reads (=140.83m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "34.568", "tooltip": "Percent of filtered reads (=113.22m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "extra_files": [{"href": "/files-processed/4DNFIC6HA2QF/@@download/4DNFIC6HA2QF.pairs.gz.px2", "file_size": 30337358, "md5sum": "8195df90c5dd90c82c2064cadc96d117", "file_format": {"display_title": "pairs_px2", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs_px2/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "file_format": "pairs_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "status": "current", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-04-06T20:16:50.991208+00:00"}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "processed file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}}], "biosample": {"biosample_type": "in vitro differentiated cells", "display_title": "4DNBS3TMS6FC", "@id": "/biosamples/4DNBS3TMS6FC/", "biosource_summary": "H1-hESC (Tier 1) differentiated to definitive endoderm", "accession": "4DNBS3TMS6FC", "biosample_category": ["H1-hESC", "In vitro Differentiation"], "@type": ["Biosample", "Item"], "status": "released", "treatments_summary": "None", "modifications_summary": "None", "uuid": "638e5d85-34b4-4259-82b9-14b1f204661c", "cell_culture_details": [{"display_title": "BiosampleCellCulture from 2020-06-24", "uuid": "cc6717b4-aadf-43ed-86a5-709a15beac1f", "@id": "/biosample-cell-cultures/cc6717b4-aadf-43ed-86a5-709a15beac1f/", "in_vitro_differentiated": "Yes", "@type": ["BiosampleCellCulture", "Item"], "status": "released", "tissue": {"@id": "/ontology-terms/UBERON:0005439/", "term_id": "UBERON:0005439", "display_title": "definitive endoderm", "@type": ["OntologyTerm", "Item"], "term_name": "definitive endoderm", "preferred_name": "definitive endoderm", "status": "released", "synonyms": ["embryonic endoderm"], "uuid": "52e444bc-62c2-4524-a29c-4aa4d1d96f26", "slim_terms": [{"status": "released", "@id": "/ontology-terms/UBERON:0000925/", "@type": ["OntologyTerm", "Item"], "display_title": "endoderm", "uuid": "111121bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosource": [{"@type": ["Biosource", "Item"], "@id": "/biosources/4DNSRV3SKQ8M/", "accession": "4DNSRV3SKQ8M", "uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "status": "released", "cell_line_tier": "Tier 1", "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "biosource_type": "stem cell derived cell line", "tissue": {"term_name": "stem cell", "term_id": "CL:0000034", "preferred_name": "stem cell", "display_title": "stem cell", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000034/", "synonyms": ["animal stem cell"], "status": "released", "slim_terms": [{"status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"term_id": "EFO:0003042", "status": "released", "term_name": "H1-hESC", "display_title": "H1-hESC", "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "@id": "/ontology-terms/EFO:0003042/", "preferred_name": "H1-hESC", "synonyms": ["H1"], "@type": ["OntologyTerm", "Item"], "slim_terms": [{"status": "current", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"display_title": "H. sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@type": ["Organism", "Item"], "status": "released", "scientific_name": "Homo sapiens", "@id": "/organisms/9606/", "name": "human", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing doubling_number"], "badge": {"warning": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "badge_icon": "/static/img/badges/biosample-icon.svg", "status": "released", "@type": ["Badge", "Item"], "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "badge_classification": "Warning", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"organ_system": ["endoderm"], "tissue_source": "definitive endoderm"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"display_title": "MNase", "status": "released", "@type": ["Enzyme", "Item"], "uuid": "e781b59c-ef3d-4ae4-9a94-4a34190bc6d2", "@id": "/enzymes/MNase/", "name": "MNase", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"field": "Enzyme", "value": "MNase", "combined": "Enzyme: MNase"}, "experiment_type": {"assay_classification": "3C via Ligation", "assay_subclassification": "DNA-DNA Pairwise Interactions", "status": "released", "@type": ["ExperimentType", "Item"], "assay_subclass_short": "Hi-C", "@id": "/experiment-types/micro-c/", "experiment_category": "Sequencing", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "uuid": "bc7899cf-8352-4360-b9be-efc3c7e3a574", "title": "Micro-C", "display_title": "Micro-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-01-04T14:56:52.700838+00:00"}, "external_references": []}, {"files": [{"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/8f1dc5cc-bd86-41d9-8957-f17173be5049/4DNFIVCPFY1Q.fastq.gz", "uuid": "8f1dc5cc-bd86-41d9-8957-f17173be5049", "@id": "/files-fastq/4DNFIVCPFY1Q/", "status": "released", "display_title": "4DNFIVCPFY1Q.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFIVCPFY1Q/@@download/4DNFIVCPFY1Q.fastq.gz", "file_type": "reads", "file_size": 10814500926, "md5sum": "4325f32b7e7a66c6423806b021de70cb", "accession": "4DNFIVCPFY1Q", "@type": ["FileFastq", "File", "Item"], "upload_key": "8f1dc5cc-bd86-41d9-8957-f17173be5049/4DNFIVCPFY1Q.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "e5eb365f-d335-4f2a-bfd3-19e4d2df1400", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIAX4KYI1/", "file_type": "reads", "accession": "4DNFIAX4KYI1", "display_title": "4DNFIAX4KYI1.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 343212794, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIVCPFY1Q/fastqc_report.html", "@id": "/quality-metrics-fastqc/d650102d-135a-4d2b-99cf-130f6a3c26d7/", "overall_quality_status": "PASS", "uuid": "d650102d-135a-4d2b-99cf-130f6a3c26d7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 2", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/e5eb365f-d335-4f2a-bfd3-19e4d2df1400/4DNFIAX4KYI1.fastq.gz", "uuid": "e5eb365f-d335-4f2a-bfd3-19e4d2df1400", "@id": "/files-fastq/4DNFIAX4KYI1/", "status": "released", "display_title": "4DNFIAX4KYI1.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFIAX4KYI1/@@download/4DNFIAX4KYI1.fastq.gz", "file_type": "reads", "file_size": 12052247879, "md5sum": "c0c7c4f01a53c5c8c110343d1fb421b3", "accession": "4DNFIAX4KYI1", "@type": ["FileFastq", "File", "Item"], "upload_key": "e5eb365f-d335-4f2a-bfd3-19e4d2df1400/4DNFIAX4KYI1.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "8f1dc5cc-bd86-41d9-8957-f17173be5049", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIVCPFY1Q/", "file_type": "reads", "accession": "4DNFIVCPFY1Q", "display_title": "4DNFIVCPFY1Q.