{"lab": {"uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "@id": "/labs/wouter-de-laat-lab/", "display_title": "Wouter de Laat, HUBRECHT", "@type": ["Lab", "Item"], "title": "Wouter de Laat, HUBRECHT", "correspondence": [{"contact_email": "dy5sYWF0QGh1YnJlY2h0LmV1", "@id": "/users/d6570f35-5a6c-4b14-a818-d1c09491adb0/", "display_title": "Wouter de Laat"}], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}, "pi": {"error": "no view permissions"}}, "award": {"status": "current", "@id": "/awards/external-award/", "project": "External", "description": "Funding source is from outside 4DN.", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@type": ["Award", "Item"], "center": "External", "display_title": "EXTERNAL AWARD", "center_title": "External", "name": "external-award", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "study": "Hi-C on human cardiac tissue", "status": "released", "aliases": ["wouter-de-laat-lab:hic_left_ventricle_p01137"], "accession": "4DNESUYU9VSU", "condition": "left ventricle - donor 01137", "description": "in situ Hi-C on primary cardiomyocytes from the left ventricle - donor 01137", "study_group": "Single Time Point and Condition", "date_created": "2023-04-20T09:45:27.409109+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "in situ Hi-C on primary human cardiomyocytes", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-07-31T14:46:03.925141+00:00"}, "public_release": "2023-05-05", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-hi-c/4DNEXMIDACIS/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "88d4f24e-a835-4b16-9c79-7e53a17f3b78", "display_title": "in situ Hi-C on heart left ventricle with DpnII - 4DNEXMIDACIS", "status": "released", "accession": "4DNEXMIDACIS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-hi-c/4DNEXQMOEZL7/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "db9b95eb-e6f0-4288-b7bc-ee7864f3437e", "display_title": "in situ Hi-C on heart left ventricle with DpnII - 4DNEXQMOEZL7", "status": "released", "accession": "4DNEXQMOEZL7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"uuid": "5842612c-2b64-45d0-9b8e-565def9381bc", "filetype": "HiglassViewConfig", "award": {"uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "display_title": "EXTERNAL AWARD", "status": "current", "@type": ["Award", "Item"], "@id": "/awards/external-award/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "4DNESUYU9VSU (in situ Hi-C on primary cardiomyocytes from the left ventricle - donor 01137): 4DNFITF7RS3P, 4DNFIMJ5UIV6, 4DNFIKPCGUQ9, 4DNFI6L9PN8E", "contributing_labs": [], "@type": ["HiglassViewConfig", "UserContent", "Item"], "lab": {"uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "@id": "/labs/wouter-de-laat-lab/", "display_title": "Wouter de Laat, HUBRECHT", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}, "@id": "/higlass-view-configs/5842612c-2b64-45d0-9b8e-565def9381bc/", "display_title": "4DNESUYU9VSU - Processed files", "name": "5842612c-2b64-45d0-9b8e-565def9381bc", "title": "4DNESUYU9VSU - Processed files", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}, "location": "tab:processed-files", "description": "auto_generated_higlass_view_config"}, {"content": {"uuid": "5ea459cc-cbfa-4d8e-897c-29bebbfd3c33", "filetype": "md", "award": {"uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "status": "current", "@type": ["Award", "Item"], "@id": "/awards/2U01CA200059-06/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "options": {"filetype": "md", "collapsible": false, "default_open": true, "convert_ext_links": true}, "@type": ["StaticSection", "UserContent", "Item"], "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "@id": "/static-sections/5ea459cc-cbfa-4d8e-897c-29bebbfd3c33/", "display_title": "delaat-ext-grant-note", "content": "This work was supported by Fondation Leducq (14CVD01) Transatlantic Network grant: \u2018Deciphering the genomic topology of atrial fibrillation\u2019", "name": "delaat-ext-grant-note", "status": "released", "content_as_html": "<div class=\"markdown-container\"><p>This work was supported by Fondation Leducq (14CVD01) Transatlantic Network grant: \u2018Deciphering the genomic topology of atrial fibrillation\u2019</p></div>", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267227777"]}}, "location": "tab:attribution"}], "static_headers": [{"lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "<b>In Situ Hi-C</b>\n\n<p>\n   In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed <i>in situ</i> inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n</p>\n<p>\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n</p>\n<p>\nSee <a href=\"https://www.sciencedirect.com/science/article/pii/S0092867414014974?via%3Dihub\">Rao et al., 2014</a> for more details.\n</p>\n\n<div>\n<img style=\"width: 600px;max-width:100%;\" src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/IsHC_fig1.png\"/>\n  <br/><br/>\n  <em>Image source: Rao et al., 2014, Figure 1A</em>\n</div>", "name": "item-page-headers.ExperimentType.insituhic", "award": {"@id": "/awards/1U01CA200059-01/", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Assay Description", "status": "released", "aliases": ["4dn-dcic-lab:experiment_infobox_hic"], "options": {"filetype": "html", "collapsible": false, "default_open": false, "convert_ext_links": true}, "date_created": "2018-09-07T18:19:43.777198+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-11-09T14:48:01.220007+00:00"}, "schema_version": "2", "@id": "/static-sections/298554ad-20e2-4449-a752-ac190123dab7/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "298554ad-20e2-4449-a752-ac190123dab7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.56c9c683-bb11-471b-b590-c656f7dc03c1"]}, "display_title": "Assay Description", "external_references": [], "content": "<b>In Situ Hi-C</b>\n\n<p>\n   In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed <i>in situ</i> inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n</p>\n<p>\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n</p>\n<p>\nSee <a href=\"https://www.sciencedirect.com/science/article/pii/S0092867414014974?via%3Dihub\">Rao et al., 2014</a> for more details.\n</p>\n\n<div>\n<img style=\"width: 600px;max-width:100%;\" src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/IsHC_fig1.png\"/>\n  <br/><br/>\n  <em>Image source: Rao et al., 2014, Figure 1A</em>\n</div>", "filetype": "html", "content_as_html": "<div class=\"html-container\"><b>In Situ Hi-C</b>\n<p>\n   In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed <i>in situ</i> inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n</p>\n<p>\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n</p>\n<p>\nSee <a href=\"https://www.sciencedirect.com/science/article/pii/S0092867414014974?via%3Dihub\" rel=\"noopener noreferrer\" target=\"_blank\">Rao et al., 2014</a> for more details.\n</p>\n<div>\n<img src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/IsHC_fig1.png\" style=\"width: 600px;max-width:100%;\"/>\n<br/><br/>\n<em>Image source: Rao et al., 2014, Figure 1A</em>\n</div></div>"}], "processed_files": [{"@type": ["FileProcessed", "File", "Item"], "status": "released", "file_size": 16571861538, "file_type_detailed": "contact list-combined (pairs)", "@id": "/files-processed/4DNFI7K16HOA/", "genome_assembly": "GRCh38", "md5sum": "dde8c217f96ac72ab79afb5ef84829f6", "file_type": "contact list-combined", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFI7K16HOA/@@download/4DNFI7K16HOA.pairs.gz", "uuid": "d505e59c-131c-430a-a1e5-47713ef8668f", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/d505e59c-131c-430a-a1e5-47713ef8668f/4DNFI7K16HOA.pairs.gz", "file_classification": "processed file", "upload_key": "d505e59c-131c-430a-a1e5-47713ef8668f/4DNFI7K16HOA.pairs.gz", "accession": "4DNFI7K16HOA", "display_title": "4DNFI7K16HOA.pairs.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-06-21T18:20:23.406165+00:00"}, "lab": {"status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "quality_metric": {"@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "@id": "/quality-metrics-pairsqc/228c17f3-5144-4da1-adbf-521891c00fb3/", "status": "released", "display_title": "QualityMetricPairsqc from 2023-04-25", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI7K16HOA/pairsqc_report.html", "Total reads": 829831487, "uuid": "228c17f3-5144-4da1-adbf-521891c00fb3", "quality_metric_summary": [{"title": "Filtered Reads", "value": "829831487", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "40.845", "tooltip": "Percent of filtered reads (=338.95m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "25.825", "tooltip": "Percent of filtered reads (=214.3m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "33.33", "tooltip": "Percent of filtered reads (=276.58m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "extra_files": [{"md5sum": "1b026e6ec9ce916f91eb912970a1f9b6", "href": "/files-processed/4DNFI7K16HOA/@@download/4DNFI7K16HOA.pairs.gz.px2", "file_size": 14783381, "file_format": {"status": "released", "@type": ["FileFormat", "Item"], "file_format": "pairs_px2", "display_title": "pairs_px2", "@id": "/file-formats/pairs_px2/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "contributing_labs": [{"status": "current", "name": "wouter-de-laat-lab", "@type": ["Lab", "Item"], "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "@id": "/labs/wouter-de-laat-lab/", "display_title": "Wouter de Laat, HUBRECHT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}], "external_references": [], "track_and_facet_info": {"dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "experimental_lab": "Wouter de Laat, HUBRECHT", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "heart left ventricle", "lab_name": "4DN