{"lab": {"uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "title": "David Zarkower, UMN", "display_title": "David Zarkower, UMN", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/david-zarkower-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}, "award": {"name": "external-award", "@id": "/awards/external-award/", "center": "External", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "center_title": "External", "status": "current", "project": "External", "display_title": "EXTERNAL AWARD", "description": "Funding source is from outside 4DN.", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["zarkower-lab:hi-c-on-mouse-sertoli-cells"], "accession": "4DNES265ETYQ", "condition": "male Sertoli cells", "description": "in situ Hi-C on primary mouse Sertoli cells from 7 day old males", "study_group": "Single Time Point and Condition", "date_created": "2021-06-02T17:26:08.883588+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "Hi-C on mouse somatic gonadal cells", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-07-17T06:46:47.917001+00:00"}, "public_release": "2021-06-22", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"accession": "4DNEXMNJ6A2Y", "status": "released", "@type": ["ExperimentHiC", "Experiment", "Item"], "display_title": "in situ Hi-C on Sertoli cell with Arima - A1, A2 - 4DNEXMNJ6A2Y", "uuid": "4cda9536-12ca-4669-98e0-2ec9510b9b94", "@id": "/experiments-hi-c/4DNEXMNJ6A2Y/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"accession": "4DNEX99DGLEF", "status": "released", "@type": ["ExperimentHiC", "Experiment", "Item"], "display_title": "in situ Hi-C on Sertoli cell with Arima - A1, A2 - 4DNEX99DGLEF", "uuid": "d8a78b5f-9425-4557-ba5b-b88de8f748da", "@id": "/experiments-hi-c/4DNEX99DGLEF/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"title": "4DNES265ETYQ - Processed files", "description": "4DNES265ETYQ (in situ Hi-C on primary mouse Sertoli cells from 7 day old males): 4DNFIB7RFFBB, 4DNFIZDHT51M, 4DNFIKPHXAGA, 4DNFIWX6RNFM", "@id": "/higlass-view-configs/f861aa08-67d7-447d-88d1-39db68ec084e/", "name": "f861aa08-67d7-447d-88d1-39db68ec084e", "contributing_labs": [], "award": {"uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@type": ["Award", "Item"], "@id": "/awards/external-award/", "status": "current", "display_title": "EXTERNAL AWARD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "David Zarkower, UMN", "@type": ["Lab", "Item"], "@id": "/labs/david-zarkower-lab/", "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}, "status": "released", "filetype": "HiglassViewConfig", "uuid": "f861aa08-67d7-447d-88d1-39db68ec084e", "display_title": "4DNES265ETYQ - Processed files", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}, "location": "tab:processed-files", "description": "auto_generated_higlass_view_config"}], "static_headers": [{"lab": {"@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "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": {"uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "status": "current", "@type": ["Award", "Item"], "@id": "/awards/1U01CA200059-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Assay Description", "status": "released", "aliases": ["4dn-dcic-lab:experiment_infobox_hic"], "options": {"filetype": "html", "collapsible": false, "default_open": false, "convert_ext_links": true}, "date_created": "2018-09-07T18:19:43.777198+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-11-09T14:48:01.220007+00:00"}, "schema_version": "2", "@id": "/static-sections/298554ad-20e2-4449-a752-ac190123dab7/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "298554ad-20e2-4449-a752-ac190123dab7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.56c9c683-bb11-471b-b590-c656f7dc03c1"]}, "display_title": "Assay Description", "external_references": [], "content": "<b>In Situ Hi-C</b>\n\n<p>\n   In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed <i>in situ</i> inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n</p>\n<p>\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n</p>\n<p>\nSee <a href=\"https://www.sciencedirect.com/science/article/pii/S0092867414014974?via%3Dihub\">Rao et al., 2014</a> for more details.\n</p>\n\n<div>\n<img style=\"width: 600px;max-width:100%;\" src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/IsHC_fig1.png\"/>\n  <br/><br/>\n  <em>Image source: Rao et al., 2014, Figure 1A</em>\n</div>", "filetype": "html", "content_as_html": "<div class=\"html-container\"><b>In Situ Hi-C</b>\n<p>\n   In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed <i>in situ</i> inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n</p>\n<p>\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n</p>\n<p>\nSee <a href=\"https://www.sciencedirect.com/science/article/pii/S0092867414014974?via%3Dihub\" rel=\"noopener noreferrer\" target=\"_blank\">Rao et al., 2014</a> for more details.\n</p>\n<div>\n<img src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/IsHC_fig1.png\" style=\"width: 600px;max-width:100%;\"/>\n<br/><br/>\n<em>Image source: Rao et al., 2014, Figure 1A</em>\n</div></div>"}], "processed_files": [{"file_size": 10875972036, "uuid": "126a894a-bb5f-4213-9332-fa3883db0d23", "href": "/files-processed/4DNFILTSAY9I/@@download/4DNFILTSAY9I.pairs.gz", "@id": "/files-processed/4DNFILTSAY9I/", "file_type": "contact list-combined", "upload_key": "126a894a-bb5f-4213-9332-fa3883db0d23/4DNFILTSAY9I.pairs.gz", "file_type_detailed": "contact list-combined (pairs)", "genome_assembly": "GRCm38", "file_format": {"display_title": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/126a894a-bb5f-4213-9332-fa3883db0d23/4DNFILTSAY9I.pairs.gz", "display_title": "4DNFILTSAY9I.pairs.gz", "file_classification": "processed file", "md5sum": "e8270d7765ef511e2eb3f45178ed7776", "accession": "4DNFILTSAY9I", "@type": ["FileProcessed", "File", "Item"], "status": "released", "contributing_labs": [{"@id": "/labs/david-zarkower-lab/", "status": "current", "display_title": "David Zarkower, UMN", "@type": ["Lab", "Item"], "name": "david-zarkower-lab", "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}], "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "extra_files": [{"file_size": 9728993, "md5sum": "aa4a7b7ee00f10620d742b7936d05101", "href": "/files-processed/4DNFILTSAY9I/@@download/4DNFILTSAY9I.pairs.gz.px2", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "display_title": "pairs_px2", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs_px2/", "file_format": "pairs_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFILTSAY9I/pairsqc_report.html", "status": "released", "Total reads": 589079877, "display_title": "QualityMetricPairsqc from 2021-06-11", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "uuid": "498e657f-fdfb-4fdb-a860-f34e0b9e2039", "@id": "/quality-metrics-pairsqc/498e657f-fdfb-4fdb-a860-f34e0b9e2039/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "589079877", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "52.773", "tooltip": "Percent of filtered reads (=310.88m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "30.533", "tooltip": "Percent of filtered reads (=179.86m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "16.694", "tooltip": "Percent of filtered reads (=98.34m)", "numberType": "percent"}]}, "external_references": [], "last_modified": {"date_modified": "2021-08-10T20:30:36.428691+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "experimental_lab": "David Zarkower, UMN", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "Arima - A1, A2", "biosource_name": "Sertoli cell", "lab_name": "4DN DCIC, HMS"}}, {"file_size": 