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 343212794, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIAX4KYI1/fastqc_report.html", "@id": "/quality-metrics-fastqc/9af179e2-8385-4ef0-8ad2-1525223266b6/", "overall_quality_status": "PASS", "uuid": "9af179e2-8385-4ef0-8ad2-1525223266b6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 2", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/17939293-03ac-4370-95a6-8cbac24df50c/4DNFI4DJEMWB.fastq.gz", "uuid": "17939293-03ac-4370-95a6-8cbac24df50c", "@id": "/files-fastq/4DNFI4DJEMWB/", "status": "released", "display_title": "4DNFI4DJEMWB.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFI4DJEMWB/@@download/4DNFI4DJEMWB.fastq.gz", "file_type": "reads", "file_size": 10757577333, "md5sum": "52c96e2307474a84dcfaf621681cc1fd", "accession": "4DNFI4DJEMWB", "@type": ["FileFastq", "File", "Item"], "upload_key": "17939293-03ac-4370-95a6-8cbac24df50c/4DNFI4DJEMWB.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "8cfd3702-50f6-4b4c-976f-f31c944ea93e", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIX31ISHK/", "file_type": "reads", "accession": "4DNFIX31ISHK", "display_title": "4DNFIX31ISHK.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 339161649, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI4DJEMWB/fastqc_report.html", "@id": "/quality-metrics-fastqc/3f771e6a-1561-4a67-82d7-f713649b1e29/", "overall_quality_status": "PASS", "uuid": "3f771e6a-1561-4a67-82d7-f713649b1e29", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 2", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/8cfd3702-50f6-4b4c-976f-f31c944ea93e/4DNFIX31ISHK.fastq.gz", "uuid": "8cfd3702-50f6-4b4c-976f-f31c944ea93e", "@id": "/files-fastq/4DNFIX31ISHK/", "status": "released", "display_title": "4DNFIX31ISHK.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFIX31ISHK/@@download/4DNFIX31ISHK.fastq.gz", "file_type": "reads", "file_size": 12093101315, "md5sum": "3e480baa7e53cb6eca71d883e8702c18", "accession": "4DNFIX31ISHK", "@type": ["FileFastq", "File", "Item"], "upload_key": "8cfd3702-50f6-4b4c-976f-f31c944ea93e/4DNFIX31ISHK.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "17939293-03ac-4370-95a6-8cbac24df50c", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFI4DJEMWB/", "file_type": "reads", "accession": "4DNFI4DJEMWB", "display_title": "4DNFI4DJEMWB.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 339161649, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIX31ISHK/fastqc_report.html", "@id": "/quality-metrics-fastqc/e9f57b65-4d74-4dd5-9fc7-9ba8fa6894e8/", "overall_quality_status": "PASS", "uuid": "e9f57b65-4d74-4dd5-9fc7-9ba8fa6894e8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 2", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}], "display_title": "Micro-C on H1-hESC (Tier 1) differentiated to definitive endoderm with MNase - 4DNEXXSXYECB", "@type": ["ExperimentHiC", "Experiment", "Item"], "status": "released", "@id": "/experiments-hi-c/4DNEXXSXYECB/", "crosslinking_method": "1% Formaldehyde and 3mM DSG", "uuid": "eed1b722-b024-4c51-bb1f-ea0ff9663fab", "accession": "4DNEXXSXYECB", "processed_files": [{"href": "/files-processed/4DNFIKCANJCE/@@download/4DNFIKCANJCE.bam", "file_classification": "processed file", "file_type": "alignments", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "90cd9d8b-633c-43e5-ba73-7c475d9b6a18", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "alignments (bam)", "md5sum": "5124f4c1087b5f962260d90d75e89c96", "accession": "4DNFIKCANJCE", "display_title": "4DNFIKCANJCE.bam", "status": "released", "genome_assembly": "GRCh38", "file_size": 64646801256, "@id": "/files-processed/4DNFIKCANJCE/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/90cd9d8b-633c-43e5-ba73-7c475d9b6a18/4DNFIKCANJCE.bam", "upload_key": "90cd9d8b-633c-43e5-ba73-7c475d9b6a18/4DNFIKCANJCE.bam", "quality_metric": {"@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-bamqc/7f0e701f-8aa4-4f88-88f4-bf1cec2c8070/", "overall_quality_status": "PASS", "display_title": "QualityMetricBamqc from 2020-07-01", "uuid": "7f0e701f-8aa4-4f88-88f4-bf1cec2c8070", "quality_metric_summary": [{"title": "Total Reads", "value": "682374443", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "4.754", "tooltip": "Percent of total reads (=32.44m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "21.007", "tooltip": "Percent of total reads (=143.34m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "11.803", "tooltip": "Percent of total reads (=80.54m)", "numberType": "percent"}, {"title": "Walks", "value": "0.004", "tooltip": "Percent of total reads (=0.03m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.146", "tooltip": "Percent of total reads (=0.99m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "status": "current", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-03-28T14:28:47.985217+00:00"}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "processed file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 2", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}}, {"href": "/files-processed/4DNFI16WMFWK/@@download/4DNFI16WMFWK.pairs.gz", "file_classification": "processed file", "file_type": "contact list-replicate", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "e5f3f10a-a266-4605-ac0e-3f698be940c9", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "contact list-replicate (pairs)", "md5sum": "72786d4d21ec745bece4f6ef7443c907", "accession": "4DNFI16WMFWK", "display_title": "4DNFI16WMFWK.pairs.gz", "status": "released", "genome_assembly": "GRCh38", "file_size": 8318223387, "@id": "/files-processed/4DNFI16WMFWK/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e5f3f10a-a266-4605-ac0e-3f698be940c9/4DNFI16WMFWK.pairs.gz", "upload_key": "e5f3f10a-a266-4605-ac0e-3f698be940c9/4DNFI16WMFWK.pairs.gz", "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI16WMFWK/pairsqc_report.html", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Total reads": 426016149, "status": "released", "@id": "/quality-metrics-pairsqc/4c1a1cf6-121f-4376-8bad-064843ba6944/", "overall_quality_status": "PASS", "display_title": "QualityMetricPairsqc from 2020-07-01", "uuid": "4c1a1cf6-121f-4376-8bad-064843ba6944", "quality_metric_summary": [{"title": "Filtered Reads", "value": "426016149", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "21.337", "tooltip": "Percent of filtered reads (=90.9m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "45.035", "tooltip": "Percent of filtered reads (=191.86m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "33.628", "tooltip": "Percent of filtered reads (=143.26m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "extra_files": [{"href": "/files-processed/4DNFI16WMFWK/@@download/4DNFI16WMFWK.pairs.gz.px2", "file_size": 31460652, "md5sum": "4ff7f3803be7fd13b3289c393be36297", "file_format": {"display_title": "pairs_px2", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs_px2/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "file_format": "pairs_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "status": "current", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-04-06T20:16:55.021846+00:00"}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "processed file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 2", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}}], "biosample": {"biosample_type": "in vitro differentiated cells", "display_title": "4DNBS3TMS6FC", "@id": "/biosamples/4DNBS3TMS6FC/", "biosource_summary": "H1-hESC (Tier 1) differentiated to definitive endoderm", "accession": "4DNBS3TMS6FC", "biosample_category": ["H1-hESC", "In vitro Differentiation"], "@type": ["Biosample", "Item"], "status": "released", "treatments_summary": "None", "modifications_summary": "None", "uuid": "638e5d85-34b4-4259-82b9-14b1f204661c", "cell_culture_details": [{"display_title": "BiosampleCellCulture from 2020-06-24", "uuid": "cc6717b4-aadf-43ed-86a5-709a15beac1f", "@id": "/biosample-cell-cultures/cc6717b4-aadf-43ed-86a5-709a15beac1f/", "in_vitro_differentiated": "Yes", "@type": ["BiosampleCellCulture", "Item"], "status": "released", "tissue": {"@id": "/ontology-terms/UBERON:0005439/", "term_id": "UBERON:0005439", "display_title": "definitive endoderm", "@type": ["OntologyTerm", "Item"], "term_name": "definitive endoderm", "preferred_name": "definitive endoderm", "status": "released", "synonyms": ["embryonic endoderm"], "uuid": "52e444bc-62c2-4524-a29c-4aa4d1d96f26", "slim_terms": [{"status": "released", "@id": "/ontology-terms/UBERON:0000925/", "@type": ["OntologyTerm", "Item"], "display_title": "endoderm", "uuid": "111121bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosource": [{"@type": ["Biosource", "Item"], "@id": "/biosources/4DNSRV3SKQ8M/", "accession": "4DNSRV3SKQ8M", "uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "status": "released", "cell_line_tier": "Tier 1", "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "biosource_type": "stem cell derived cell line", "tissue": {"term_name": "stem cell", "term_id": "CL:0000034", "preferred_name": "stem cell", "display_title": "stem cell", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000034/", "synonyms": ["animal stem cell"], "status": "released", "slim_terms": [{"status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"term_id": "EFO:0003042", "status": "released", "term_name": "H1-hESC", "display_title": "H1-hESC", "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "@id": "/ontology-terms/EFO:0003042/", "preferred_name": "H1-hESC", "synonyms": ["H1"], "@type": ["OntologyTerm", "Item"], "slim_terms": [{"status": "current", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"display_title": "H. sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@type": ["Organism", "Item"], "status": "released", "scientific_name": "Homo sapiens", "@id": "/organisms/9606/", "name": "human", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing doubling_number"], "badge": {"warning": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "badge_icon": "/static/img/badges/biosample-icon.svg", "status": "released", "@type": ["Badge", "Item"], "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "badge_classification": "Warning", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"organ_system": ["endoderm"], "tissue_source": "definitive endoderm"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"display_title": "MNase", "status": "released", "@type": ["Enzyme", "Item"], "uuid": "e781b59c-ef3d-4ae4-9a94-4a34190bc6d2", "@id": "/enzymes/MNase/", "name": "MNase", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"field": "Enzyme", "value": "MNase", "combined": "Enzyme: MNase"}, "experiment_type": {"assay_classification": "3C via Ligation", "assay_subclassification": "DNA-DNA Pairwise Interactions", "status": "released", "@type": ["ExperimentType", "Item"], "assay_subclass_short": "Hi-C", "@id": "/experiment-types/micro-c/", "experiment_category": "Sequencing", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "uuid": "bc7899cf-8352-4360-b9be-efc3c7e3a574", "title": "Micro-C", "display_title": "Micro-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-01-04T14:56:23.982824+00:00"}, "external_references": []}, {"files": [{"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/c7af7b15-94bb-4d0c-aa0a-1003585dcf13/4DNFI8EY7OGB.fastq.gz", "uuid": "c7af7b15-94bb-4d0c-aa0a-1003585dcf13", "@id": "/files-fastq/4DNFI8EY7OGB/", "status": "released", "display_title": "4DNFI8EY7OGB.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFI8EY7OGB/@@download/4DNFI8EY7OGB.fastq.gz", "file_type": "reads", "file_size": 11009118772, "md5sum": "1e02d097aafecccd97c483290987cfe2", "accession": "4DNFI8EY7OGB", "@type": ["FileFastq", "File", "Item"], "upload_key": "c7af7b15-94bb-4d0c-aa0a-1003585dcf13/4DNFI8EY7OGB.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "f6926a1d-8d55-4f21-9d11-9b8d1ab53325", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIIKLOA21/", "file_type": "reads", "accession": "4DNFIIKLOA21", "display_title": "4DNFIIKLOA21.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 349681840, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI8EY7OGB/fastqc_report.html", "@id": "/quality-metrics-fastqc/918a4889-3895-4138-8e9b-59793198a762/", "overall_quality_status": "PASS", "uuid": "918a4889-3895-4138-8e9b-59793198a762", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 3", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/f6926a1d-8d55-4f21-9d11-9b8d1ab53325/4DNFIIKLOA21.fastq.gz", "uuid": "f6926a1d-8d55-4f21-9d11-9b8d1ab53325", "@id": "/files-fastq/4DNFIIKLOA21/", "status": "released", "display_title": "4DNFIIKLOA21.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFIIKLOA21/@@download/4DNFIIKLOA21.fastq.gz", "file_type": "reads", "file_size": 12238919715, "md5sum": "5ef31df04c5272d064fee86db9ae11c2", "accession": "4DNFIIKLOA21", "@type": ["FileFastq", "File", "Item"], "upload_key": "f6926a1d-8d55-4f21-9d11-9b8d1ab53325/4DNFIIKLOA21.