DCIC, HMS"}}, {"@type": ["FileProcessed", "File", "Item"], "status": "released", "file_size": 7555130881, "file_type_detailed": "contact matrix (hic)", "@id": "/files-processed/4DNFIM351CAA/", "genome_assembly": "GRCh38", "md5sum": "01f0bcd1cd99045a43a382647db110ed", "file_type": "contact matrix", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/hic/", "display_title": "hic", "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFIM351CAA/@@download/4DNFIM351CAA.hic", "uuid": "7f902a51-7a0a-41d8-acfa-c29b3420faac", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/7f902a51-7a0a-41d8-acfa-c29b3420faac/4DNFIM351CAA.hic", "file_classification": "processed file", "upload_key": "7f902a51-7a0a-41d8-acfa-c29b3420faac/4DNFIM351CAA.hic", "accession": "4DNFIM351CAA", "display_title": "4DNFIM351CAA.hic", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-06-21T18:18:50.550692+00:00"}, "lab": {"status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"status": "current", "name": "wouter-de-laat-lab", "@type": ["Lab", "Item"], "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "@id": "/labs/wouter-de-laat-lab/", "display_title": "Wouter de Laat, HUBRECHT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}], "external_references": [], "track_and_facet_info": {"dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "experimental_lab": "Wouter de Laat, HUBRECHT", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "heart left ventricle", "lab_name": "4DN DCIC, HMS"}}, {"@type": ["FileProcessed", "File", "Item"], "status": "released", "file_size": 5115429530, "file_type_detailed": "contact matrix (mcool)", "@id": "/files-processed/4DNFITF7RS3P/", "genome_assembly": "GRCh38", "md5sum": "de4a1daec241e835b02ca10821aae25f", "file_type": "contact matrix", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/mcool/", "display_title": "mcool", "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "higlass_uid": "075a026d-28c3-41f9-9639-49e59ee3dab4", "href": "/files-processed/4DNFITF7RS3P/@@download/4DNFITF7RS3P.mcool", "notes_to_tsv": ["WARNING - Due to a bug in the version of cooler (0.8.3) used in the current 4DN standard Hi-C processing pipeline some pixels may occur mulitple times at a single resolution with different counts being reported for each occurence.  This duplication does not affect the higlass display of these files, howevver, downstream analyses using this file may encounter issues due to this pixel duplication.  The counts from the duplicate pixels can be aggregated to determine the correct count value at that location. If this issue is problematic for your needs you should consider regenerating the matrices from the merged pairs file of the associated dataset using a more recent version of cooler.  We are working to update the pipeline but do not yet have a predicted date for when this issue will be resolved."], "uuid": "c8a48814-0ff7-41c3-914d-41952f77bf94", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c8a48814-0ff7-41c3-914d-41952f77bf94/4DNFITF7RS3P.mcool", "file_classification": "processed file", "upload_key": "c8a48814-0ff7-41c3-914d-41952f77bf94/4DNFITF7RS3P.mcool", "accession": "4DNFITF7RS3P", "display_title": "4DNFITF7RS3P.mcool", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-08-25T17:48:06.239943+00:00"}, "lab": {"status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "quality_metric": {"@type": ["QualityMetricMcool", "QualityMetric", "Item"], "overall_quality_status": "PASS", "@id": "/quality-metrics-mcool/f7ac3c42-1d45-4050-a18e-b54bcbaa2239/", "status": "released", "display_title": "QualityMetricMcool from 2023-04-25", "uuid": "f7ac3c42-1d45-4050-a18e-b54bcbaa2239", "quality_metric_summary": [{"title": "Failed Balancing", "value": "None", "tooltip": "Resolutions where balancing failed", "numberType": "string"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"display_title": "4DNFITF7RS3P - contact matrix for heart left ventricle in situ Hi-C DpnII", "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "6dd21868-ca0d-4eef-b292-b909381259ad", "@id": "/higlass-view-configs/6dd21868-ca0d-4eef-b292-b909381259ad/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "contributing_labs": [{"status": "current", "name": "wouter-de-laat-lab", "@type": ["Lab", "Item"], "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "@id": "/labs/wouter-de-laat-lab/", "display_title": "Wouter de Laat, HUBRECHT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}], "external_references": [], "track_and_facet_info": {"dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "experimental_lab": "Wouter de Laat, HUBRECHT", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "heart left ventricle", "lab_name": "4DN DCIC, HMS", "track_title": "contact matrix for heart left ventricle in situ Hi-C DpnII"}}, {"@type": ["FileProcessed", "File", "Item"], "status": "released", "file_size": 213310, "file_type_detailed": "compartments (bw)", "@id": "/files-processed/4DNFIMJ5UIV6/", "genome_assembly": "GRCh38", "md5sum": "f95ad39bc4b6d8ef47cffcb0e7b7770f", "file_type": "compartments", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "higlass_uid": "7d1af9f7-3dbb-44a2-a01e-b40bf9254bff", "href": "/files-processed/4DNFIMJ5UIV6/@@download/4DNFIMJ5UIV6.bw", "uuid": "f3bcfaa8-d903-469b-9de3-2534f59a4425", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f3bcfaa8-d903-469b-9de3-2534f59a4425/4DNFIMJ5UIV6.bw", "file_classification": "processed file", "upload_key": "f3bcfaa8-d903-469b-9de3-2534f59a4425/4DNFIMJ5UIV6.bw", "accession": "4DNFIMJ5UIV6", "display_title": "4DNFIMJ5UIV6.bw", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-06-21T18:48:12.608258+00:00"}, "lab": {"status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"display_title": "4DNFIMJ5UIV6 - compartments for heart left ventricle in situ Hi-C DpnII", "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "124ddaa4-e47c-481d-8aa6-1a7da6ce80f6", "@id": "/higlass-view-configs/124ddaa4-e47c-481d-8aa6-1a7da6ce80f6/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "contributing_labs": [{"status": "current", "name": "wouter-de-laat-lab", "@type": ["Lab", "Item"], "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "@id": "/labs/wouter-de-laat-lab/", "display_title": "Wouter de Laat, HUBRECHT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}], "external_references": [], "track_and_facet_info": {"dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "experimental_lab": "Wouter de Laat, HUBRECHT", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "heart left ventricle", "lab_name": "4DN DCIC, HMS", "track_title": "compartments for heart left ventricle in situ Hi-C DpnII"}}, {"@type": ["FileProcessed", "File", "Item"], "status": "released", "file_size": 149480, "file_type_detailed": "boundaries (bed)", "@id": "/files-processed/4DNFIKPCGUQ9/", "genome_assembly": "GRCh38", "md5sum": "b019a0570512f805bc5823f5093686d9", "file_type": "boundaries", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bed/", "display_title": "bed", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "higlass_uid": "BnlGynPiTiCfwv9PxPXFNw", "href": "/files-processed/4DNFIKPCGUQ9/@@download/4DNFIKPCGUQ9.bed.gz", "uuid": "3b7a512c-1ae8-4de9-b117-d7831eb549b2", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/3b7a512c-1ae8-4de9-b117-d7831eb549b2/4DNFIKPCGUQ9.bed.gz", "file_classification": "processed file", "upload_key": "3b7a512c-1ae8-4de9-b117-d7831eb549b2/4DNFIKPCGUQ9.bed.gz", "accession": "4DNFIKPCGUQ9", "display_title": "4DNFIKPCGUQ9.bed.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-06-21T18:48:14.584843+00:00"}, "lab": {"status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "extra_files": [{"md5sum": "7d1c50003ff46c921609f5e84f2444c6", "href": "/files-processed/4DNFIKPCGUQ9/@@download/4DNFIKPCGUQ9.beddb", "use_for": "visualization", "file_size": 1738752, "file_format": {"status": "released", "@type": ["FileFormat", "Item"], "file_format": "beddb", "display_title": "beddb", "@id": "/file-formats/beddb/", "uuid": "76dc8c06-67d8-487b-8fc8-d841752a0b60", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"display_title": "4DNFIKPCGUQ9 - boundaries for heart left ventricle in situ Hi-C DpnII", "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "4593a97d-cfc4-46f1-a28d-f668f33a86e9", "@id": "/higlass-view-configs/4593a97d-cfc4-46f1-a28d-f668f33a86e9/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "contributing_labs": [{"status": "current", "name": "wouter-de-laat-lab", "@type": ["Lab", "Item"], "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "@id": "/labs/wouter-de-laat-lab/", "display_title": "Wouter de Laat, HUBRECHT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}], "external_references": [], "track_and_facet_info": {"dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "experimental_lab": "Wouter de Laat, HUBRECHT", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "heart left ventricle", "lab_name": "4DN DCIC, HMS", "track_title": "boundaries for heart left ventricle in situ Hi-C DpnII"}}, {"@type": ["FileProcessed", "File", "Item"], "status": "released", "file_size": 8549199, "file_type_detailed": "insulation score-diamond (bw)", "@id": "/files-processed/4DNFI6L9PN8E/", "genome_assembly": "GRCh38", "md5sum": "174613a12ce2d61cb44065a85baccec8", "file_type": "insulation score-diamond", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "higlass_uid": "44186f8a-441c-44ae-9d8a-8e26fbb5fd30", "href": "/files-processed/4DNFI6L9PN8E/@@download/4DNFI6L9PN8E.bw", "uuid": "14e952a2-0424-4ebe-a965-292b0ed06663", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/14e952a2-0424-4ebe-a965-292b0ed06663/4DNFI6L9PN8E.bw", "file_classification": "processed