4145484985, "uuid": "8597cdae-8319-42d9-9175-3f77aaee34e1", "href": "/files-processed/4DNFIQWS3632/@@download/4DNFIQWS3632.hic", "@id": "/files-processed/4DNFIQWS3632/", "file_type": "contact matrix", "upload_key": "8597cdae-8319-42d9-9175-3f77aaee34e1/4DNFIQWS3632.hic", "file_type_detailed": "contact matrix (hic)", "genome_assembly": "GRCm38", "file_format": {"display_title": "hic", "@id": "/file-formats/hic/", "@type": ["FileFormat", "Item"], "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8597cdae-8319-42d9-9175-3f77aaee34e1/4DNFIQWS3632.hic", "display_title": "4DNFIQWS3632.hic", "file_classification": "processed file", "md5sum": "c4be7ec43ef31e2e6afb20fa7aaeb569", "accession": "4DNFIQWS3632", "@type": ["FileProcessed", "File", "Item"], "status": "released", "contributing_labs": [{"@id": "/labs/david-zarkower-lab/", "status": "current", "display_title": "David Zarkower, UMN", "@type": ["Lab", "Item"], "name": "david-zarkower-lab", "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}], "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "external_references": [], "last_modified": {"date_modified": "2021-08-10T20:29:34.726724+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "experimental_lab": "David Zarkower, UMN", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "Arima - A1, A2", "biosource_name": "Sertoli cell", "lab_name": "4DN DCIC, HMS"}}, {"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."], "file_size": 2838340170, "uuid": "59d58dfb-ad17-407b-bf87-f70ee8af6eeb", "href": "/files-processed/4DNFIB7RFFBB/@@download/4DNFIB7RFFBB.mcool", "@id": "/files-processed/4DNFIB7RFFBB/", "file_type": "contact matrix", "upload_key": "59d58dfb-ad17-407b-bf87-f70ee8af6eeb/4DNFIB7RFFBB.mcool", "file_type_detailed": "contact matrix (mcool)", "genome_assembly": "GRCm38", "higlass_uid": "8bf144b4-9fe7-475d-ab5f-7f7163ceda5c", "file_format": {"display_title": "mcool", "@id": "/file-formats/mcool/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/59d58dfb-ad17-407b-bf87-f70ee8af6eeb/4DNFIB7RFFBB.mcool", "display_title": "4DNFIB7RFFBB.mcool", "file_classification": "processed file", "md5sum": "c44f0b2de97edf4dcb86917753e52c1c", "accession": "4DNFIB7RFFBB", "@type": ["FileProcessed", "File", "Item"], "status": "released", "contributing_labs": [{"@id": "/labs/david-zarkower-lab/", "status": "current", "display_title": "David Zarkower, UMN", "@type": ["Lab", "Item"], "name": "david-zarkower-lab", "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}], "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "quality_metric": {"status": "released", "display_title": "QualityMetricMcool from 2021-06-11", "@type": ["QualityMetricMcool", "QualityMetric", "Item"], "overall_quality_status": "PASS", "uuid": "d5768e04-33d2-4b70-9cad-8afee05594ee", "@id": "/quality-metrics-mcool/d5768e04-33d2-4b70-9cad-8afee05594ee/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Failed Balancing", "value": "None", "tooltip": "Resolutions where balancing failed", "numberType": "string"}]}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "8fa844de-7f84-45fb-b691-938dab843b5a", "status": "released", "display_title": "4DNFIB7RFFBB - contact matrix for Sertoli cell in situ Hi-C Arima - A1, A2", "@id": "/higlass-view-configs/8fa844de-7f84-45fb-b691-938dab843b5a/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "external_references": [], "last_modified": {"date_modified": "2023-08-25T17:48:54.903795+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "experimental_lab": "David Zarkower, UMN", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "Arima - A1, A2", "biosource_name": "Sertoli cell", "lab_name": "4DN DCIC, HMS", "track_title": "contact matrix for Sertoli cell in situ Hi-C Arima - A1, A2"}}, {"file_size": 7627972, "uuid": "d32fa5cb-d07c-4c49-a979-847f380a9f0b", "href": "/files-processed/4DNFIZDHT51M/@@download/4DNFIZDHT51M.bw", "@id": "/files-processed/4DNFIZDHT51M/", "file_type": "insulation score-diamond", "upload_key": "d32fa5cb-d07c-4c49-a979-847f380a9f0b/4DNFIZDHT51M.bw", "file_type_detailed": "insulation score-diamond (bw)", "genome_assembly": "GRCm38", "higlass_uid": "b42ee0d1-a6a7-49c5-b981-e5a96fcf2b69", "file_format": {"display_title": "bw", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/d32fa5cb-d07c-4c49-a979-847f380a9f0b/4DNFIZDHT51M.bw", "display_title": "4DNFIZDHT51M.bw", "file_classification": "processed file", "md5sum": "4d44930af52d31d2c7795074ddce8b5b", "accession": "4DNFIZDHT51M", "@type": ["FileProcessed", "File", "Item"], "status": "released", "contributing_labs": [{"@id": "/labs/david-zarkower-lab/", "status": "current", "display_title": "David Zarkower, UMN", "@type": ["Lab", "Item"], "name": "david-zarkower-lab", "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}], "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/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": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "ba63a3fa-4ce6-48b4-98fe-0d74aa6ed767", "status": "released", "display_title": "4DNFIZDHT51M - insulation score-diamond for Sertoli cell in situ Hi-C Arima - A1, A2", "@id": "/higlass-view-configs/ba63a3fa-4ce6-48b4-98fe-0d74aa6ed767/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "external_references": [], "last_modified": {"date_modified": "2021-08-10T20:46:00.694834+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "experimental_lab": "David Zarkower, UMN", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "Arima - A1, A2", "biosource_name": "Sertoli cell", "lab_name": "4DN DCIC, HMS", "track_title": "insulation score-diamond for Sertoli cell in situ Hi-C Arima - A1, A2"}}, {"file_size": 193061, "uuid": "c98952c5-9872-488e-9f3f-7a699bf0891e", "href": "/files-processed/4DNFIKPHXAGA/@@download/4DNFIKPHXAGA.bw", "@id": "/files-processed/4DNFIKPHXAGA/", "file_type": "compartments", "upload_key": "c98952c5-9872-488e-9f3f-7a699bf0891e/4DNFIKPHXAGA.bw", "file_type_detailed": "compartments (bw)", "genome_assembly": "GRCm38", "higlass_uid": "7b9f5c01-a32d-4303-8a2a-72e576c720f4", "file_format": {"display_title": "bw", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c98952c5-9872-488e-9f3f-7a699bf0891e/4DNFIKPHXAGA.bw", "display_title": "4DNFIKPHXAGA.bw", "file_classification": "processed file", "md5sum": "a3d44b4ce5e15d0badaa90172560ae52", "accession": "4DNFIKPHXAGA", "@type": ["FileProcessed", "File", "Item"], "status": "released", "contributing_labs": [{"@id": "/labs/david-zarkower-lab/", "status": "current", "display_title": "David Zarkower, UMN", "@type": ["Lab", "Item"], "name": "david-zarkower-lab", "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}], "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/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": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "64541543-ad28-4002-afaf-0c874666b15f", "status": "released", "display_title": "4DNFIKPHXAGA - compartments for Sertoli cell in situ Hi-C Arima - A1, A2", "@id": "/higlass-view-configs/64541543-ad28-4002-afaf-0c874666b15f/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "external_references": [], "last_modified": {"date_modified": "2021-08-10T20:46:01.948995+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "experimental_lab": "David Zarkower, UMN", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "Arima - A1, A2", "biosource_name": "Sertoli cell", "lab_name": "4DN DCIC, HMS", "track_title": "compartments for Sertoli cell in situ Hi-C Arima - A1, A2"}}, {"file_size": 148045, "uuid": "62b64107-a6f9-4a01-a1b0-dd5387d0042d", "href": "/files-processed/4DNFIWX6RNFM/@@download/4DNFIWX6RNFM.bed.gz", "@id": "/files-processed/4DNFIWX6RNFM/", "file_type": "boundaries", "upload_key": "62b64107-a6f9-4a01-a1b0-dd5387d0042d/4DNFIWX6RNFM.bed.gz", "file_type_detailed": "boundaries (bed)", "genome_assembly": "GRCm38", "higlass_uid": "E2T6NWOGTv2DLEColoeUOA", "file_format": {"display_title": "bed", "@id": "/file-formats/bed/", "@type": ["FileFormat", "Item"], "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/62b64107-a6f9-4a01-a1b0-dd5387d0042d/4DNFIWX6RNFM.bed.gz", "display_title": "4DNFIWX6RNFM.bed.gz", "file_classification": "processed file", "md5sum": "12e8a02a441ca55f1609761fa0ce9061", "accession": "4DNFIWX6RNFM", "@type": ["FileProcessed", "File", "Item"], "status": "released", "contributing_labs": [{"@id": "/labs/david-zarkower-lab/", "status": "current", "display_title": "David Zarkower, UMN", "@type": ["Lab", "Item"], "name": "david-zarkower-lab", "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}], "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "extra_files": [{"file_size": 1721344, "md5sum": "27dbfb4ff4ef3ec9c349a18d0ae85bef", "use_for": "visualization", "href": "/files-processed/4DNFIWX6RNFM/@@download/4DNFIWX6RNFM.beddb", "file_format": {"status": "released", "uuid": "76dc8c06-67d8-487b-8fc8-d841752a0b60", "display_title": "beddb", "@type": ["FileFormat", "Item"], "@id": "/file-formats/beddb/", "file_format": "beddb", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "b9010440-7c90-478e-ba74-669e6b359861", "status": "released", "display_title": "4DNFIWX6RNFM - boundaries for Sertoli cell in situ Hi-C Arima - A1, A2", "@id": "/higlass-view-configs/b9010440-7c90-478e-ba74-669e6b359861/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "external_references": [], "last_modified": {"date_modified": "2021-08-10T20:45:59.512919+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "experimental_lab": "David Zarkower, UMN", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "Arima - A1, A2", "biosource_name": "Sertoli cell", "lab_name": "4DN DCIC, HMS", "track_title": "boundaries for Sertoli cell in situ Hi-C Arima - A1, A2"}}], "project_release": "2021-06-22", "experiments_in_set": [{"@type": ["ExperimentHiC", "Experiment", "Item"], "@id": "/experiments-hi-c/4DNEXMNJ6A2Y/", "status": "released", "dbxrefs": ["GEO:GSM5184267", "SRA:SRX10404230"], "crosslinking_method": "2% Formaldehyde", "files": [{"upload_key": "e92fe746-6417-4f27-86ca-80ef396913c6/4DNFI3QKVF8U.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "1", "display_title": "4DNFI3QKVF8U.fastq.gz", "@id": "/files-fastq/4DNFI3QKVF8U/", "file_size": 5904123033, "accession": "4DNFI3QKVF8U", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/e92fe746-6417-4f27-86ca-80ef396913c6/4DNFI3QKVF8U.fastq.gz", "href": "/files-fastq/4DNFI3QKVF8U/@@download/4DNFI3QKVF8U.fastq.gz", "@type": ["FileFastq", "File", "Item"], "uuid": "e92fe746-6417-4f27-86ca-80ef396913c6", "file_classification": "raw file", "md5sum": "9fea5cb3b0ecd781d38c1af0566fc319", "status": "released", "file_type": "reads", "dbxrefs": ["SRA:SRR14027544"], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "fc71f67d-b83a-4f87-bd6d-445e5bafb1ed", "display_title": "4DNFIJZTIYRI.fastq.gz", "accession": "4DNFIJZTIYRI", "status": "released", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFIJZTIYRI/", "file_type": "reads", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"Total Sequences": 62135045, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI3QKVF8U/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/5a6956d7-95d2-4cac-9a6b-5c1947c83739/", "uuid": "5a6956d7-95d2-4cac-9a6b-5c1947c83739", "Sequence length": "150", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2021-06-02", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR14027544", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR14027544"}], "lab": {"name": "david-zarkower-lab", "@type": ["Lab", "Item"], "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "@id": "/labs/david-zarkower-lab/", "display_title": "David Zarkower, UMN", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}, "track_and_facet_info": {"experimental_lab": "David Zarkower, UMN", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "Sertoli cell", "lab_name": "David Zarkower, UMN"}}, {"upload_key": "fc71f67d-b83a-4f87-bd6d-445e5bafb1ed/4DNFIJZTIYRI.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "2", "display_title": "4DNFIJZTIYRI.fastq.gz", "@id": "/files-fastq/4DNFIJZTIYRI/", "file_size": 6452110885, "accession": "4DNFIJZTIYRI", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/fc71f67d-b83a-4f87-bd6d-445e5bafb1ed/4DNFIJZTIYRI.fastq.gz", "href": "/files-fastq/4DNFIJZTIYRI/@@download/4DNFIJZTIYRI.fastq.gz", "@type": ["FileFastq", "File", "Item"], "uuid": "fc71f67d-b83a-4f87-bd6d-445e5bafb1ed", "file_classification": "raw file", "md5sum": "d5c79385f7a1d3efb5a6e17d2666cbd2", "status": "released", "file_type": "reads", "dbxrefs": ["SRA:SRR14027544"], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "e92fe746-6417-4f27-86ca-80ef396913c6", "display_title": "4DNFI3QKVF8U.fastq.gz", "accession": "4DNFI3QKVF8U", "status": "released", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFI3QKVF8U/", "file_type": "reads", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"Total Sequences": 62135045, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJZTIYRI/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/a5427d0a-e171-458b-8826-16bd7aa181aa/", "uuid": "a5427d0a-e171-458b-8826-16bd7aa181aa", "Sequence length": "150", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2021-06-02", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR14027544", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR14027544"}], "lab": {"name": "david-zarkower-lab", "@type": ["Lab", "Item"], "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "@id": "/labs/david-zarkower-lab/", "display_title": "David Zarkower, UMN", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}, "track_and_facet_info": {"experimental_lab": "David Zarkower, UMN", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "Sertoli cell", "lab_name": "David Zarkower, UMN"}}, {"upload_key": "9b017903-d71e-4cdc-821c-ebbb2f2c0144/4DNFI73Y49KO.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "1", "display_title": "4DNFI73Y49KO.fastq.gz", "@id": "/files-fastq/4DNFI73Y49KO/", "file_size": 35205729542, "accession": "4DNFI73Y49KO", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/9b017903-d71e-4cdc-821c-ebbb2f2c0144/4DNFI73Y49KO.fastq.gz", "href": "/files-fastq/4DNFI73Y49KO/@@download/4DNFI73Y49KO.fastq.gz", "@type": ["FileFastq", "File", "Item"], "uuid": "9b017903-d71e-4cdc-821c-ebbb2f2c0144", "file_classification": "raw file", "md5sum": "65d2e61b8deb13b4b83bd6a8519d6b33", "status": "released", "file_type": "reads", "dbxrefs": ["SRA:SRR14027545"], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "632fd410-9104-4385-aeb2-967599838a9e", "display_title": "4DNFIJZULQLL.fastq.gz", "accession": "4DNFIJZULQLL", "status": "released", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFIJZULQLL/", "file_type": "reads", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"Total Sequences": 459269359, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI73Y49KO/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/b7c27c79-173e-4606-a23f-28de943e7a43/", "uuid": "b7c27c79-173e-4606-a23f-28de943e7a43", "Sequence length": "150", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2021-06-02", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR14027545", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR14027545"}], "lab": {"name": "david-zarkower-lab", "@type": ["Lab", "Item"], "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "@id": "/labs/david-zarkower-lab/", "display_title": "David Zarkower, UMN", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}, "track_and_facet_info": {"experimental_lab": "David Zarkower, UMN", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "Sertoli cell", "lab_name": "David Zarkower, UMN"}}, {"upload_key": "632fd410-9104-4385-aeb2-967599838a9e/4DNFIJZULQLL.