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "c7af7b15-94bb-4d0c-aa0a-1003585dcf13", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFI8EY7OGB/", "file_type": "reads", "accession": "4DNFI8EY7OGB", "display_title": "4DNFI8EY7OGB.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 349681840, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIIKLOA21/fastqc_report.html", "@id": "/quality-metrics-fastqc/5ef66812-e052-4fd8-9fe6-7db4569abde6/", "overall_quality_status": "PASS", "uuid": "5ef66812-e052-4fd8-9fe6-7db4569abde6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 3", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/e5574d1e-4cd7-459b-b4d2-fbabd1843531/4DNFI6273E4N.fastq.gz", "uuid": "e5574d1e-4cd7-459b-b4d2-fbabd1843531", "@id": "/files-fastq/4DNFI6273E4N/", "status": "released", "display_title": "4DNFI6273E4N.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFI6273E4N/@@download/4DNFI6273E4N.fastq.gz", "file_type": "reads", "file_size": 10784656507, "md5sum": "b574a910a914f284814a8a21c15b1b11", "accession": "4DNFI6273E4N", "@type": ["FileFastq", "File", "Item"], "upload_key": "e5574d1e-4cd7-459b-b4d2-fbabd1843531/4DNFI6273E4N.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "5deebc6f-6283-483f-bdf6-48b2db483da9", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIKXBFJN1/", "file_type": "reads", "accession": "4DNFIKXBFJN1", "display_title": "4DNFIKXBFJN1.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 337958516, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI6273E4N/fastqc_report.html", "@id": "/quality-metrics-fastqc/e27fb47d-4a4e-42ea-8999-0276f53a9a95/", "overall_quality_status": "PASS", "uuid": "e27fb47d-4a4e-42ea-8999-0276f53a9a95", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 3", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/5deebc6f-6283-483f-bdf6-48b2db483da9/4DNFIKXBFJN1.fastq.gz", "uuid": "5deebc6f-6283-483f-bdf6-48b2db483da9", "@id": "/files-fastq/4DNFIKXBFJN1/", "status": "released", "display_title": "4DNFIKXBFJN1.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFIKXBFJN1/@@download/4DNFIKXBFJN1.fastq.gz", "file_type": "reads", "file_size": 12055246072, "md5sum": "5e775e67c4f8c0e863d40a5c17e56409", "accession": "4DNFIKXBFJN1", "@type": ["FileFastq", "File", "Item"], "upload_key": "5deebc6f-6283-483f-bdf6-48b2db483da9/4DNFIKXBFJN1.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "e5574d1e-4cd7-459b-b4d2-fbabd1843531", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFI6273E4N/", "file_type": "reads", "accession": "4DNFI6273E4N", "display_title": "4DNFI6273E4N.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 337958516, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIKXBFJN1/fastqc_report.html", "@id": "/quality-metrics-fastqc/a5d16525-2562-4948-af7b-08dee1803f40/", "overall_quality_status": "PASS", "uuid": "a5d16525-2562-4948-af7b-08dee1803f40", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 3", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}], "display_title": "Micro-C on H1-hESC (Tier 1) differentiated to definitive endoderm with MNase - 4DNEXSCJ4HOI", "@type": ["ExperimentHiC", "Experiment", "Item"], "status": "released", "@id": "/experiments-hi-c/4DNEXSCJ4HOI/", "crosslinking_method": "1% Formaldehyde and 3mM DSG", "uuid": "11ab026a-aceb-48cb-ba75-f03ee00d60e4", "accession": "4DNEXSCJ4HOI", "processed_files": [{"href": "/files-processed/4DNFIDUYHPWU/@@download/4DNFIDUYHPWU.bam", "file_classification": "processed file", "file_type": "alignments", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "044b9512-a0c9-49c6-b9fc-d08c2217522c", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "alignments (bam)", "md5sum": "beeacb48c341fc07aa69a08d9da64bc7", "accession": "4DNFIDUYHPWU", "display_title": "4DNFIDUYHPWU.bam", "status": "released", "genome_assembly": "GRCh38", "file_size": 66151024999, "@id": "/files-processed/4DNFIDUYHPWU/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/044b9512-a0c9-49c6-b9fc-d08c2217522c/4DNFIDUYHPWU.bam", "upload_key": "044b9512-a0c9-49c6-b9fc-d08c2217522c/4DNFIDUYHPWU.bam", "quality_metric": {"@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-bamqc/264dfdc3-4d34-4cdd-b7ea-698f25153091/", "overall_quality_status": "PASS", "display_title": "QualityMetricBamqc from 2020-07-01", "uuid": "264dfdc3-4d34-4cdd-b7ea-698f25153091", "quality_metric_summary": [{"title": "Total Reads", "value": "687640356", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "4.597", "tooltip": "Percent of total reads (=31.61m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "21.019", "tooltip": "Percent of total reads (=144.53m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "9.603", "tooltip": "Percent of total reads (=66.03m)", "numberType": "percent"}, {"title": "Walks", "value": "0.004", "tooltip": "Percent of total reads (=0.03m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.153", "tooltip": "Percent of total reads (=1.05m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "status": "current", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-03-28T14:28:46.378222+00:00"}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "processed file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 3", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}}, {"href": "/files-processed/4DNFIP8UA8FE/@@download/4DNFIP8UA8FE.pairs.gz", "file_classification": "processed file", "file_type": "contact list-replicate", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "a4115cb5-990e-42ad-a7b1-fbacddbb3ddd", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "contact list-replicate (pairs)", "md5sum": "e6bf12100de14fbb30429fc5ffabdbe9", "accession": "4DNFIP8UA8FE", "display_title": "4DNFIP8UA8FE.pairs.gz", "status": "released", "genome_assembly": "GRCh38", "file_size": 8732994025, "@id": "/files-processed/4DNFIP8UA8FE/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a4115cb5-990e-42ad-a7b1-fbacddbb3ddd/4DNFIP8UA8FE.pairs.gz", "upload_key": "a4115cb5-990e-42ad-a7b1-fbacddbb3ddd/4DNFIP8UA8FE.pairs.gz", "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIP8UA8FE/pairsqc_report.html", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Total reads": 445430506, "status": "released", "@id": "/quality-metrics-pairsqc/43bc211b-df34-4ea5-b990-62044b18fc4d/", "overall_quality_status": "PASS", "display_title": "QualityMetricPairsqc from 2020-07-01", "uuid": "43bc211b-df34-4ea5-b990-62044b18fc4d", "quality_metric_summary": [{"title": "Filtered Reads", "value": "445430506", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "20.984", "tooltip": "Percent of filtered reads (=93.47m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "43.325", "tooltip": "Percent