file", "upload_key": "14e952a2-0424-4ebe-a965-292b0ed06663/4DNFI6L9PN8E.bw", "accession": "4DNFI6L9PN8E", "display_title": "4DNFI6L9PN8E.bw", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-06-21T18:48:16.244247+00:00"}, "lab": {"status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"display_title": "4DNFI6L9PN8E - insulation score-diamond for heart left ventricle in situ Hi-C DpnII", "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "7a2ada14-8eaf-4f8d-b49b-cdcd8b1c97b6", "@id": "/higlass-view-configs/7a2ada14-8eaf-4f8d-b49b-cdcd8b1c97b6/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "contributing_labs": [{"status": "current", "name": "wouter-de-laat-lab", "@type": ["Lab", "Item"], "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "@id": "/labs/wouter-de-laat-lab/", "display_title": "Wouter de Laat, HUBRECHT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}], "external_references": [], "track_and_facet_info": {"dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "experimental_lab": "Wouter de Laat, HUBRECHT", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "heart left ventricle", "lab_name": "4DN DCIC, HMS", "track_title": "insulation score-diamond for heart left ventricle in situ Hi-C DpnII"}}], "project_release": "2023-05-05", "experiments_in_set": [{"display_title": "in situ Hi-C on heart left ventricle with DpnII - 4DNEXMIDACIS", "files": [{"uuid": "b53677fc-555d-4042-9671-3d5e596d1470", "md5sum": "e4979709c2d265898e093e486f6d92d9", "file_classification": "raw file", "href": "/files-fastq/4DNFIWJPM2RB/@@download/4DNFIWJPM2RB.fastq.gz", "accession": "4DNFIWJPM2RB", "@id": "/files-fastq/4DNFIWJPM2RB/", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_size": 23313588569, "file_type_detailed": "reads (fastq)", "upload_key": "b53677fc-555d-4042-9671-3d5e596d1470/4DNFIWJPM2RB.fastq.gz", "display_title": "4DNFIWJPM2RB.fastq.gz", "status": "restricted", "related_files": [{"relationship_type": "paired with", "file": {"status": "restricted", "display_title": "4DNFI4H95T4L.fastq.gz", "@id": "/files-fastq/4DNFI4H95T4L/", "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFI4H95T4L", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "uuid": "351c4faf-bf7e-4ac6-b348-d3dd9b1ab2d7", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/7c9f8912-1aa9-4a64-a049-114757ec67c1/", "Total Sequences": 295684538, "overall_quality_status": "PASS", "uuid": "7c9f8912-1aa9-4a64-a049-114757ec67c1", "Sequence length": "100", "display_title": "QualityMetricFastqc from 2023-04-21", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIWJPM2RB/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "Wouter de Laat, HUBRECHT"}, "lab": {"@type": ["Lab", "Item"], "status": "current", "display_title": "Wouter de Laat, HUBRECHT", "@id": "/labs/wouter-de-laat-lab/", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"uuid": "351c4faf-bf7e-4ac6-b348-d3dd9b1ab2d7", "md5sum": "bbcf5dc52881f1aaf3212fb6ff6cda89", "file_classification": "raw file", "href": "/files-fastq/4DNFI4H95T4L/@@download/4DNFI4H95T4L.fastq.gz", "accession": "4DNFI4H95T4L", "@id": "/files-fastq/4DNFI4H95T4L/", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_size": 23499054397, "file_type_detailed": "reads (fastq)", "upload_key": "351c4faf-bf7e-4ac6-b348-d3dd9b1ab2d7/4DNFI4H95T4L.fastq.gz", "display_title": "4DNFI4H95T4L.fastq.gz", "status": "restricted", "related_files": [{"relationship_type": "paired with", "file": {"status": "restricted", "display_title": "4DNFIWJPM2RB.fastq.gz", "@id": "/files-fastq/4DNFIWJPM2RB/", "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFIWJPM2RB", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "uuid": "b53677fc-555d-4042-9671-3d5e596d1470", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/0c767d63-4933-4b51-b3f1-958d82e578da/", "Total Sequences": 295684538, "overall_quality_status": "PASS", "uuid": "0c767d63-4933-4b51-b3f1-958d82e578da", "Sequence length": "100", "display_title": "QualityMetricFastqc from 2023-04-21", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI4H95T4L/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "Wouter de Laat, HUBRECHT"}, "lab": {"@type": ["Lab", "Item"], "status": "current", "display_title": "Wouter de Laat, HUBRECHT", "@id": "/labs/wouter-de-laat-lab/", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"uuid": "1c16db77-6934-4284-98bd-709c54c3d457", "md5sum": "9f1a78a49fd9cde47fd375be0a76936b", "file_classification": "raw file", "href": "/files-fastq/4DNFIWBJD3P9/@@download/4DNFIWBJD3P9.fastq.gz", "accession": "4DNFIWBJD3P9", "@id": "/files-fastq/4DNFIWBJD3P9/", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_size": 1672172248, "file_type_detailed": "reads (fastq)", "upload_key": "1c16db77-6934-4284-98bd-709c54c3d457/4DNFIWBJD3P9.fastq.gz", "display_title": "4DNFIWBJD3P9.fastq.gz", "status": "restricted", "related_files": [{"relationship_type": "paired with", "file": {"status": "restricted", "display_title": "4DNFIZ9WAWJL.fastq.gz", "@id": "/files-fastq/4DNFIZ9WAWJL/", "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFIZ9WAWJL", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "uuid": "312f2a4e-2db4-440d-992b-f527c7dab53b", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/3b782167-c831-49ae-b200-2f11b243c550/", "Total Sequences": 30849455, "overall_quality_status": "PASS", "uuid": "3b782167-c831-49ae-b200-2f11b243c550", "Sequence length": "35-76", "display_title": "QualityMetricFastqc from 2023-04-21", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIWBJD3P9/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "Wouter de Laat, HUBRECHT"}, "lab": {"@type": ["Lab", "Item"], "status": "current", "display_title": "Wouter de Laat, HUBRECHT", "@id": "/labs/wouter-de-laat-lab/", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"uuid": "312f2a4e-2db4-440d-992b-f527c7dab53b", "md5sum": "0c615b9b58917ebd37ca3fe916e7bbcf", "file_classification": "raw file", "href": "/files-fastq/4DNFIZ9WAWJL/@@download/4DNFIZ9WAWJL.fastq.gz", "accession": "4DNFIZ9WAWJL", "@id": "/files-fastq/4DNFIZ9WAWJL/", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_size": 1744637347, "file_type_detailed": "reads (fastq)", "upload_key": "312f2a4e-2db4-440d-992b-f527c7dab53b/4DNFIZ9WAWJL.fastq.gz", "display_title": "4DNFIZ9WAWJL.fastq.gz", "status": "restricted", "related_files": [{"relationship_type": "paired with", "file": {"status": "restricted", "display_title": "4DNFIWBJD3P9.fastq.gz", "@id": "/files-fastq/4DNFIWBJD3P9/", "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFIWBJD3P9", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "uuid": "1c16db77-6934-4284-98bd-709c54c3d457", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/7a2b6a0a-63dd-4fed-ba1c-195766d3705e/", "Total Sequences": 30849455, "overall_quality_status": "PASS", "uuid": "7a2b6a0a-63dd-4fed-ba1c-195766d3705e", "Sequence length": "55-76", "display_title": "QualityMetricFastqc from 2023-04-21", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIZ9WAWJL/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "Wouter de Laat, HUBRECHT"}, "lab": {"@type": ["Lab", "Item"], "status": "current", "display_title": "Wouter de Laat, HUBRECHT", "@id": "/labs/wouter-de-laat-lab/", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"uuid": "5c2bdc4a-d809-422b-a051-9121e9b9426a", "md5sum": "74f4d794fa864303d1855c6fb00f4e0f", "file_classification": "raw file", "href": "/files-fastq/4DNFIZ1DKSWK/@@download/4DNFIZ1DKSWK.fastq.gz", "accession": "4DNFIZ1DKSWK", "@id": "/files-fastq/4DNFIZ1DKSWK/", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_size": 2142636471, "file_type_detailed": "reads (fastq)", "upload_key": "5c2bdc4a-d809-422b-a051-9121e9b9426a/4DNFIZ1DKSWK.fastq.gz", "display_title": "4DNFIZ1DKSWK.fastq.gz", "status": "restricted", "related_files": [{"relationship_type": "paired with", "file": {"status": "restricted", "display_title": "4DNFI2DCNFQX.fastq.gz", "@id": "/files-fastq/4DNFI2DCNFQX/", "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFI2DCNFQX", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "uuid": "e6ebe9ae-f7a9-4937-92c8-1e113b5515fa", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/b58e6574-6d2e-4c1b-aa4c-6faf2126e4a3/", "Total Sequences": 37148005, "overall_quality_status": "PASS", "uuid": "b58e6574-6d2e-4c1b-aa4c-6faf2126e4a3", "Sequence length": "35-76", "display_title": "QualityMetricFastqc from 2023-04-21", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIZ1DKSWK/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "Wouter de Laat, HUBRECHT"}, "lab": {"@type": ["Lab", "Item"], "status": "current", "display_title": "Wouter de Laat, HUBRECHT", "@id": "/labs/wouter-de-laat-lab/", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"uuid": "e6ebe9ae-f7a9-4937-92c8-1e113b5515fa", "md5sum": "180bb8711786aaadce863415e85f3362", "file_classification": "raw file", "href": "/files-fastq/4DNFI2DCNFQX/@@download/4DNFI2DCNFQX.fastq.gz", "accession": "4DNFI2DCNFQX", "@id": "/files-fastq/4DNFI2DCNFQX/", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_size": 2196457702, "file_type_detailed": "reads (fastq)", "upload_key": "e6ebe9ae-f7a9-4937-92c8-1e113b5515fa/4DNFI2DCNFQX.fastq.gz", "display_title": "4DNFI2DCNFQX.fastq.gz", "status": "restricted", "related_files": [{"relationship_type": "paired with", "file": {"status": "restricted", "display_title": "4DNFIZ1DKSWK.fastq.gz", "@id": "/files-fastq/4DNFIZ1DKSWK/", "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFIZ1DKSWK", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "uuid": "5c2bdc4a-d809-422b-a051-9121e9b9426a", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/2627fc13-ea92-455f-8e0b-3c56abe71565/", "Total Sequences": 37148005, "overall_quality_status": "PASS", "uuid": "2627fc13-ea92-455f-8e0b-3c56abe71565", "Sequence