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "2", "display_title": "4DNFIJZULQLL.fastq.gz", "@id": "/files-fastq/4DNFIJZULQLL/", "file_size": 35883167338, "accession": "4DNFIJZULQLL", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/632fd410-9104-4385-aeb2-967599838a9e/4DNFIJZULQLL.fastq.gz", "href": "/files-fastq/4DNFIJZULQLL/@@download/4DNFIJZULQLL.fastq.gz", "@type": ["FileFastq", "File", "Item"], "uuid": "632fd410-9104-4385-aeb2-967599838a9e", "file_classification": "raw file", "md5sum": "3e997986221163a62a904d9c7dcb58ab", "status": "released", "file_type": "reads", "dbxrefs": ["SRA:SRR14027545"], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "9b017903-d71e-4cdc-821c-ebbb2f2c0144", "display_title": "4DNFI73Y49KO.fastq.gz", "accession": "4DNFI73Y49KO", "status": "released", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFI73Y49KO/", "file_type": "reads", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"Total Sequences": 459269359, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJZULQLL/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/afab40c7-b000-404d-bf15-73bb521e0692/", "uuid": "afab40c7-b000-404d-bf15-73bb521e0692", "Sequence length": "150", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2021-06-02", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR14027545", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR14027545"}], "lab": {"name": "david-zarkower-lab", "@type": ["Lab", "Item"], "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "@id": "/labs/david-zarkower-lab/", "display_title": "David Zarkower, UMN", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}, "track_and_facet_info": {"experimental_lab": "David Zarkower, UMN", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "Sertoli cell", "lab_name": "David Zarkower, UMN"}}], "accession": "4DNEXMNJ6A2Y", "display_title": "in situ Hi-C on Sertoli cell with Arima - A1, A2 - 4DNEXMNJ6A2Y", "uuid": "4cda9536-12ca-4669-98e0-2ec9510b9b94", "biosample": {"status": "released", "modifications_summary": "None", "biosample_category": ["Primary Cells"], "biosample_type": "primary cells", "@id": "/biosamples/4DNBSLA8NRR5/", "treatments_summary": "None", "biosource_summary": "Sertoli cell", "accession": "4DNBSLA8NRR5", "@type": ["Biosample", "Item"], "display_title": "4DNBSLA8NRR5", "uuid": "ee3a7a56-a8f9-497f-892b-9cdfd629e541", "biosource": [{"uuid": "2c69ce50-c2a2-4000-ba32-3186383e9807", "display_title": "Sertoli cell - 4DNSR73BT2A2", "@id": "/biosources/4DNSR73BT2A2/", "accession": "4DNSR73BT2A2", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "status": "released", "biosource_type": "primary cell", "tissue": {"uuid": "c108f0e6-61a1-42c0-876f-19d3a7231112", "@id": "/ontology-terms/CL:0000216/", "preferred_name": "Sertoli cell", "@type": ["OntologyTerm", "Item"], "term_name": "Sertoli cell", "term_id": "CL:0000216", "status": "released", "display_title": "Sertoli cell", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000990/", "display_title": "reproductive system", "status": "released", "uuid": "111127bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000926/", "display_title": "mesoderm", "status": "released", "uuid": "111120bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000991/", "display_title": "gonad", "status": "released", "uuid": "111164bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"display_title": "M. musculus", "name": "mouse", "@id": "/organisms/10090/", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "scientific_name": "Mus musculus", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"@type": ["OntologyTerm", "Item"], "display_title": "Sertoli cell", "term_id": "CL:0000216", "status": "released", "uuid": "c108f0e6-61a1-42c0-876f-19d3a7231112", "term_name": "Sertoli cell", "@id": "/ontology-terms/CL:0000216/", "preferred_name": "Sertoli cell", "slim_terms": [{"status": "released", "@id": "/ontology-terms/UBERON:0000990/", "display_title": "reproductive system", "uuid": "111127bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/ontology-terms/UBERON:0000926/", "display_title": "mesoderm", "uuid": "111120bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "current", "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/ontology-terms/UBERON:0000991/", "display_title": "gonad", "uuid": "111164bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"organ_system": ["reproductive system", "mesoderm", "gonad"], "tissue_source": "Sertoli cell"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"href": "/files-processed/4DNFI17EU7ZH/@@download/4DNFI17EU7ZH.bam", "file_type_detailed": "alignments (bam)", "uuid": "ee106e80-f81f-4248-88f8-a21e3d5fc843", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ee106e80-f81f-4248-88f8-a21e3d5fc843/4DNFI17EU7ZH.bam", "@id": "/files-processed/4DNFI17EU7ZH/", "status": "released", "display_title": "4DNFI17EU7ZH.bam", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFI17EU7ZH", "file_type": "alignments", "file_classification": "processed file", "upload_key": "ee106e80-f81f-4248-88f8-a21e3d5fc843/4DNFI17EU7ZH.bam", "file_size": 125240221970, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "540f770877d2ccfc5716a9a347020ffb", "quality_metric": {"uuid": "14380843-5118-4716-a63c-91d0441e22dc", "overall_quality_status": "PASS", "status": "released", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "@id": "/quality-metrics-bamqc/14380843-5118-4716-a63c-91d0441e22dc/", "display_title": "QualityMetricBamqc from 2021-06-25", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Reads", "value": "521404404", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "9.074", "tooltip": "Percent of total reads (=47.31m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "8.951", "tooltip": "Percent of total reads (=46.67m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "11.34", "tooltip": "Percent of total reads (=59.13m)", "numberType": "percent"}, {"title": "Walks", "value": "14.668", "tooltip": "Percent of total reads (=76.48m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.061", "tooltip": "Percent of total reads (=0.32m)", "numberType": "percent"}]}, "lab": {"@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "display_title": "4DN DCIC, HMS", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/david-zarkower-lab/", "name": "david-zarkower-lab", "display_title": "David Zarkower, UMN", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}], "external_references": [], "track_and_facet_info": {"experimental_lab": "David Zarkower, UMN", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "Sertoli cell", "lab_name": "4DN DCIC, HMS"}, "last_modified": {"date_modified": "2021-08-10T20:53:37.233727+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"href": "/files-processed/4DNFIAHA9Q1B/@@download/4DNFIAHA9Q1B.pairs.gz", "file_type_detailed": "contact list-replicate (pairs)", "uuid": "d783f402-b8c8-4c1c-be68-d1d6f05f29e5", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/d783f402-b8c8-4c1c-be68-d1d6f05f29e5/4DNFIAHA9Q1B.pairs.gz", "@id": "/files-processed/4DNFIAHA9Q1B/", "status": "released", "display_title": "4DNFIAHA9Q1B.pairs.gz", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIAHA9Q1B", "file_type": "contact list-replicate", "file_classification": "processed