of filtered reads (=192.98m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "35.691", "tooltip": "Percent of filtered reads (=158.98m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "extra_files": [{"href": "/files-processed/4DNFIP8UA8FE/@@download/4DNFIP8UA8FE.pairs.gz.px2", "file_size": 32086064, "md5sum": "1f59243f037f22205475858dc89071ed", "file_format": {"display_title": "pairs_px2", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs_px2/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "file_format": "pairs_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "status": "current", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-04-06T20:16:54.321171+00:00"}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "processed file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 3", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}}], "biosample": {"biosample_type": "in vitro differentiated cells", "display_title": "4DNBS3TMS6FC", "@id": "/biosamples/4DNBS3TMS6FC/", "biosource_summary": "H1-hESC (Tier 1) differentiated to definitive endoderm", "accession": "4DNBS3TMS6FC", "biosample_category": ["H1-hESC", "In vitro Differentiation"], "@type": ["Biosample", "Item"], "status": "released", "treatments_summary": "None", "modifications_summary": "None", "uuid": "638e5d85-34b4-4259-82b9-14b1f204661c", "cell_culture_details": [{"display_title": "BiosampleCellCulture from 2020-06-24", "uuid": "cc6717b4-aadf-43ed-86a5-709a15beac1f", "@id": "/biosample-cell-cultures/cc6717b4-aadf-43ed-86a5-709a15beac1f/", "in_vitro_differentiated": "Yes", "@type": ["BiosampleCellCulture", "Item"], "status": "released", "tissue": {"@id": "/ontology-terms/UBERON:0005439/", "term_id": "UBERON:0005439", "display_title": "definitive endoderm", "@type": ["OntologyTerm", "Item"], "term_name": "definitive endoderm", "preferred_name": "definitive endoderm", "status": "released", "synonyms": ["embryonic endoderm"], "uuid": "52e444bc-62c2-4524-a29c-4aa4d1d96f26", "slim_terms": [{"status": "released", "@id": "/ontology-terms/UBERON:0000925/", "@type": ["OntologyTerm", "Item"], "display_title": "endoderm", "uuid": "111121bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosource": [{"@type": ["Biosource", "Item"], "@id": "/biosources/4DNSRV3SKQ8M/", "accession": "4DNSRV3SKQ8M", "uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "status": "released", "cell_line_tier": "Tier 1", "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "biosource_type": "stem cell derived cell line", "tissue": {"term_name": "stem cell", "term_id": "CL:0000034", "preferred_name": "stem cell", "display_title": "stem cell", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000034/", "synonyms": ["animal stem cell"], "status": "released", "slim_terms": [{"status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"term_id": "EFO:0003042", "status": "released", "term_name": "H1-hESC", "display_title": "H1-hESC", "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "@id": "/ontology-terms/EFO:0003042/", "preferred_name": "H1-hESC", "synonyms": ["H1"], "@type": ["OntologyTerm", "Item"], "slim_terms": [{"status": "current", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"display_title": "H. sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@type": ["Organism", "Item"], "status": "released", "scientific_name": "Homo sapiens", "@id": "/organisms/9606/", "name": "human", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing doubling_number"], "badge": {"warning": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "badge_icon": "/static/img/badges/biosample-icon.svg", "status": "released", "@type": ["Badge", "Item"], "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "badge_classification": "Warning", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"organ_system": ["endoderm"], "tissue_source": "definitive endoderm"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"display_title": "MNase", "status": "released", "@type": ["Enzyme", "Item"], "uuid": "e781b59c-ef3d-4ae4-9a94-4a34190bc6d2", "@id": "/enzymes/MNase/", "name": "MNase", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"field": "Enzyme", "value": "MNase", "combined": "Enzyme: MNase"}, "experiment_type": {"assay_classification": "3C via Ligation", "assay_subclassification": "DNA-DNA Pairwise Interactions", "status": "released", "@type": ["ExperimentType", "Item"], "assay_subclass_short": "Hi-C", "@id": "/experiment-types/micro-c/", "experiment_category": "Sequencing", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "uuid": "bc7899cf-8352-4360-b9be-efc3c7e3a574", "title": "Micro-C", "display_title": "Micro-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-01-04T14:57:18.767903+00:00"}, "external_references": []}, {"files": [{"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/33de7ecd-8e7a-456f-95cf-1779bc5bb0de/4DNFIXW4XIZP.fastq.gz", "uuid": "33de7ecd-8e7a-456f-95cf-1779bc5bb0de", "@id": "/files-fastq/4DNFIXW4XIZP/", "status": "released", "display_title": "4DNFIXW4XIZP.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFIXW4XIZP/@@download/4DNFIXW4XIZP.fastq.gz", "file_type": "reads", "file_size": 10678696969, "md5sum": "cb147dacc33752b06f768c9ae576c260", "accession": "4DNFIXW4XIZP", "@type": ["FileFastq", "File", "Item"], "upload_key": "33de7ecd-8e7a-456f-95cf-1779bc5bb0de/4DNFIXW4XIZP.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "d3b9ef66-addf-4e7a-ac22-f9500fb6277a", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIIXDBT6Y/", "file_type": "reads", "accession": "4DNFIIXDBT6Y", "display_title": "4DNFIIXDBT6Y.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 330801748, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIXW4XIZP/fastqc_report.html", "@id": "/quality-metrics-fastqc/a70fa6f9-0e70-4054-bde9-8d2f2a3e7e5a/", "overall_quality_status": "PASS", "uuid": "a70fa6f9-0e70-4054-bde9-8d2f2a3e7e5a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 4", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/d3b9ef66-addf-4e7a-ac22-f9500fb6277a/4DNFIIXDBT6Y.fastq.gz", "uuid": "d3b9ef66-addf-4e7a-ac22-f9500fb6277a", "@id": "/files-fastq/4DNFIIXDBT6Y/", "status": "released", "display_title": "4DNFIIXDBT6Y.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFIIXDBT6Y/@@download/4DNFIIXDBT6Y.fastq.gz", "file_type": "reads", "file_size": 11773392898, "md5sum": "6985f4db71de351d2d009f2abe3b6519", "accession": "4DNFIIXDBT6Y", "@type": ["FileFastq", "File", "Item"], "upload_key": "d3b9ef66-addf-4e7a-ac22-f9500fb6277a/4DNFIIXDBT6Y.