length": "55-76", "display_title": "QualityMetricFastqc from 2023-04-21", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI2DCNFQX/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "Wouter de Laat, HUBRECHT"}, "lab": {"@type": ["Lab", "Item"], "status": "current", "display_title": "Wouter de Laat, HUBRECHT", "@id": "/labs/wouter-de-laat-lab/", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"uuid": "7b64c955-b7e6-4176-97bf-9784c87f96be", "md5sum": "2050df64e2b77aa4f3b8e5956063cafd", "file_classification": "raw file", "href": "/files-fastq/4DNFIDL96859/@@download/4DNFIDL96859.fastq.gz", "accession": "4DNFIDL96859", "@id": "/files-fastq/4DNFIDL96859/", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_size": 11745978089, "file_type_detailed": "reads (fastq)", "upload_key": "7b64c955-b7e6-4176-97bf-9784c87f96be/4DNFIDL96859.fastq.gz", "display_title": "4DNFIDL96859.fastq.gz", "status": "restricted", "related_files": [{"relationship_type": "paired with", "file": {"status": "restricted", "display_title": "4DNFIYRTP87E.fastq.gz", "@id": "/files-fastq/4DNFIYRTP87E/", "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFIYRTP87E", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "uuid": "de6523c6-2e0b-4200-beac-15048d4069c2", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/d7f3cb38-1c3c-4ffc-b04d-88c5d4d672a5/", "Total Sequences": 456004454, "overall_quality_status": "PASS", "uuid": "d7f3cb38-1c3c-4ffc-b04d-88c5d4d672a5", "Sequence length": "51", "display_title": "QualityMetricFastqc from 2023-04-21", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIDL96859/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "Wouter de Laat, HUBRECHT"}, "lab": {"@type": ["Lab", "Item"], "status": "current", "display_title": "Wouter de Laat, HUBRECHT", "@id": "/labs/wouter-de-laat-lab/", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"uuid": "de6523c6-2e0b-4200-beac-15048d4069c2", "md5sum": "1dafaadace44f3f68f3bb4d4c1258271", "file_classification": "raw file", "href": "/files-fastq/4DNFIYRTP87E/@@download/4DNFIYRTP87E.fastq.gz", "accession": "4DNFIYRTP87E", "@id": "/files-fastq/4DNFIYRTP87E/", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_size": 12145281446, "file_type_detailed": "reads (fastq)", "upload_key": "de6523c6-2e0b-4200-beac-15048d4069c2/4DNFIYRTP87E.fastq.gz", "display_title": "4DNFIYRTP87E.fastq.gz", "status": "restricted", "related_files": [{"relationship_type": "paired with", "file": {"status": "restricted", "display_title": "4DNFIDL96859.fastq.gz", "@id": "/files-fastq/4DNFIDL96859/", "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFIDL96859", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "uuid": "7b64c955-b7e6-4176-97bf-9784c87f96be", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/1f7de3d9-886e-4c09-9858-412e7a452015/", "Total Sequences": 456004454, "overall_quality_status": "PASS", "uuid": "1f7de3d9-886e-4c09-9858-412e7a452015", "Sequence length": "51", "display_title": "QualityMetricFastqc from 2023-04-21", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIYRTP87E/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "Wouter de Laat, HUBRECHT"}, "lab": {"@type": ["Lab", "Item"], "status": "current", "display_title": "Wouter de Laat, HUBRECHT", "@id": "/labs/wouter-de-laat-lab/", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}], "@type": ["ExperimentHiC", "Experiment", "Item"], "crosslinking_method": "2% Formaldehyde", "@id": "/experiments-hi-c/4DNEXMIDACIS/", "accession": "4DNEXMIDACIS", "status": "released", "uuid": "88d4f24e-a835-4b16-9c79-7e53a17f3b78", "biosample": {"display_title": "4DNBSSYFDFSU", "accession": "4DNBSSYFDFSU", "treatments_summary": "None", "uuid": "8a9e7d5d-1fe0-4c31-96eb-c4f69518cb58", "status": "released", "biosample_category": ["Multicellular Tissue"], "biosample_type": "tissue", "modifications_summary": "None", "@id": "/biosamples/4DNBSSYFDFSU/", "biosource_summary": "heart left ventricle", "@type": ["Biosample", "Item"], "biosource": [{"display_title": "heart left ventricle - 4DNSRPQXZDBC", "@id": "/biosources/4DNSRPQXZDBC/", "accession": "4DNSRPQXZDBC", "cell_line_tier": "Unclassified", "biosource_type": "tissue", "@type": ["Biosource", "Item"], "uuid": "f70eeb3f-0b4d-4755-8cb8-40e9a3d0e204", "status": "released", "tissue": {"synonyms": ["left cardiac ventricle", "left ventricle", "left ventricle of heart", "cardiac left ventricle"], "term_name": "heart left ventricle", "term_id": "UBERON:0002084", "status": "released", "@id": "/ontology-terms/UBERON:0002084/", "display_title": "heart left ventricle", "preferred_name": "heart left ventricle", "@type": ["OntologyTerm", "Item"], "uuid": "5c3cfbf3-fc0a-482f-aa54-09163a7af31b", "slim_terms": [{"display_title": "circulatory system", "@id": "/ontology-terms/UBERON:0001009/", "status": "released", "uuid": "111131bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "mesoderm", "@id": "/ontology-terms/UBERON:0000926/", "status": "released", "uuid": "111120bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "heart", "@id": "/ontology-terms/UBERON:0000948/", "status": "released", "uuid": "111187bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "name": "human", "@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "scientific_name": "Homo sapiens", "@type": ["Organism", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"tissue_source": "heart left ventricle", "organ_system": ["circulatory system", "mesoderm", "heart"]}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "other_processed_files": [{"title": "HiC Processing Pipeline - v0.3.0", "type": "preliminary", "description": "These are files generated using the updated Hi-C processing pipeline. They should be largely similar to those available in the Processed Files tab, which were generated with the previous version of the standard pipeline.  One potential difference of note is that the version of cooler used to generate the mcool file has a bug fix to prevent a pixel duplication issue which is observed in some files generated by the previous version of the pipeline.  Another notable difference is that a filter is applied to remove reads with MAPQ scores below 30 prior to mcool file generation.", "files": [{"uuid": "37f1c3b3-4a82-4703-9b0d-b51c152e4ab1", "genome_assembly": "GRCh38", "href": "/files-processed/4DNFIXNEABGE/@@download/4DNFIXNEABGE.bam", "file_type": "alignments", "@type": ["FileProcessed", "File", "Item"], "file_size": 132749136960, "file_type_detailed": "alignments (bam)", "@id": "/files-processed/4DNFIXNEABGE/", "accession": "4DNFIXNEABGE", "md5sum": "68c9b75074a64bcce4cc319716fb410d", "display_title": "4DNFIXNEABGE.bam", "status": "restricted", "contributing_labs": [{"@id": "/labs/wouter-de-laat-lab/", "display_title": "Wouter de Laat, HUBRECHT", "status": "current", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}], "lab": {"@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "file_format": "bam", "@id": "/file-formats/bam/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-10-04T17:26:52.744590+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "4DN DCIC, HMS"}}, {"uuid": "fd25fbc9-53a9-44a5-9b24-1cee586832de", "genome_assembly": "GRCh38", "href": "/files-processed/4DNFINBTOW1E/@@download/4DNFINBTOW1E.pairs.gz", "file_type": "contact list-replicate", "@type": ["FileProcessed", "File", "Item"], "file_size": 9285460742, "file_type_detailed": "contact list-replicate (pairs)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/fd25fbc9-53a9-44a5-9b24-1cee586832de/4DNFINBTOW1E.pairs.gz", "@id": "/files-processed/4DNFINBTOW1E/", "accession": "4DNFINBTOW1E", "md5sum": "1ebb8952d98e8df22c898622fe57e3fd", "display_title": "4DNFINBTOW1E.pairs.gz", "status": "released", "contributing_labs": [{"@id": "/labs/wouter-de-laat-lab/", "display_title": "Wouter de Laat, HUBRECHT", "status": "current", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}], "quality_metric": {"@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "uuid": "ac48a1c0-e5ce-4747-85cc-9b2b92bec1cb", "display_title": "QualityMetricPairsqc from 2024-07-10", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFINBTOW1E/pairsqc_report.html", "overall_quality_status": "PASS", "@id": "/quality-metrics-pairsqc/ac48a1c0-e5ce-4747-85cc-9b2b92bec1cb/", "status": "released", "quality_metric_summary": [{"title": "Filtered Reads", "value": "460922685", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "40.517", "tooltip": "Percent of filtered reads (=186.75m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "27.327", "tooltip": "Percent of filtered reads (=125.96m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "32.156", "tooltip": "Percent of filtered reads (=148.21m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "pairs", "file_format": "pairs", "@id": "/file-formats/pairs/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-08-07T23:57:14.081693+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "4DN DCIC, HMS"}}]}], "processed_files": [{"file_size": 133343753757, "href": "/files-processed/4DNFI64YSDVU/@@download/4DNFI64YSDVU.bam", "@id": "/files-processed/4DNFI64YSDVU/", "status": "restricted", "file_format": {"display_title": "bam", "status": "released", "@id": "/file-formats/bam/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_type": "alignments", "md5sum": "a94287e30bd805dff101b7fa8dade2fb", "accession": "4DNFI64YSDVU", "file_type_detailed": "alignments (bam)", "@type": ["FileProcessed", "File", "Item"], "upload_key": "8e2eb129-57f1-4ae4-9750-821fdcc02b59/4DNFI64YSDVU.bam", "file_classification": "processed file", "display_title": "4DNFI64YSDVU.bam", "genome_assembly": "GRCh38", "uuid": "8e2eb129-57f1-4ae4-9750-821fdcc02b59", "contributing_labs": [{"@id": "/labs/wouter-de-laat-lab/", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "display_title": "Wouter