file", "upload_key": "d783f402-b8c8-4c1c-be68-d1d6f05f29e5/4DNFIAHA9Q1B.pairs.gz", "file_size": 5870068974, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "59418577b5f0107f75e0b7e865cba28c", "quality_metric": {"uuid": "f767c5d5-4c13-47b6-9b77-93c78abe35d6", "overall_quality_status": "PASS", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIAHA9Q1B/pairsqc_report.html", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Total reads": 291818223, "@id": "/quality-metrics-pairsqc/f767c5d5-4c13-47b6-9b77-93c78abe35d6/", "display_title": "QualityMetricPairsqc from 2021-06-10", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "291818223", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "53.778", "tooltip": "Percent of filtered reads (=156.93m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "29.915", "tooltip": "Percent of filtered reads (=87.3m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "16.307", "tooltip": "Percent of filtered reads (=47.59m)", "numberType": "percent"}]}, "lab": {"@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "display_title": "4DN DCIC, HMS", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "extra_files": [{"href": "/files-processed/4DNFIAHA9Q1B/@@download/4DNFIAHA9Q1B.pairs.gz.px2", "file_size": 19830150, "md5sum": "a3ea7eb201c8ee5400bea0504f5b2ad6", "file_format": {"file_format": "pairs_px2", "display_title": "pairs_px2", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "@id": "/file-formats/pairs_px2/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "contributing_labs": [{"uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/david-zarkower-lab/", "name": "david-zarkower-lab", "display_title": "David Zarkower, UMN", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}], "external_references": [], "track_and_facet_info": {"experimental_lab": "David Zarkower, UMN", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "Sertoli cell", "lab_name": "4DN DCIC, HMS"}, "last_modified": {"date_modified": "2021-08-10T20:47:07.778881+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "other_processed_files": [{"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.", "type": "preliminary", "title": "HiC Processing Pipeline - v0.3.0", "files": [{"@type": ["FileProcessed", "File", "Item"], "status": "released", "md5sum": "231a3309d178167278070ffaa7dc02de", "uuid": "1070b77b-6263-40a6-b982-29d382d207cf", "@id": "/files-processed/4DNFI4NGCGCK/", "file_type": "alignments", "file_type_detailed": "alignments (bam)", "accession": "4DNFI4NGCGCK", "href": "/files-processed/4DNFI4NGCGCK/@@download/4DNFI4NGCGCK.bam", "genome_assembly": "GRCm38", "display_title": "4DNFI4NGCGCK.bam", "file_size": 121167337643, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/1070b77b-6263-40a6-b982-29d382d207cf/4DNFI4NGCGCK.bam", "lab": {"status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "status": "released", "file_format": "bam", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"status": "current", "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "name": "david-zarkower-lab", "display_title": "David Zarkower, UMN", "@id": "/labs/david-zarkower-lab/", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}], "track_and_facet_info": {"experimental_lab": "David Zarkower, UMN", "experiment_type": "in situ Hi-C", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "Sertoli cell", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2024-08-08T00:10:09.735029+00:00"}}, {"@type": ["FileProcessed", "File", "Item"], "status": "released", "md5sum": "a67431d5f8898f80eecebc8b418ca218", "uuid": "ac05eb15-1caf-4899-8e83-53c3b3389944", "@id": "/files-processed/4DNFISZOBAR5/", "file_type": "contact list-replicate", "file_type_detailed": "contact list-replicate (pairs)", "accession": "4DNFISZOBAR5", "href": "/files-processed/4DNFISZOBAR5/@@download/4DNFISZOBAR5.pairs.gz", "genome_assembly": "GRCm38", "display_title": "4DNFISZOBAR5.pairs.gz", "file_size": 6194086897, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ac05eb15-1caf-4899-8e83-53c3b3389944/4DNFISZOBAR5.pairs.gz", "lab": {"status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"status": "current", "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "name": "david-zarkower-lab", "display_title": "David Zarkower, UMN", "@id": "/labs/david-zarkower-lab/", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}], "quality_metric": {"overall_quality_status": "PASS", "display_title": "QualityMetricPairsqc from 2024-07-04", "uuid": "28a5afd0-4726-43e5-8f4a-5cbcebeb6666", "status": "released", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "@id": "/quality-metrics-pairsqc/28a5afd0-4726-43e5-8f4a-5cbcebeb6666/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFISZOBAR5/pairsqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "329579457", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "53.608", "tooltip": "Percent of filtered reads (=176.68m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "29.491", "tooltip": "Percent of filtered reads (=97.2m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "16.901", "tooltip": "Percent of filtered reads (=55.7m)", "numberType": "percent"}]}, "track_and_facet_info": {"experimental_lab": "David Zarkower, UMN", "experiment_type": "in situ Hi-C", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "Sertoli cell", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2024-08-08T00:01:46.914520+00:00"}}]}], "digestion_enzyme": {"uuid": "1b967af3-f275-4480-93d7-c6ce62a908c6", "display_title": "Arima - A1, A2", "@type": ["Enzyme", "Item"], "name": "Arima - A1, A2", "@id": "/enzymes/Arima%20-%20A1,%20A2/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "@type": ["ExperimentType", "Item"], "assay_subclass_short": "Hi-C", "@id": "/experiment-types/in-situ-hi-c/", "assay_subclassification": "DNA-DNA Pairwise Interactions", "display_title": "in situ Hi-C", "title": "in situ Hi-C", "status": "released", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "experiment_category": "Sequencing", "assay_classification": "3C via Ligation", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"value": "Arima - A1, A2", "combined": "Enzyme: Arima - A1, A2", "field": "Enzyme"}, "last_modified": {"date_modified": "2024-07-16T15:02:04.515183+00:00"}, "external_references": [{"ref": "GEO:GSM5184267", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5184267"}, {"ref": "SRA:SRX10404230", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX10404230"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["ExperimentHiC", "Experiment", "Item"], "@id": "/experiments-hi-c/4DNEX99DGLEF/", "status": "released", "dbxrefs": ["GEO:GSM5184268", "SRA:SRX10404231"], "crosslinking_method": "2% Formaldehyde", "files": [{"upload_key": "11a49adc-2679-471e-9471-621e3c6f4eff/4DNFI9622X7Z.