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "33de7ecd-8e7a-456f-95cf-1779bc5bb0de", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIXW4XIZP/", "file_type": "reads", "accession": "4DNFIXW4XIZP", "display_title": "4DNFIXW4XIZP.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 330801748, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIIXDBT6Y/fastqc_report.html", "@id": "/quality-metrics-fastqc/5d6701a2-823e-4218-8a78-03145d9a520f/", "overall_quality_status": "PASS", "uuid": "5d6701a2-823e-4218-8a78-03145d9a520f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 4", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/ea1b0980-53f3-4241-85c2-b997d741c113/4DNFIOX4UIYA.fastq.gz", "uuid": "ea1b0980-53f3-4241-85c2-b997d741c113", "@id": "/files-fastq/4DNFIOX4UIYA/", "status": "released", "display_title": "4DNFIOX4UIYA.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFIOX4UIYA/@@download/4DNFIOX4UIYA.fastq.gz", "file_type": "reads", "file_size": 10910136071, "md5sum": "30975544ef098b627a115e6b4e8f0fed", "accession": "4DNFIOX4UIYA", "@type": ["FileFastq", "File", "Item"], "upload_key": "ea1b0980-53f3-4241-85c2-b997d741c113/4DNFIOX4UIYA.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "c7fee06c-1fc8-402b-b27b-b8256814fc91", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFI19ZMQNB/", "file_type": "reads", "accession": "4DNFI19ZMQNB", "display_title": "4DNFI19ZMQNB.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 343778885, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIOX4UIYA/fastqc_report.html", "@id": "/quality-metrics-fastqc/b76832af-3095-4199-b9e8-669690996d32/", "overall_quality_status": "PASS", "uuid": "b76832af-3095-4199-b9e8-669690996d32", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 4", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}, {"file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/c7fee06c-1fc8-402b-b27b-b8256814fc91/4DNFI19ZMQNB.fastq.gz", "uuid": "c7fee06c-1fc8-402b-b27b-b8256814fc91", "@id": "/files-fastq/4DNFI19ZMQNB/", "status": "released", "display_title": "4DNFI19ZMQNB.fastq.gz", "file_type_detailed": "reads (fastq)", "href": "/files-fastq/4DNFI19ZMQNB/@@download/4DNFI19ZMQNB.fastq.gz", "file_type": "reads", "file_size": 12166814351, "md5sum": "d160b147f3e4a829645f05ad395c53ae", "accession": "4DNFI19ZMQNB", "@type": ["FileFastq", "File", "Item"], "upload_key": "c7fee06c-1fc8-402b-b27b-b8256814fc91/4DNFI19ZMQNB.fastq.gz", "paired_end": "2", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "display_title": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@type": ["Lab", "Item"], "name": "job-dekker-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "ea1b0980-53f3-4241-85c2-b997d741c113", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIOX4UIYA/", "file_type": "reads", "accession": "4DNFIOX4UIYA", "display_title": "4DNFIOX4UIYA.fastq.gz", "paired_end": "1", "file_format": {"@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"display_title": "QualityMetricFastqc from 2020-06-26", "Total Sequences": 343778885, "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "50", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI19ZMQNB/fastqc_report.html", "@id": "/quality-metrics-fastqc/05714b35-a9c9-458f-8788-954bde9bf03a/", "overall_quality_status": "PASS", "uuid": "05714b35-a9c9-458f-8788-954bde9bf03a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "raw file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 4", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}}], "display_title": "Micro-C on H1-hESC (Tier 1) differentiated to definitive endoderm with MNase - 4DNEX2ZUALZI", "@type": ["ExperimentHiC", "Experiment", "Item"], "status": "released", "@id": "/experiments-hi-c/4DNEX2ZUALZI/", "crosslinking_method": "1% Formaldehyde and 3mM DSG", "uuid": "ba35dd84-26cd-4fa8-b94f-dd574d4e1da8", "accession": "4DNEX2ZUALZI", "processed_files": [{"href": "/files-processed/4DNFIWKNPRHK/@@download/4DNFIWKNPRHK.bam", "file_classification": "processed file", "file_type": "alignments", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "1540b3f3-a9ae-4572-9b90-5c2216f1a290", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "alignments (bam)", "md5sum": "611764c26dabaf930dff023116bbab49", "accession": "4DNFIWKNPRHK", "display_title": "4DNFIWKNPRHK.bam", "status": "released", "genome_assembly": "GRCh38", "file_size": 63770731514, "@id": "/files-processed/4DNFIWKNPRHK/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/1540b3f3-a9ae-4572-9b90-5c2216f1a290/4DNFIWKNPRHK.bam", "upload_key": "1540b3f3-a9ae-4572-9b90-5c2216f1a290/4DNFIWKNPRHK.bam", "quality_metric": {"@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "status": "released", "@id": "/quality-metrics-bamqc/1d903ee0-2564-4c9f-893c-980f8e239973/", "overall_quality_status": "PASS", "display_title": "QualityMetricBamqc from 2020-07-01", "uuid": "1d903ee0-2564-4c9f-893c-980f8e239973", "quality_metric_summary": [{"title": "Total Reads", "value": "674580633", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "4.474", "tooltip": "Percent of total reads (=30.18m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "21.373", "tooltip": "Percent of total reads (=144.18m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "13.976", "tooltip": "Percent of total reads (=94.28m)", "numberType": "percent"}, {"title": "Walks", "value": "0.004", "tooltip": "Percent of total reads (=0.03m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.144", "tooltip": "Percent of total reads (=0.97m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "status": "current", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-03-28T14:28:44.737535+00:00"}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "processed file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 4", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}}, {"href": "/files-processed/4DNFISPHZI17/@@download/4DNFISPHZI17.pairs.gz", "file_classification": "processed file", "file_type": "contact list-replicate", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "f25e3ce2-14df-4704-be3a-64dbc44da8dd", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "contact list-replicate (pairs)", "md5sum": "0c80aa7db127ea6a4839b50119aac660", "accession": "4DNFISPHZI17", "display_title": "4DNFISPHZI17.pairs.gz", "status": "released", "genome_assembly": "GRCh38", "file_size": 7954052152, "@id": "/files-processed/4DNFISPHZI17/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f25e3ce2-14df-4704-be3a-64dbc44da8dd/4DNFISPHZI17.pairs.gz", "upload_key": "f25e3ce2-14df-4704-be3a-64dbc44da8dd/4DNFISPHZI17.pairs.gz", "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFISPHZI17/pairsqc_report.html", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Total