de Laat, HUBRECHT", "name": "wouter-de-laat-lab", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}], "external_references": [], "quality_metric": {"@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "@id": "/quality-metrics-bamqc/3c553072-0fa6-42fc-926d-3edcf509ed4f/", "status": "released", "overall_quality_status": "PASS", "display_title": "QualityMetricBamqc from 2023-04-24", "uuid": "3c553072-0fa6-42fc-926d-3edcf509ed4f", "quality_metric_summary": [{"title": "Total Reads", "value": "819686452", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "15.852", "tooltip": "Percent of total reads (=129.94m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "19.573", "tooltip": "Percent of total reads (=160.44m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "5.301", "tooltip": "Percent of total reads (=43.45m)", "numberType": "percent"}, {"title": "Walks", "value": "7.126", "tooltip": "Percent of total reads (=58.41m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.206", "tooltip": "Percent of total reads (=1.69m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "last_modified": {"date_modified": "2023-09-25T20:26:58.579239+00:00"}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 9555575639, "href": "/files-processed/4DNFI9RQJ8IK/@@download/4DNFI9RQJ8IK.pairs.gz", "@id": "/files-processed/4DNFI9RQJ8IK/", "status": "released", "file_format": {"display_title": "pairs", "status": "released", "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_type": "contact list-replicate", "md5sum": "a9713225cdcd31a97a9fef76de8e6240", "accession": "4DNFI9RQJ8IK", "file_type_detailed": "contact list-replicate (pairs)", "@type": ["FileProcessed", "File", "Item"], "upload_key": "eb88e50f-72f1-4596-b2c0-31c817c8a59a/4DNFI9RQJ8IK.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/eb88e50f-72f1-4596-b2c0-31c817c8a59a/4DNFI9RQJ8IK.pairs.gz", "file_classification": "processed file", "display_title": "4DNFI9RQJ8IK.pairs.gz", "genome_assembly": "GRCh38", "uuid": "eb88e50f-72f1-4596-b2c0-31c817c8a59a", "contributing_labs": [{"@id": "/labs/wouter-de-laat-lab/", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "display_title": "Wouter de Laat, HUBRECHT", "name": "wouter-de-laat-lab", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}], "extra_files": [{"md5sum": "c8232d5d617a3e527cf3f4ef4d364d2a", "file_size": 31242590, "href": "/files-processed/4DNFI9RQJ8IK/@@download/4DNFI9RQJ8IK.pairs.gz.px2", "file_format": {"file_format": "pairs_px2", "@type": ["FileFormat", "Item"], "display_title": "pairs_px2", "@id": "/file-formats/pairs_px2/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "@id": "/quality-metrics-pairsqc/edffead5-ad90-4f54-abce-5b0b26ab0b86/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI9RQJ8IK/pairsqc_report.html", "overall_quality_status": "PASS", "display_title": "QualityMetricPairsqc from 2023-04-24", "Total reads": 427450537, "uuid": "edffead5-ad90-4f54-abce-5b0b26ab0b86", "quality_metric_summary": [{"title": "Filtered Reads", "value": "427450537", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "40.509", "tooltip": "Percent of filtered reads (=173.16m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "27.563", "tooltip": "Percent of filtered reads (=117.82m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "31.928", "tooltip": "Percent of filtered reads (=136.47m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "last_modified": {"date_modified": "2023-06-21T18:34:13.355567+00:00"}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "external_references": [], "digestion_enzyme": {"@id": "/enzymes/DpnII/", "status": "released", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "display_title": "DpnII", "@type": ["Enzyme", "Item"], "name": "DpnII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-07-19T12:44:18.505134+00:00"}, "experiment_type": {"assay_subclassification": "DNA-DNA Pairwise Interactions", "experiment_category": "Sequencing", "status": "released", "@id": "/experiment-types/in-situ-hi-c/", "title": "in situ Hi-C", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "assay_classification": "3C via Ligation", "@type": ["ExperimentType", "Item"], "display_title": "in situ Hi-C", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "assay_subclass_short": "Hi-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"field": "Enzyme", "combined": "Enzyme: DpnII", "value": "DpnII"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "in situ Hi-C on heart left ventricle with DpnII - 4DNEXQMOEZL7", "files": [{"uuid": "06cced5f-3c9d-469c-9ccf-af165b0b8a06", "md5sum": "ff86a831d474283cbc7e218dcd718e3f", "file_classification": "raw file", "href": "/files-fastq/4DNFIFPFX7PA/@@download/4DNFIFPFX7PA.fastq.gz", "accession": "4DNFIFPFX7PA", "@id": "/files-fastq/4DNFIFPFX7PA/", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_size": 18757684371, "file_type_detailed": "reads (fastq)", "upload_key": "06cced5f-3c9d-469c-9ccf-af165b0b8a06/4DNFIFPFX7PA.fastq.gz", "display_title": "4DNFIFPFX7PA.fastq.gz", "status": "restricted", "related_files": [{"relationship_type": "paired with", "file": {"status": "restricted", "display_title": "4DNFIR37BYXO.fastq.gz", "@id": "/files-fastq/4DNFIR37BYXO/", "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFIR37BYXO", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "uuid": "cf93bf80-fe66-4f53-aaaa-8d88daa02f4b", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/87e61a0a-d512-4deb-a9d3-fbe9ad0f225a/", "Total Sequences": 235970567, "overall_quality_status": "PASS", "uuid": "87e61a0a-d512-4deb-a9d3-fbe9ad0f225a", "Sequence length": "100", "display_title": "QualityMetricFastqc from 2023-04-21", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIFPFX7PA/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "Wouter de Laat, HUBRECHT"}, "lab": {"@type": ["Lab", "Item"], "status": "current", "display_title": "Wouter de Laat, HUBRECHT", "@id": "/labs/wouter-de-laat-lab/", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"uuid": "cf93bf80-fe66-4f53-aaaa-8d88daa02f4b", "md5sum": "4284963de15069405a2f0b4612f0bf87", "file_classification": "raw file", "href": "/files-fastq/4DNFIR37BYXO/@@download/4DNFIR37BYXO.fastq.gz", "accession": "4DNFIR37BYXO", "@id": "/files-fastq/4DNFIR37BYXO/", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_size": 18963594671, "file_type_detailed": "reads (fastq)", "upload_key": "cf93bf80-fe66-4f53-aaaa-8d88daa02f4b/4DNFIR37BYXO.fastq.gz", "display_title": "4DNFIR37BYXO.fastq.gz", "status": "restricted", "related_files": [{"relationship_type": "paired with", "file": {"status": "restricted", "display_title": "4DNFIFPFX7PA.fastq.gz", "@id": "/files-fastq/4DNFIFPFX7PA/", "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFIFPFX7PA", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "uuid": "06cced5f-3c9d-469c-9ccf-af165b0b8a06", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/7b8b5642-1a41-42ef-a65a-54770d19b1fe/", "Total Sequences": 235970567, "overall_quality_status": "PASS", "uuid": "7b8b5642-1a41-42ef-a65a-54770d19b1fe", "Sequence length": "100", "display_title": "QualityMetricFastqc from 2023-04-21", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIR37BYXO/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "Wouter de Laat, HUBRECHT"}, "lab": {"@type": ["Lab", "Item"], "status": "current", "display_title": "Wouter de Laat, HUBRECHT", "@id": "/labs/wouter-de-laat-lab/", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"uuid": "058a014d-c80c-41a9-be0e-2d2a86d79419", "md5sum": "ca173ada02393c26b9b9e14fc6db48ff", "file_classification": "raw file", "href": "/files-fastq/4DNFIGZWYDI1/@@download/4DNFIGZWYDI1.fastq.gz", "accession": "4DNFIGZWYDI1", "@id": "/files-fastq/4DNFIGZWYDI1/", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_size": 3320893974, "file_type_detailed": "reads (fastq)", "upload_key": "058a014d-c80c-41a9-be0e-2d2a86d79419/4DNFIGZWYDI1.fastq.gz", "display_title": "4DNFIGZWYDI1.fastq.gz", "status": "restricted", "related_files": [{"relationship_type": "paired with", "file": {"status": "restricted", "display_title": "4DNFI9CL9TNZ.fastq.gz", "@id": "/files-fastq/4DNFI9CL9TNZ/", "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFI9CL9TNZ", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "uuid": "541aec86-b7fd-46b8-b367-063c99aa917d", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/f9a8bd0d-3193-4465-a318-f50431ed0527/", "Total Sequences": 60868985, "overall_quality_status": "PASS", "uuid": "f9a8bd0d-3193-4465-a318-f50431ed0527", "Sequence length": "35-76", "display_title": "QualityMetricFastqc from 2023-04-21", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIGZWYDI1/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "Wouter de Laat, HUBRECHT"}, "lab": {"@type": ["Lab", "Item"], "status": "current", "display_title": "Wouter de Laat, HUBRECHT", "@id": "/labs/wouter-de-laat-lab/", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"uuid": "541aec86-b7fd-46b8-b367-063c99aa917d", "md5sum": "b87a8e710d74057aa8f03c54c9b2634e", "file_classification": "raw file", "href": "/files-fastq/4DNFI9CL9TNZ/@@download/4DNFI9CL9TNZ.fastq.gz", "accession": "4DNFI9CL9TNZ", "@id": "/files-fastq/4DNFI9CL9TNZ/", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_size": 3459655437, "file_type_detailed": "reads (fastq)", "upload_key": "541aec86-b7fd-46b8-b367-063c99aa917d/4DNFI9CL9TNZ.fastq.gz", "display_title": "4DNFI9CL9TNZ.fastq.gz", "status": "restricted", "related_files": [{"relationship_type": "paired