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "1", "display_title": "4DNFI9622X7Z.fastq.gz", "@id": "/files-fastq/4DNFI9622X7Z/", "file_size": 5804912422, "accession": "4DNFI9622X7Z", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/11a49adc-2679-471e-9471-621e3c6f4eff/4DNFI9622X7Z.fastq.gz", "href": "/files-fastq/4DNFI9622X7Z/@@download/4DNFI9622X7Z.fastq.gz", "@type": ["FileFastq", "File", "Item"], "uuid": "11a49adc-2679-471e-9471-621e3c6f4eff", "file_classification": "raw file", "md5sum": "a88d70b09b1e74f563ed0c03d36a1273", "status": "released", "file_type": "reads", "dbxrefs": ["SRA:SRR14027546"], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "2cff64ca-30ca-4a6a-aad1-2cdd0f763762", "display_title": "4DNFIH5SEZR7.fastq.gz", "accession": "4DNFIH5SEZR7", "status": "released", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFIH5SEZR7/", "file_type": "reads", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"Total Sequences": 61899146, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI9622X7Z/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/3ae05f1e-c5b7-4f69-b8a4-dffac6352066/", "uuid": "3ae05f1e-c5b7-4f69-b8a4-dffac6352066", "Sequence length": "150", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2021-06-02", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR14027546", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR14027546"}], "lab": {"name": "david-zarkower-lab", "@type": ["Lab", "Item"], "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "@id": "/labs/david-zarkower-lab/", "display_title": "David Zarkower, UMN", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}, "track_and_facet_info": {"experimental_lab": "David Zarkower, UMN", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "Sertoli cell", "lab_name": "David Zarkower, UMN"}}, {"upload_key": "2cff64ca-30ca-4a6a-aad1-2cdd0f763762/4DNFIH5SEZR7.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "2", "display_title": "4DNFIH5SEZR7.fastq.gz", "@id": "/files-fastq/4DNFIH5SEZR7/", "file_size": 6209742131, "accession": "4DNFIH5SEZR7", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/2cff64ca-30ca-4a6a-aad1-2cdd0f763762/4DNFIH5SEZR7.fastq.gz", "href": "/files-fastq/4DNFIH5SEZR7/@@download/4DNFIH5SEZR7.fastq.gz", "@type": ["FileFastq", "File", "Item"], "uuid": "2cff64ca-30ca-4a6a-aad1-2cdd0f763762", "file_classification": "raw file", "md5sum": "7c60d632719866213543856efd250afb", "status": "released", "file_type": "reads", "dbxrefs": ["SRA:SRR14027546"], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "11a49adc-2679-471e-9471-621e3c6f4eff", "display_title": "4DNFI9622X7Z.fastq.gz", "accession": "4DNFI9622X7Z", "status": "released", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFI9622X7Z/", "file_type": "reads", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"Total Sequences": 61899146, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIH5SEZR7/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/a27c0306-80fb-4978-ac17-59dba1c0beef/", "uuid": "a27c0306-80fb-4978-ac17-59dba1c0beef", "Sequence length": "150", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2021-06-02", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR14027546", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR14027546"}], "lab": {"name": "david-zarkower-lab", "@type": ["Lab", "Item"], "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "@id": "/labs/david-zarkower-lab/", "display_title": "David Zarkower, UMN", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}, "track_and_facet_info": {"experimental_lab": "David Zarkower, UMN", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "Sertoli cell", "lab_name": "David Zarkower, UMN"}}, {"upload_key": "191ae6f4-f688-4914-aa72-0df1630cfde5/4DNFIRKS2SCL.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "1", "display_title": "4DNFIRKS2SCL.fastq.gz", "@id": "/files-fastq/4DNFIRKS2SCL/", "file_size": 36914267891, "accession": "4DNFIRKS2SCL", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/191ae6f4-f688-4914-aa72-0df1630cfde5/4DNFIRKS2SCL.fastq.gz", "href": "/files-fastq/4DNFIRKS2SCL/@@download/4DNFIRKS2SCL.fastq.gz", "@type": ["FileFastq", "File", "Item"], "uuid": "191ae6f4-f688-4914-aa72-0df1630cfde5", "file_classification": "raw file", "md5sum": "70b1e65b4bddd832a0ab5328ac6b7cc0", "status": "released", "file_type": "reads", "dbxrefs": ["SRA:SRR14027547"], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "3738e4c8-d0d9-427b-ae77-7a42a442c702", "display_title": "4DNFIVGN7A11.fastq.gz", "accession": "4DNFIVGN7A11", "status": "released", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFIVGN7A11/", "file_type": "reads", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"Total Sequences": 482881594, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIRKS2SCL/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/b8af6f94-1ad8-41ea-b0ce-e53d9f90fcee/", "uuid": "b8af6f94-1ad8-41ea-b0ce-e53d9f90fcee", "Sequence length": "150", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2021-06-02", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR14027547", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR14027547"}], "lab": {"name": "david-zarkower-lab", "@type": ["Lab", "Item"], "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "@id": "/labs/david-zarkower-lab/", "display_title": "David Zarkower, UMN", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}, "track_and_facet_info": {"experimental_lab": "David Zarkower, UMN", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "Sertoli cell", "lab_name": "David Zarkower, UMN"}}, {"upload_key": "3738e4c8-d0d9-427b-ae77-7a42a442c702/4DNFIVGN7A11.fastq.gz", "file_type_detailed": "reads (fastq)", "paired_end": "2", "display_title": "4DNFIVGN7A11.fastq.gz", "@id": "/files-fastq/4DNFIVGN7A11/", "file_size": 37264323998, "accession": "4DNFIVGN7A11", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/3738e4c8-d0d9-427b-ae77-7a42a442c702/4DNFIVGN7A11.fastq.gz", "href": "/files-fastq/4DNFIVGN7A11/@@download/4DNFIVGN7A11.fastq.gz", "@type": ["FileFastq", "File", "Item"], "uuid": "3738e4c8-d0d9-427b-ae77-7a42a442c702", "file_classification": "raw file", "md5sum": "420b9497e736e1b303bcf51f32228a36", "status": "released", "file_type": "reads", "dbxrefs": ["SRA:SRR14027547"], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "191ae6f4-f688-4914-aa72-0df1630cfde5", "display_title": "4DNFIRKS2SCL.fastq.gz", "accession": "4DNFIRKS2SCL", "status": "released", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFIRKS2SCL/", "file_type": "reads", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"Total Sequences": 482881594, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIVGN7A11/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/c8e47e25-aa5e-4910-8d53-3b388bba8838/", "uuid": "c8e47e25-aa5e-4910-8d53-3b388bba8838", "Sequence length": "150", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2021-06-02", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR14027547", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR14027547"}], "lab": {"name": "david-zarkower-lab", "@type": ["Lab", "Item"], "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "@id": "/labs/david-zarkower-lab/", "display_title": "David Zarkower, UMN", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}, "track_and_facet_info": {"experimental_lab": "David Zarkower, UMN", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "Sertoli cell", "lab_name": "David Zarkower, UMN"}}], "accession": "4DNEX99DGLEF", "display_title": "in situ Hi-C on Sertoli cell with Arima - A1, A2 - 4DNEX99DGLEF", "uuid": "d8a78b5f-9425-4557-ba5b-b88de8f748da", "biosample": {"status": "released", "modifications_summary": "None", "biosample_category": ["Primary Cells"], "biosample_type": "primary cells", "@id": "/biosamples/4DNBSTHASN1X/", "treatments_summary": "None", "biosource_summary": "Sertoli cell", "accession": "4DNBSTHASN1X", "@type": ["Biosample", "Item"], "display_title": "4DNBSTHASN1X", "uuid": "1ff12d51-f895-4554-941f-c95def6d835e", "biosource": [{"uuid": "2c69ce50-c2a2-4000-ba32-3186383e9807", "display_title": "Sertoli cell - 4DNSR73BT2A2", "@id": "/biosources/4DNSR73BT2A2/", "accession": "4DNSR73BT2A2", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "status": "released", "biosource_type": "primary cell", "tissue": {"uuid": "c108f0e6-61a1-42c0-876f-19d3a7231112", "@id": "/ontology-terms/CL:0000216/", "preferred_name": "Sertoli cell", "@type": ["OntologyTerm", "Item"], "term_name": "Sertoli