reads": 405917878, "status": "released", "@id": "/quality-metrics-pairsqc/623813c5-2530-400f-bbec-fe5f2ab3a92b/", "overall_quality_status": "PASS", "display_title": "QualityMetricPairsqc from 2020-06-30", "uuid": "623813c5-2530-400f-bbec-fe5f2ab3a92b", "quality_metric_summary": [{"title": "Filtered Reads", "value": "405917878", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "20.244", "tooltip": "Percent of filtered reads (=82.17m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "44.417", "tooltip": "Percent of filtered reads (=180.3m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "35.339", "tooltip": "Percent of filtered reads (=143.45m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"@id": "/labs/job-dekker-lab/", "@type": ["Lab", "Item"], "display_title": "Job Dekker, UMMS", "status": "current", "name": "job-dekker-lab", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "extra_files": [{"href": "/files-processed/4DNFISPHZI17/@@download/4DNFISPHZI17.pairs.gz.px2", "file_size": 31531401, "md5sum": "9e0d107962e5ca94528479db5614f75b", "file_format": {"display_title": "pairs_px2", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs_px2/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "file_format": "pairs_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "status": "current", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-04-06T20:16:53.526571+00:00"}, "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "processed file", "assay_info": "MNase", "dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "replicate_info": "Biorep 2, Techrep 4", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "4DN DCIC, HMS"}}], "biosample": {"biosample_type": "in vitro differentiated cells", "display_title": "4DNBS3TMS6FC", "@id": "/biosamples/4DNBS3TMS6FC/", "biosource_summary": "H1-hESC (Tier 1) differentiated to definitive endoderm", "accession": "4DNBS3TMS6FC", "biosample_category": ["H1-hESC", "In vitro Differentiation"], "@type": ["Biosample", "Item"], "status": "released", "treatments_summary": "None", "modifications_summary": "None", "uuid": "638e5d85-34b4-4259-82b9-14b1f204661c", "cell_culture_details": [{"display_title": "BiosampleCellCulture from 2020-06-24", "uuid": "cc6717b4-aadf-43ed-86a5-709a15beac1f", "@id": "/biosample-cell-cultures/cc6717b4-aadf-43ed-86a5-709a15beac1f/", "in_vitro_differentiated": "Yes", "@type": ["BiosampleCellCulture", "Item"], "status": "released", "tissue": {"@id": "/ontology-terms/UBERON:0005439/", "term_id": "UBERON:0005439", "display_title": "definitive endoderm", "@type": ["OntologyTerm", "Item"], "term_name": "definitive endoderm", "preferred_name": "definitive endoderm", "status": "released", "synonyms": ["embryonic endoderm"], "uuid": "52e444bc-62c2-4524-a29c-4aa4d1d96f26", "slim_terms": [{"status": "released", "@id": "/ontology-terms/UBERON:0000925/", "@type": ["OntologyTerm", "Item"], "display_title": "endoderm", "uuid": "111121bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosource": [{"@type": ["Biosource", "Item"], "@id": "/biosources/4DNSRV3SKQ8M/", "accession": "4DNSRV3SKQ8M", "uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "status": "released", "cell_line_tier": "Tier 1", "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "biosource_type": "stem cell derived cell line", "tissue": {"term_name": "stem cell", "term_id": "CL:0000034", "preferred_name": "stem cell", "display_title": "stem cell", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000034/", "synonyms": ["animal stem cell"], "status": "released", "slim_terms": [{"status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"term_id": "EFO:0003042", "status": "released", "term_name": "H1-hESC", "display_title": "H1-hESC", "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "@id": "/ontology-terms/EFO:0003042/", "preferred_name": "H1-hESC", "synonyms": ["H1"], "@type": ["OntologyTerm", "Item"], "slim_terms": [{"status": "current", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"display_title": "H. sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@type": ["Organism", "Item"], "status": "released", "scientific_name": "Homo sapiens", "@id": "/organisms/9606/", "name": "human", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing doubling_number"], "badge": {"warning": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "badge_icon": "/static/img/badges/biosample-icon.svg", "status": "released", "@type": ["Badge", "Item"], "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "badge_classification": "Warning", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"organ_system": ["endoderm"], "tissue_source": "definitive endoderm"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"display_title": "MNase", "status": "released", "@type": ["Enzyme", "Item"], "uuid": "e781b59c-ef3d-4ae4-9a94-4a34190bc6d2", "@id": "/enzymes/MNase/", "name": "MNase", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"field": "Enzyme", "value": "MNase", "combined": "Enzyme: MNase"}, "experiment_type": {"assay_classification": "3C via Ligation", "assay_subclassification": "DNA-DNA Pairwise Interactions", "status": "released", "@type": ["ExperimentType", "Item"], "assay_subclass_short": "Hi-C", "@id": "/experiment-types/micro-c/", "experiment_category": "Sequencing", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "uuid": "bc7899cf-8352-4360-b9be-efc3c7e3a574", "title": "Micro-C", "display_title": "Micro-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-01-04T14:56:25.647529+00:00"}, "external_references": []}], "experimentset_type": "replicate", "completed_processes": ["insulation_scores_and_boundaries_v1", "HiC_Pipeline_0.2.7", "compartments_v1.2"], "other_processed_files": [{"type": "supplementary", "files": [{"accession": "4DNFIRZ6N2M1", "file_type": "compartments", "@type": ["FileProcessed", "File", "Item"], "file_format": {"uuid": "dba26778-f40a-4561-a552-65539702ded4", "display_title": "compressed_txt", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "abfb39bd-0f59-4978-95f8-7b7db78dec91", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "href": "/files-processed/4DNFIRZ6N2M1/@@download/4DNFIRZ6N2M1.txt.gz", "md5sum": "8a433c4aec2beeef66a7d0e9c8643ec2", "file_type_detailed": "compartments (compressed_txt)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/abfb39bd-0f59-4978-95f8-7b7db78dec91/4DNFIRZ6N2M1.txt.gz", "status": "released", "display_title": "4DNFIRZ6N2M1.txt.gz", "@id": "/files-processed/4DNFIRZ6N2M1/", "genome_assembly": "GRCh38", "file_size": 