with", "file": {"status": "restricted", "display_title": "4DNFIGZWYDI1.fastq.gz", "@id": "/files-fastq/4DNFIGZWYDI1/", "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFIGZWYDI1", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "uuid": "058a014d-c80c-41a9-be0e-2d2a86d79419", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/366b60e7-e976-46c4-b060-c54666dc711d/", "Total Sequences": 60868985, "overall_quality_status": "PASS", "uuid": "366b60e7-e976-46c4-b060-c54666dc711d", "Sequence length": "55-76", "display_title": "QualityMetricFastqc from 2023-04-21", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI9CL9TNZ/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "Wouter de Laat, HUBRECHT"}, "lab": {"@type": ["Lab", "Item"], "status": "current", "display_title": "Wouter de Laat, HUBRECHT", "@id": "/labs/wouter-de-laat-lab/", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"uuid": "287b49ce-7bab-45b4-bd04-99b03c71f824", "md5sum": "0e4f8fe758ae4df3de7b19385db581cc", "file_classification": "raw file", "href": "/files-fastq/4DNFIDLNINSG/@@download/4DNFIDLNINSG.fastq.gz", "accession": "4DNFIDLNINSG", "@id": "/files-fastq/4DNFIDLNINSG/", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_size": 3118909462, "file_type_detailed": "reads (fastq)", "upload_key": "287b49ce-7bab-45b4-bd04-99b03c71f824/4DNFIDLNINSG.fastq.gz", "display_title": "4DNFIDLNINSG.fastq.gz", "status": "restricted", "related_files": [{"relationship_type": "paired with", "file": {"status": "restricted", "display_title": "4DNFICTZIJRA.fastq.gz", "@id": "/files-fastq/4DNFICTZIJRA/", "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFICTZIJRA", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "uuid": "747f2d4e-da4e-4b42-8882-ca822678d54d", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/f95982d7-0415-4df8-a1c0-2f668cdf5ca2/", "Total Sequences": 53659157, "overall_quality_status": "PASS", "uuid": "f95982d7-0415-4df8-a1c0-2f668cdf5ca2", "Sequence length": "35-76", "display_title": "QualityMetricFastqc from 2023-04-21", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIDLNINSG/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "Wouter de Laat, HUBRECHT"}, "lab": {"@type": ["Lab", "Item"], "status": "current", "display_title": "Wouter de Laat, HUBRECHT", "@id": "/labs/wouter-de-laat-lab/", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"uuid": "747f2d4e-da4e-4b42-8882-ca822678d54d", "md5sum": "fe09d68e886303b75a194651af8b470d", "file_classification": "raw file", "href": "/files-fastq/4DNFICTZIJRA/@@download/4DNFICTZIJRA.fastq.gz", "accession": "4DNFICTZIJRA", "@id": "/files-fastq/4DNFICTZIJRA/", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_size": 3191865558, "file_type_detailed": "reads (fastq)", "upload_key": "747f2d4e-da4e-4b42-8882-ca822678d54d/4DNFICTZIJRA.fastq.gz", "display_title": "4DNFICTZIJRA.fastq.gz", "status": "restricted", "related_files": [{"relationship_type": "paired with", "file": {"status": "restricted", "display_title": "4DNFIDLNINSG.fastq.gz", "@id": "/files-fastq/4DNFIDLNINSG/", "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFIDLNINSG", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "uuid": "287b49ce-7bab-45b4-bd04-99b03c71f824", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/4161815e-be93-4309-955e-286b9f361395/", "Total Sequences": 53659157, "overall_quality_status": "PASS", "uuid": "4161815e-be93-4309-955e-286b9f361395", "Sequence length": "55-76", "display_title": "QualityMetricFastqc from 2023-04-21", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFICTZIJRA/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "Wouter de Laat, HUBRECHT"}, "lab": {"@type": ["Lab", "Item"], "status": "current", "display_title": "Wouter de Laat, HUBRECHT", "@id": "/labs/wouter-de-laat-lab/", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"uuid": "b50be245-3114-45de-bc5e-76a24f6a9bd2", "md5sum": "ff60d8463d26d9ca21d5123e019b01ff", "file_classification": "raw file", "href": "/files-fastq/4DNFI7VGE92F/@@download/4DNFI7VGE92F.fastq.gz", "accession": "4DNFI7VGE92F", "@id": "/files-fastq/4DNFI7VGE92F/", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_size": 10119670521, "file_type_detailed": "reads (fastq)", "upload_key": "b50be245-3114-45de-bc5e-76a24f6a9bd2/4DNFI7VGE92F.fastq.gz", "display_title": "4DNFI7VGE92F.fastq.gz", "status": "restricted", "related_files": [{"relationship_type": "paired with", "file": {"status": "restricted", "display_title": "4DNFIDENFMJJ.fastq.gz", "@id": "/files-fastq/4DNFIDENFMJJ/", "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFIDENFMJJ", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "uuid": "5033d7fa-07e7-4dec-9066-503ffd17823f", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/172884a2-9182-40b3-b1cd-eb5c0eba262d/", "Total Sequences": 391393994, "overall_quality_status": "PASS", "uuid": "172884a2-9182-40b3-b1cd-eb5c0eba262d", "Sequence length": "51", "display_title": "QualityMetricFastqc from 2023-04-21", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI7VGE92F/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "Wouter de Laat, HUBRECHT"}, "lab": {"@type": ["Lab", "Item"], "status": "current", "display_title": "Wouter de Laat, HUBRECHT", "@id": "/labs/wouter-de-laat-lab/", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"uuid": "5033d7fa-07e7-4dec-9066-503ffd17823f", "md5sum": "e19024e24cfeb52f0b322a10fbfd199b", "file_classification": "raw file", "href": "/files-fastq/4DNFIDENFMJJ/@@download/4DNFIDENFMJJ.fastq.gz", "accession": "4DNFIDENFMJJ", "@id": "/files-fastq/4DNFIDENFMJJ/", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_size": 10472971033, "file_type_detailed": "reads (fastq)", "upload_key": "5033d7fa-07e7-4dec-9066-503ffd17823f/4DNFIDENFMJJ.fastq.gz", "display_title": "4DNFIDENFMJJ.fastq.gz", "status": "restricted", "related_files": [{"relationship_type": "paired with", "file": {"status": "restricted", "display_title": "4DNFI7VGE92F.fastq.gz", "@id": "/files-fastq/4DNFI7VGE92F/", "file_type_detailed": "reads (fastq)", "file_type": "reads", "accession": "4DNFI7VGE92F", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "uuid": "b50be245-3114-45de-bc5e-76a24f6a9bd2", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@id": "/quality-metrics-fastqc/be52367b-ea57-4e48-8961-fffc061ae00a/", "Total Sequences": 391393994, "overall_quality_status": "PASS", "uuid": "be52367b-ea57-4e48-8961-fffc061ae00a", "Sequence length": "51", "display_title": "QualityMetricFastqc from 2023-04-21", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIDENFMJJ/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "Wouter de Laat, HUBRECHT"}, "lab": {"@type": ["Lab", "Item"], "status": "current", "display_title": "Wouter de Laat, HUBRECHT", "@id": "/labs/wouter-de-laat-lab/", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}], "@type": ["ExperimentHiC", "Experiment", "Item"], "crosslinking_method": "2% Formaldehyde", "@id": "/experiments-hi-c/4DNEXQMOEZL7/", "accession": "4DNEXQMOEZL7", "status": "released", "uuid": "db9b95eb-e6f0-4288-b7bc-ee7864f3437e", "biosample": {"display_title": "4DNBSAXOXUGD", "accession": "4DNBSAXOXUGD", "treatments_summary": "None", "uuid": "7e468be4-13fd-463a-b37c-3a08f2bb1579", "status": "released", "biosample_category": ["Multicellular Tissue"], "biosample_type": "tissue", "modifications_summary": "None", "@id": "/biosamples/4DNBSAXOXUGD/", "biosource_summary": "heart left ventricle", "@type": ["Biosample", "Item"], "biosource": [{"display_title": "heart left ventricle - 4DNSRPQXZDBC", "@id": "/biosources/4DNSRPQXZDBC/", "accession": "4DNSRPQXZDBC", "cell_line_tier": "Unclassified", "biosource_type": "tissue", "@type": ["Biosource", "Item"], "uuid": "f70eeb3f-0b4d-4755-8cb8-40e9a3d0e204", "status": "released", "tissue": {"synonyms": ["left cardiac ventricle", "left ventricle", "left ventricle of heart", "cardiac left ventricle"], "term_name": "heart left ventricle", "term_id": "UBERON:0002084", "status": "released", "@id": "/ontology-terms/UBERON:0002084/", "display_title": "heart left ventricle", "preferred_name": "heart left ventricle", "@type": ["OntologyTerm", "Item"], "uuid": "5c3cfbf3-fc0a-482f-aa54-09163a7af31b", "slim_terms": [{"display_title": "circulatory system", "@id": "/ontology-terms/UBERON:0001009/", "status": "released", "uuid": "111131bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "mesoderm", "@id": "/ontology-terms/UBERON:0000926/", "status": "released", "uuid": "111120bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "heart", "@id": "/ontology-terms/UBERON:0000948/", "status": "released", "uuid": "111187bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "name": "human", "@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "scientific_name": "Homo sapiens", "@type": ["Organism", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"tissue_source": "heart left ventricle", "organ_system": ["circulatory system", "mesoderm", "heart"]}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "other_processed_files": [{"title": "HiC Processing Pipeline - v0.3.0", "type": "preliminary", "description": "These are files generated using the updated Hi-C processing pipeline. They should be largely similar to those available in the Processed Files tab, which were generated with the previous version of the standard pipeline.  One potential difference of note is that the version of cooler used to generate the mcool file has a bug fix to prevent a pixel duplication issue which is observed in some files generated by the previous version of the pipeline.  