cell", "term_id": "CL:0000216", "status": "released", "display_title": "Sertoli cell", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000990/", "display_title": "reproductive system", "status": "released", "uuid": "111127bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000926/", "display_title": "mesoderm", "status": "released", "uuid": "111120bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0000991/", "display_title": "gonad", "status": "released", "uuid": "111164bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"display_title": "M. musculus", "name": "mouse", "@id": "/organisms/10090/", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "scientific_name": "Mus musculus", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"@type": ["OntologyTerm", "Item"], "display_title": "Sertoli cell", "term_id": "CL:0000216", "status": "released", "uuid": "c108f0e6-61a1-42c0-876f-19d3a7231112", "term_name": "Sertoli cell", "@id": "/ontology-terms/CL:0000216/", "preferred_name": "Sertoli cell", "slim_terms": [{"status": "released", "@id": "/ontology-terms/UBERON:0000990/", "display_title": "reproductive system", "uuid": "111127bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/ontology-terms/UBERON:0000926/", "display_title": "mesoderm", "uuid": "111120bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "current", "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/ontology-terms/UBERON:0000991/", "display_title": "gonad", "uuid": "111164bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue_organ_info": {"organ_system": ["reproductive system", "mesoderm", "gonad"], "tissue_source": "Sertoli cell"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"href": "/files-processed/4DNFIABW2TRH/@@download/4DNFIABW2TRH.bam", "file_type_detailed": "alignments (bam)", "uuid": "f97a746b-9462-43b9-9ca3-bc1285876276", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f97a746b-9462-43b9-9ca3-bc1285876276/4DNFIABW2TRH.bam", "@id": "/files-processed/4DNFIABW2TRH/", "status": "released", "display_title": "4DNFIABW2TRH.bam", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIABW2TRH", "file_type": "alignments", "file_classification": "processed file", "upload_key": "f97a746b-9462-43b9-9ca3-bc1285876276/4DNFIABW2TRH.bam", "file_size": 134046645830, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "d06000a71433c87c7cccabc7ad7c834e", "quality_metric": {"uuid": "87a8071b-baf0-4de8-9af6-ba4dda4ef707", "overall_quality_status": "PASS", "status": "released", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "@id": "/quality-metrics-bamqc/87a8071b-baf0-4de8-9af6-ba4dda4ef707/", "display_title": "QualityMetricBamqc from 2021-06-25", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Reads", "value": "544780740", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "9.346", "tooltip": "Percent of total reads (=50.91m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "8.024", "tooltip": "Percent of total reads (=43.71m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "10.486", "tooltip": "Percent of total reads (=57.12m)", "numberType": "percent"}, {"title": "Walks", "value": "17.58", "tooltip": "Percent of total reads (=95.77m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.066", "tooltip": "Percent of total reads (=0.36m)", "numberType": "percent"}]}, "lab": {"@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "display_title": "4DN DCIC, HMS", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/david-zarkower-lab/", "name": "david-zarkower-lab", "display_title": "David Zarkower, UMN", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}], "external_references": [], "track_and_facet_info": {"experimental_lab": "David Zarkower, UMN", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "Sertoli cell", "lab_name": "4DN DCIC, HMS"}, "last_modified": {"date_modified": "2021-08-10T20:46:32.148981+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"href": "/files-processed/4DNFIGA7F8K9/@@download/4DNFIGA7F8K9.pairs.gz", "file_type_detailed": "contact list-replicate (pairs)", "uuid": "144798a3-a143-4850-8f2b-8887de6f0556", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/144798a3-a143-4850-8f2b-8887de6f0556/4DNFIGA7F8K9.pairs.gz", "@id": "/files-processed/4DNFIGA7F8K9/", "status": "released", "display_title": "4DNFIGA7F8K9.pairs.gz", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIGA7F8K9", "file_type": "contact list-replicate", "file_classification": "processed file", "upload_key": "144798a3-a143-4850-8f2b-8887de6f0556/4DNFIGA7F8K9.pairs.gz", "file_size": 5943699488, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "9728eaef960372109a134d302825f881", "quality_metric": {"uuid": "5db8fd57-f847-43b3-bab2-4bf1d2c2d50f", "overall_quality_status": "PASS", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIGA7F8K9/pairsqc_report.html", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Total reads": 297261654, "@id": "/quality-metrics-pairsqc/5db8fd57-f847-43b3-bab2-4bf1d2c2d50f/", "display_title": "QualityMetricPairsqc from 2021-06-10", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "297261654", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "51.787", "tooltip": "Percent of filtered reads (=153.94m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "31.14", "tooltip": "Percent of filtered reads (=92.57m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "17.073", "tooltip": "Percent of filtered reads (=50.75m)", "numberType": "percent"}]}, "lab": {"@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "display_title": "4DN DCIC, HMS", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "extra_files": [{"href": "/files-processed/4DNFIGA7F8K9/@@download/4DNFIGA7F8K9.pairs.gz.px2", "file_size": 19928856, "md5sum": "20b13e6a69b8d3338381b1f010ee3d09", "file_format": {"file_format": "pairs_px2", "display_title": "pairs_px2", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "@id": "/file-formats/pairs_px2/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "contributing_labs": [{"uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/david-zarkower-lab/", "name": "david-zarkower-lab", "display_title": "David Zarkower, UMN", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}], "external_references": [], "track_and_facet_info": {"experimental_lab": "David Zarkower, UMN", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "Sertoli cell", "lab_name": "4DN DCIC, HMS"}, "last_modified": {"date_modified": "2021-08-10T20:39:27.969051+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "other_processed_files": [{"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.", "type": "preliminary", "title": "HiC Processing Pipeline - v0.3.0", "files": [{"@type": ["FileProcessed", "File", "Item"], "status": "released", "md5sum": "6bccb4ae50a3c89248ac0a962e9cf772", "uuid": "11bf1df8-b4fd-4bbf-b9c7-0556702aac3c", "@id": "/files-processed/4DNFI31A9MK9/", "file_type": "alignments", "file_type_detailed": "alignments (bam)", "accession": "4DNFI31A9MK9", "href": "/files-processed/4DNFI31A9MK9/@@download/4DNFI31A9MK9.bam", "genome_assembly": "GRCm38", "display_title": "4DNFI31A9MK9.bam", "file_size": 128566386683, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/11bf1df8-b4fd-4bbf-b9c7-0556702aac3c/4DNFI31A9MK9.bam", "lab": {"status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "status": "released", "file_format": "bam", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"status": "current", "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "name": "david-zarkower-lab", "display_title": "David Zarkower, UMN", "@id": "/labs/david-zarkower-lab/", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}], "track_and_facet_info": {"experimental_lab": "David