1051536, "track_and_facet_info": {"dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "Compartment, insulation and loop calls - Dekker Lab", "experiment_type": "Micro-C", "assay_info": "MNase", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "last_modified": {"date_modified": "2021-12-16T07:02:18.662526+00:00"}, "lab": {"status": "current", "display_title": "Job Dekker, UMMS", "name": "job-dekker-lab", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "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"]}}, {"accession": "4DNFIC5YU5BU", "file_type": "compartments", "@type": ["FileProcessed", "File", "Item"], "file_format": {"uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "display_title": "bw", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "98b54481-3810-4745-a150-fda01b8df7c5", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "href": "/files-processed/4DNFIC5YU5BU/@@download/4DNFIC5YU5BU.bw", "md5sum": "36cde4ed78c9af118b18909006173c55", "file_type_detailed": "compartments (bw)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/98b54481-3810-4745-a150-fda01b8df7c5/4DNFIC5YU5BU.bw", "status": "released", "display_title": "4DNFIC5YU5BU.bw", "@id": "/files-processed/4DNFIC5YU5BU/", "higlass_uid": "4bdae633-0a5f-4e8a-8812-5c23fe0486a4", "genome_assembly": "GRCh38", "file_size": 322251, "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"display_title": "4DNFIC5YU5BU - compartments for H1-hESC (Tier 1) differentiated to definitive endoderm Micro-C MNase", "@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/ef37389c-83d2-44f9-82f5-bbd6b60c8451/", "uuid": "ef37389c-83d2-44f9-82f5-bbd6b60c8451", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "track_and_facet_info": {"dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "Compartment, insulation and loop calls - Dekker Lab", "experiment_type": "Micro-C", "assay_info": "MNase", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS", "track_title": "compartments for H1-hESC (Tier 1) differentiated to definitive endoderm Micro-C MNase"}, "last_modified": {"date_modified": "2021-12-16T07:02:09.122330+00:00"}, "lab": {"status": "current", "display_title": "Job Dekker, UMMS", "name": "job-dekker-lab", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "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"]}}, {"accession": "4DNFIHA37UQC", "file_type": "insulation score", "@type": ["FileProcessed", "File", "Item"], "file_format": {"uuid": "dba26778-f40a-4561-a552-65539702ded4", "display_title": "compressed_txt", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/compressed_txt/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "bf368a0e-de73-40b5-92d3-6f438637f19d", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "href": "/files-processed/4DNFIHA37UQC/@@download/4DNFIHA37UQC.txt.gz", "md5sum": "d88d91e25c625c307ae45eb7bdbeb600", "file_type_detailed": "insulation score (compressed_txt)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/bf368a0e-de73-40b5-92d3-6f438637f19d/4DNFIHA37UQC.txt.gz", "status": "released", "display_title": "4DNFIHA37UQC.txt.gz", "@id": "/files-processed/4DNFIHA37UQC/", "genome_assembly": "GRCh38", "file_size": 4829802, "track_and_facet_info": {"dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "Compartment, insulation and loop calls - Dekker Lab", "experiment_type": "Micro-C", "assay_info": "MNase", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "last_modified": {"date_modified": "2021-12-16T07:01:59.880129+00:00"}, "lab": {"status": "current", "display_title": "Job Dekker, UMMS", "name": "job-dekker-lab", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "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"]}}, {"accession": "4DNFI49A9Z1K", "file_type": "dot calls", "@type": ["FileProcessed", "File", "Item"], "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f556118b2c", "display_title": "bedpe", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bedpe/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "4f568bd9-a205-486d-ab67-8b275aac1210", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "href": "/files-processed/4DNFI49A9Z1K/@@download/4DNFI49A9Z1K.bedpe.gz", "md5sum": "58b655c4934a09be4f5cf21876ba74e2", "file_type_detailed": "dot calls (bedpe)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/4f568bd9-a205-486d-ab67-8b275aac1210/4DNFI49A9Z1K.bedpe.gz", "status": "released", "display_title": "4DNFI49A9Z1K.bedpe.gz", "@id": "/files-processed/4DNFI49A9Z1K/", "genome_assembly": "GRCh38", "file_size": 2756544, "track_and_facet_info": {"dataset": "Micro-C on H1-DE cells - protocol variations", "condition": "Formaldehyde+DSG, H1-DE (Tier 1)", "experimental_lab": "Job Dekker, UMMS", "replicate_info": "merged replicates", "experiment_bucket": "Compartment, insulation and loop calls - Dekker Lab", "experiment_type": "Micro-C", "assay_info": "MNase", "biosource_name": "H1-hESC (Tier 1) differentiated to definitive endoderm", "lab_name": "Job Dekker, UMMS"}, "last_modified": {"date_modified": "2021-12-16T07:01:51.902196+00:00"}, "lab": {"status": "current", "display_title": "Job Dekker, UMMS", "name": "job-dekker-lab", "@type": ["Lab", "Item"], "@id": "/labs/job-dekker-lab/", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "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"]}}], "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": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "description": "Supplementary Files (Compartment, insulation and loop calls - Dekker Lab) for 4DNESW1SPPTD (Micro-C experiments on H1 derived endoderm, differentiated using the 4DN protocol.): 4DNFIC5YU5BU", "display_title": "4DNESW1SPPTD - Compartment, insulation and loop calls - Dekker Lab", "status": "released", "uuid": "f6ee4e1f-16f8-45d3-ae1f-edf45e7709b8", "@id": "/higlass-view-configs/f6ee4e1f-16f8-45d3-ae1f-edf45e7709b8/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}, "last_modified": {"date_modified": "2021-01-25T06:04:08.888184+00:00"}}}], "@id": "/experiment-set-replicates/4DNESW1SPPTD/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "f3b092bb-3498-491f-8bbb-ef24f16ad4cc", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESW1SPPTD", "external_references": [], "pubs_using": [], "publications_of_set": [], "number_of_experiments": 8, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSMW55C3H/", "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": "/biosamples/4DNBS3TMS6FC/", "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."}}}]}, "validation-errors": []}