Another notable difference is that a filter is applied to remove reads with MAPQ scores below 30 prior to mcool file generation.", "files": [{"uuid": "0e99ab54-6bc3-438c-9833-525fbc84b755", "genome_assembly": "GRCh38", "href": "/files-processed/4DNFIKMAOCGT/@@download/4DNFIKMAOCGT.bam", "file_type": "alignments", "@type": ["FileProcessed", "File", "Item"], "file_size": 120055307473, "file_type_detailed": "alignments (bam)", "@id": "/files-processed/4DNFIKMAOCGT/", "accession": "4DNFIKMAOCGT", "md5sum": "a9507bbe4899b5ccd9422ca982e0f3de", "display_title": "4DNFIKMAOCGT.bam", "status": "restricted", "contributing_labs": [{"@id": "/labs/wouter-de-laat-lab/", "display_title": "Wouter de Laat, HUBRECHT", "status": "current", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}], "lab": {"@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "file_format": "bam", "@id": "/file-formats/bam/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-10-04T17:26:51.907550+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "4DN DCIC, HMS"}}, {"uuid": "426d230b-f3ca-4ff0-9427-12d8f526d90e", "genome_assembly": "GRCh38", "href": "/files-processed/4DNFIP2TPTDX/@@download/4DNFIP2TPTDX.pairs.gz", "file_type": "contact list-replicate", "@type": ["FileProcessed", "File", "Item"], "file_size": 8723184758, "file_type_detailed": "contact list-replicate (pairs)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/426d230b-f3ca-4ff0-9427-12d8f526d90e/4DNFIP2TPTDX.pairs.gz", "@id": "/files-processed/4DNFIP2TPTDX/", "accession": "4DNFIP2TPTDX", "md5sum": "f96cbd94d97dd5613f4d439dec0f3945", "display_title": "4DNFIP2TPTDX.pairs.gz", "status": "released", "contributing_labs": [{"@id": "/labs/wouter-de-laat-lab/", "display_title": "Wouter de Laat, HUBRECHT", "status": "current", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}], "quality_metric": {"@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "uuid": "08e38768-6e13-46f5-a208-16d4e49b887b", "display_title": "QualityMetricPairsqc from 2024-07-10", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIP2TPTDX/pairsqc_report.html", "overall_quality_status": "PASS", "@id": "/quality-metrics-pairsqc/08e38768-6e13-46f5-a208-16d4e49b887b/", "status": "released", "quality_metric_summary": [{"title": "Filtered Reads", "value": "427669791", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "41.12", "tooltip": "Percent of filtered reads (=175.86m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "23.898", "tooltip": "Percent of filtered reads (=102.2m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "34.983", "tooltip": "Percent of filtered reads (=149.61m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "pairs", "file_format": "pairs", "@id": "/file-formats/pairs/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-08-07T23:56:09.058126+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "4DN DCIC, HMS"}}]}], "processed_files": [{"file_size": 120404817339, "href": "/files-processed/4DNFIBR476U7/@@download/4DNFIBR476U7.bam", "@id": "/files-processed/4DNFIBR476U7/", "status": "restricted", "file_format": {"display_title": "bam", "status": "released", "@id": "/file-formats/bam/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_type": "alignments", "md5sum": "98b126e1e38716a2e82cf2d877dc519c", "accession": "4DNFIBR476U7", "file_type_detailed": "alignments (bam)", "@type": ["FileProcessed", "File", "Item"], "upload_key": "454e6b69-9a04-47d5-b2aa-07bcb6d2870c/4DNFIBR476U7.bam", "file_classification": "processed file", "display_title": "4DNFIBR476U7.bam", "genome_assembly": "GRCh38", "uuid": "454e6b69-9a04-47d5-b2aa-07bcb6d2870c", "contributing_labs": [{"@id": "/labs/wouter-de-laat-lab/", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "display_title": "Wouter de Laat, HUBRECHT", "name": "wouter-de-laat-lab", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}], "external_references": [], "quality_metric": {"@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "@id": "/quality-metrics-bamqc/bf1b7d6c-dd09-48d4-86b7-ce4110e2bce0/", "status": "released", "overall_quality_status": "PASS", "display_title": "QualityMetricBamqc from 2023-04-24", "uuid": "bf1b7d6c-dd09-48d4-86b7-ce4110e2bce0", "quality_metric_summary": [{"title": "Total Reads", "value": "741892703", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "14.847", "tooltip": "Percent of total reads (=110.15m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "19.755", "tooltip": "Percent of total reads (=146.56m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "5.041", "tooltip": "Percent of total reads (=37.4m)", "numberType": "percent"}, {"title": "Walks", "value": "6.119", "tooltip": "Percent of total reads (=45.4m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.25", "tooltip": "Percent of total reads (=1.85m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "last_modified": {"date_modified": "2023-09-25T20:27:03.486248+00:00"}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 9108095697, "href": "/files-processed/4DNFIGU8Z277/@@download/4DNFIGU8Z277.pairs.gz", "@id": "/files-processed/4DNFIGU8Z277/", "status": "released", "file_format": {"display_title": "pairs", "status": "released", "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_type": "contact list-replicate", "md5sum": "022c2dc13335f06fd07bd81b2560a1b4", "accession": "4DNFIGU8Z277", "file_type_detailed": "contact list-replicate (pairs)", "@type": ["FileProcessed", "File", "Item"], "upload_key": "5e8f51a9-3553-418d-b81f-ee9bb38af24d/4DNFIGU8Z277.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/5e8f51a9-3553-418d-b81f-ee9bb38af24d/4DNFIGU8Z277.pairs.gz", "file_classification": "processed file", "display_title": "4DNFIGU8Z277.pairs.gz", "genome_assembly": "GRCh38", "uuid": "5e8f51a9-3553-418d-b81f-ee9bb38af24d", "contributing_labs": [{"@id": "/labs/wouter-de-laat-lab/", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "display_title": "Wouter de Laat, HUBRECHT", "name": "wouter-de-laat-lab", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}], "extra_files": [{"md5sum": "0557e386a4baf7ac578223392bacf72e", "file_size": 31382700, "href": "/files-processed/4DNFIGU8Z277/@@download/4DNFIGU8Z277.pairs.gz.px2", "file_format": {"file_format": "pairs_px2", "@type": ["FileFormat", "Item"], "display_title": "pairs_px2", "@id": "/file-formats/pairs_px2/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "@id": "/quality-metrics-pairsqc/c5dfb6e6-34de-419b-8f59-0ec9ef7f10bf/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIGU8Z277/pairsqc_report.html", "overall_quality_status": "PASS", "display_title": "QualityMetricPairsqc from 2023-04-24", "Total reads": 402380950, "uuid": "c5dfb6e6-34de-419b-8f59-0ec9ef7f10bf", "quality_metric_summary": [{"title": "Filtered Reads", "value": "402380950", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "41.202", "tooltip": "Percent of filtered reads (=165.79m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "23.979", "tooltip": "Percent of filtered reads (=96.49m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "34.82", "tooltip": "Percent of filtered reads (=140.11m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "last_modified": {"date_modified": "2023-06-21T18:40:22.916213+00:00"}, "track_and_facet_info": {"experimental_lab": "Wouter de Laat, HUBRECHT", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "DpnII", "dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "heart left ventricle", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "external_references": [], "digestion_enzyme": {"@id": "/enzymes/DpnII/", "status": "released", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "display_title": "DpnII", "@type": ["Enzyme", "Item"], "name": "DpnII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-07-19T12:44:19.126119+00:00"}, "experiment_type": {"assay_subclassification": "DNA-DNA Pairwise Interactions", "experiment_category": "Sequencing", "status": "released", "@id": "/experiment-types/in-situ-hi-c/", "title": "in situ Hi-C", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "assay_classification": "3C via Ligation", "@type": ["ExperimentType", "Item"], "display_title": "in situ Hi-C", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "assay_subclass_short": "Hi-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"field": "Enzyme", "combined": "Enzyme: DpnII", "value": "DpnII"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experimentset_type": "replicate", "completed_processes": ["compartments_v1.2", "HiC_Pipeline_0.2.7", "HiC_Pipeline_0.3.0", "insulation_scores_and_boundaries_v1"], "other_processed_files": [{"type": "preliminary", "files": [{"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e5e9d70e-a9ce-4717-9c5b-66069ef38992/4DNFIBZHWV2U.pairs.gz", "display_title": "4DNFIBZHWV2U.pairs.gz", "md5sum": "cae0ad158c8e6c6b477e710507b0a268", "accession": "4DNFIBZHWV2U", "href": "/files-processed/4DNFIBZHWV2U/@@download/4DNFIBZHWV2U.pairs.gz", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/pairs/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "genome_assembly": "GRCh38", "file_type_detailed": "contact list-combined (pairs)", "file_size": 14874080985, "file_type": "contact list-combined", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIBZHWV2U/", "uuid": "e5e9d70e-a9ce-4717-9c5b-66069ef38992", "status": "released", "lab": {"name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@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"]}, "contributing_labs": [{"@id": "/labs/wouter-de-laat-lab/", "status": "current", "display_title": "Wouter de Laat, HUBRECHT", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}], "track_and_facet_info": {"dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "experimental_lab": "Wouter de Laat, HUBRECHT", "replicate_info": "merged replicates", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "heart left ventricle", "lab_name": "4DN DCIC, HMS"}, "quality_metric": {"@id": "/quality-metrics-pairsqc/62aeed16-15ee-4b45-914f-28e1479b5497/", "uuid": "62aeed16-15ee-4b45-914f-28e1479b5497", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIBZHWV2U/pairsqc_report.html", "display_title": "QualityMetricPairsqc from 2024-07-11", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "754843809", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "41.122", "tooltip": "Percent of filtered reads (=310.41m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "26.714", "tooltip": "Percent of filtered reads (=201.65m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "32.164", "tooltip": "Percent of filtered reads (=242.79m)", "numberType": "percent"}]}, "last_modified": {"date_modified": "2024-08-07T21:33:53.336768+00:00"}}, {"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/7ef80bfb-0329-447d-b971-a972de0b8cd1/4DNFIFUBA8FE.hic", "display_title": "4DNFIFUBA8FE.hic", "md5sum": "d763b2c183116a492bdb97bbfcf151b2", "accession": "4DNFIFUBA8FE", "href": "/files-processed/4DNFIFUBA8FE/@@download/4DNFIFUBA8FE.hic", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "hic", "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "status": "released", "@id": "/file-formats/hic/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "genome_assembly": "GRCh38", "file_type_detailed": "contact matrix (hic)", "file_size": 6895378209, "file_type": "contact matrix", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIFUBA8FE/", "uuid": "7ef80bfb-0329-447d-b971-a972de0b8cd1", "status": "released", "lab": {"name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@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"]}, "contributing_labs": [{"@id": "/labs/wouter-de-laat-lab/", "status": "current", "display_title": "Wouter de Laat, HUBRECHT", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}], "track_and_facet_info": {"dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "experimental_lab": "Wouter de Laat, HUBRECHT", "replicate_info": "merged replicates", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "heart left ventricle", "lab_name": "4DN DCIC, HMS"}, "last_modified": {"date_modified": "2024-08-07T21:32:00.980343+00:00"}}, {"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/db72b22c-b183-478e-9aca-14823a5d0ddb/4DNFI1KY33QV.mcool", "display_title": "4DNFI1KY33QV.mcool", "md5sum": "13b54e706b25e9057379a96d2316c334", "accession": "4DNFI1KY33QV", "href": "/files-processed/4DNFI1KY33QV/@@download/4DNFI1KY33QV.mcool", "higlass_uid": "b8556f48-8dbb-48aa-93fc-bc1c923c6111", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "mcool", "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "status": "released", "@id": "/file-formats/mcool/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "genome_assembly": "GRCh38", "file_type_detailed": "contact matrix (mcool)", "file_size": 4652748916, "file_type": "contact matrix", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI1KY33QV/", "uuid": "db72b22c-b183-478e-9aca-14823a5d0ddb", "status": "released", "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@id": "/higlass-view-configs/87eec188-64c0-42c3-9d6e-4d8b3beb77df/", "status": "released", "uuid": "87eec188-64c0-42c3-9d6e-4d8b3beb77df", "display_title": "4DNFI1KY33QV - contact matrix for heart left ventricle in situ Hi-C DpnII", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "lab": {"name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@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"]}, "contributing_labs": [{"@id": "/labs/wouter-de-laat-lab/", "status": "current", "display_title": "Wouter de Laat, HUBRECHT", "name": "wouter-de-laat-lab", "uuid": "496e33a9-da2f-4593-ac39-88262b6e4f26", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.496e33a9-da2f-4593-ac39-88262b6e4f26"]}}], "track_and_facet_info": {"dataset": "in situ Hi-C on primary human cardiomyocytes", "condition": "left ventricle - donor 01137", "experimental_lab": "Wouter de Laat, HUBRECHT", "replicate_info": "merged replicates", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "heart left ventricle", "lab_name": "4DN DCIC, HMS", "track_title": "contact matrix for heart left ventricle in situ Hi-C DpnII"}, "quality_metric": {"@id": "/quality-metrics-mcool/ae00ad75-d018-4901-a3ac-d8cedbb56750/", "uuid": "ae00ad75-d018-4901-a3ac-d8cedbb56750", "@type": ["QualityMetricMcool", "QualityMetric", "Item"], "overall_quality_status": "PASS", "status": "released", "display_title": "QualityMetricMcool from 2024-07-11", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Failed Balancing", "value": "None", "tooltip": "Resolutions where balancing failed", "numberType": "string"}]}, "last_modified": {"date_modified": "2024-08-07T21:46:15.136727+00:00"}}], "title": "HiC Processing Pipeline - v0.3.0", "description": "These are files generated using the updated Hi-C processing pipeline. They should be largely similar to those available in the Processed Files tab, which were generated with the previous version of the standard pipeline.  One potential difference of note is that the version of cooler used to generate the mcool file has a bug fix to prevent a pixel duplication issue which is observed in some files generated by the previous version of the pipeline.  Another notable difference is that a filter is applied to remove reads with MAPQ scores below 30 prior to mcool file generation.", "higlass_view_config": {"description": "Supplementary Files (HiC Processing Pipeline - v0.3.0) for 4DNESUYU9VSU (in situ Hi-C on primary cardiomyocytes from the left ventricle - donor 01137): 4DNFI1KY33QV", "status": "released", "@id": "/higlass-view-configs/e1085df2-1754-4266-b099-f40d2abd2b4f/", "display_title": "4DNESUYU9VSU - HiC Processing Pipeline - v0.3.0", "uuid": "e1085df2-1754-4266-b099-f40d2abd2b4f", "@type": ["HiglassViewConfig", "UserContent", "Item"], "last_modified": {"date_modified": "2024-07-31T21:01:21.734012+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "@id": "/experiment-set-replicates/4DNESUYU9VSU/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "cbb92a16-2e57-4f26-adfc-5dd5996058fd", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESUYU9VSU", "external_references": [], "produced_in_pub": {"display_title": "Bianchi V et al. (2019) doi:10.1101/705715", "authors": ["Bianchi V", "Geeven G", "Tucker N", "Hilvering CRE", "Hall AW", "Roselli C", "Hill MC", "Martin JF", "Margulies KB", "Ellinor PT", "deLaat W"], "short_attribution": "Bianchi V et al. (2019)", "date_published": "2019-07-17", "uuid": "395b511a-5db1-4080-b5a7-b180769b7328", "ID": "doi:10.1101/705715", "@type": ["Publication", "Item"], "status": "current", "@id": "/publications/395b511a-5db1-4080-b5a7-b180769b7328/", "title": "Detailed Regulatory Interaction Map of the Human Heart Facilitates Gene Discovery for Cardiovascular Disease", "url": "http://biorxiv.org/lookup/doi/10.1101/705715", "abstract": "Most disease-associated variants identified by population based genetic studies are non-coding, which compromises finding causative genes and mechanisms. Presumably they interact through looping with nearby genes to modulate transcription. Hi-C provides the most complete and unbiased method for genome-wide identification of potential regulatory interactions, but finding chromatin loops in Hi-C data remains difficult and tissue specific data are limited. We have generated Hi-C data from primary cardiac tissue and developed a method, peakHiC, for sensitive and quantitative loop calling to uncover the human heart regulatory interactome. We identify complex CTCF-dependent and -independent contact networks, with loops between coding and non-coding gene promoters, shared enhancers and repressive sites. Across the genome, enhancer interaction strength correlates with gene transcriptional output and loop dynamics follows CTCF, cohesin and H3K27Ac occupancy levels. Finally, we demonstrate that intersection of the human heart regulatory interactome with cardiovascular disease variants facilitates prioritizing disease-causative genes.", "journal": "bioRxiv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"@id": "/publications/395b511a-5db1-4080-b5a7-b180769b7328/", "display_title": "Bianchi V et al. (2019) doi:10.1101/705715", "ID": "doi:10.1101/705715", "@type": ["Publication", "Item"], "abstract": "Most disease-associated variants identified by population based genetic studies are non-coding, which compromises finding causative genes and mechanisms. Presumably they interact through looping with nearby genes to modulate transcription. Hi-C provides the most complete and unbiased method for genome-wide identification of potential regulatory interactions, but finding chromatin loops in Hi-C data remains difficult and tissue specific data are limited. We have generated Hi-C data from primary cardiac tissue and developed a method, peakHiC, for sensitive and quantitative loop calling to uncover the human heart regulatory interactome. We identify complex CTCF-dependent and -independent contact networks, with loops between coding and non-coding gene promoters, shared enhancers and repressive sites. Across the genome, enhancer interaction strength correlates with gene transcriptional output and loop dynamics follows CTCF, cohesin and H3K27Ac occupancy levels. Finally, we demonstrate that intersection of the human heart regulatory interactome with cardiovascular disease variants facilitates prioritizing disease-causative genes.", "journal": "bioRxiv", "authors": ["Bianchi V", "Geeven G", "Tucker N", "Hilvering CRE", "Hall AW", "Roselli C", "Hill MC", "Martin JF", "Margulies KB", "Ellinor PT", "deLaat W"], "title": "Detailed Regulatory Interaction Map of the Human Heart Facilitates Gene Discovery for Cardiovascular Disease", "status": "current", "date_published": "2019-07-17", "uuid": "395b511a-5db1-4080-b5a7-b180769b7328", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 2, "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}