Zarkower, UMN", "experiment_type": "in situ Hi-C", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "Sertoli cell", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2024-08-08T00:01:00.158914+00:00"}}, {"@type": ["FileProcessed", "File", "Item"], "status": "released", "md5sum": "71d4c0b8bacbb0c1c597a7df3ac92486", "uuid": "6eabcc08-f188-49d4-b7ee-31343df5e078", "@id": "/files-processed/4DNFIA1B2H2G/", "file_type": "contact list-replicate", "file_type_detailed": "contact list-replicate (pairs)", "accession": "4DNFIA1B2H2G", "href": "/files-processed/4DNFIA1B2H2G/@@download/4DNFIA1B2H2G.pairs.gz", "genome_assembly": "GRCm38", "display_title": "4DNFIA1B2H2G.pairs.gz", "file_size": 6535495298, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/6eabcc08-f188-49d4-b7ee-31343df5e078/4DNFIA1B2H2G.pairs.gz", "lab": {"status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"status": "current", "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "name": "david-zarkower-lab", "display_title": "David Zarkower, UMN", "@id": "/labs/david-zarkower-lab/", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}], "quality_metric": {"overall_quality_status": "PASS", "display_title": "QualityMetricPairsqc from 2024-07-05", "uuid": "9f3f413a-b4fb-4005-9429-021042f7463c", "status": "released", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "@id": "/quality-metrics-pairsqc/9f3f413a-b4fb-4005-9429-021042f7463c/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIA1B2H2G/pairsqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "349670015", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "51.612", "tooltip": "Percent of filtered reads (=180.47m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "30.939", "tooltip": "Percent of filtered reads (=108.18m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "17.449", "tooltip": "Percent of filtered reads (=61.02m)", "numberType": "percent"}]}, "track_and_facet_info": {"experimental_lab": "David Zarkower, UMN", "experiment_type": "in situ Hi-C", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "Sertoli cell", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2024-08-07T23:53:23.615041+00:00"}}]}], "digestion_enzyme": {"uuid": "1b967af3-f275-4480-93d7-c6ce62a908c6", "display_title": "Arima - A1, A2", "@type": ["Enzyme", "Item"], "name": "Arima - A1, A2", "@id": "/enzymes/Arima%20-%20A1,%20A2/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "@type": ["ExperimentType", "Item"], "assay_subclass_short": "Hi-C", "@id": "/experiment-types/in-situ-hi-c/", "assay_subclassification": "DNA-DNA Pairwise Interactions", "display_title": "in situ Hi-C", "title": "in situ Hi-C", "status": "released", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "experiment_category": "Sequencing", "assay_classification": "3C via Ligation", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"value": "Arima - A1, A2", "combined": "Enzyme: Arima - A1, A2", "field": "Enzyme"}, "last_modified": {"date_modified": "2024-07-16T15:02:05.281491+00:00"}, "external_references": [{"ref": "GEO:GSM5184268", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5184268"}, {"ref": "SRA:SRX10404231", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX10404231"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experimentset_type": "replicate", "completed_processes": ["compartments_v1.2", "HiC_Pipeline_0.3.0", "insulation_scores_and_boundaries_v1", "HiC_Pipeline_0.2.7"], "other_processed_files": [{"type": "supplementary", "files": [{"file_type_detailed": "balanced normalized contact matrix (mcool)", "display_title": "4DNFI82S5W3G.mcool", "href": "/files-processed/4DNFI82S5W3G/@@download/4DNFI82S5W3G.mcool", "uuid": "5fa8460f-e521-4a9f-b908-aac711b65290", "accession": "4DNFI82S5W3G", "file_type": "balanced normalized contact matrix", "higlass_uid": "8c17367f-ad9a-419c-9bdb-6aafcd1a7813", "status": "released", "md5sum": "fafa31ebba2f1f840f1eae55d9c1df4a", "@id": "/files-processed/4DNFI82S5W3G/", "@type": ["FileProcessed", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/5fa8460f-e521-4a9f-b908-aac711b65290/4DNFI82S5W3G.mcool", "genome_assembly": "GRCm38", "file_format": {"uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/mcool/", "display_title": "mcool", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available.", "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."], "file_size": 600921225, "lab": {"@id": "/labs/david-zarkower-lab/", "display_title": "David Zarkower, UMN", "@type": ["Lab", "Item"], "status": "current", "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "name": "david-zarkower-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"uuid": "7b56a023-bef8-4f51-b558-f1538b9013c0", "status": "released", "@id": "/higlass-view-configs/7b56a023-bef8-4f51-b558-f1538b9013c0/", "display_title": "4DNFI82S5W3G - balanced normalized contact matrix for Sertoli cell in situ Hi-C Arima - A1, A2", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "quality_metric": {"display_title": "QualityMetricMcool from 2021-06-22", "@id": "/quality-metrics-mcool/dccdb9b4-d6de-46c9-8f9d-e955930fbf75/", "@type": ["QualityMetricMcool", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "uuid": "dccdb9b4-d6de-46c9-8f9d-e955930fbf75", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Failed Balancing", "value": "None", "tooltip": "Resolutions where balancing failed", "numberType": "string"}]}, "track_and_facet_info": {"dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "experimental_lab": "David Zarkower, UMN", "replicate_info": "merged replicates", "experiment_bucket": "Derived data file provided by the Zarkower Lab", "experiment_type": "in situ Hi-C", "assay_info": "Arima - A1, A2", "biosource_name": "Sertoli cell", "lab_name": "David Zarkower, UMN", "track_title": "balanced normalized contact matrix for Sertoli cell in situ Hi-C Arima - A1, A2"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-08-25T17:48:53.728068+00:00"}}, {"file_type_detailed": "dot calls (bedpe)", "display_title": "4DNFI51UYBV4.bedpe.gz", "href": "/files-processed/4DNFI51UYBV4/@@download/4DNFI51UYBV4.bedpe.gz", "uuid": "b0f4f17b-ccc1-49b0-a78b-99c6f924093f", "accession": "4DNFI51UYBV4", "file_type": "dot calls", "status": "released", "md5sum": "2d37bd3a565083019bb2413225a0c1e6", "@id": "/files-processed/4DNFI51UYBV4/", "@type": ["FileProcessed", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/b0f4f17b-ccc1-49b0-a78b-99c6f924093f/4DNFI51UYBV4.bedpe.gz", "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f556118b2c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bedpe/", "display_title": "bedpe", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "file_size": 646389, "lab": {"@id": "/labs/david-zarkower-lab/", "display_title": "David Zarkower, UMN", "@type": ["Lab", "Item"], "status": "current", "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "name": "david-zarkower-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}, "track_and_facet_info": {"dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "experimental_lab": "David Zarkower, UMN", "replicate_info": "merged replicates", "experiment_bucket": "Derived data file provided by the Zarkower Lab", "experiment_type": "in situ Hi-C", "assay_info": "Arima - A1, A2", "biosource_name": "Sertoli cell", "lab_name": "David Zarkower, UMN"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-12-16T07:00:34.355440+00:00"}}, {"file_type_detailed": "compartments (bw)", "display_title": "4DNFI9WBQ8NU.bw", "href": "/files-processed/4DNFI9WBQ8NU/@@download/4DNFI9WBQ8NU.bw", "uuid": "6452dbe7-d2c7-40ba-a4b2-7b87c5a9fcd8", "accession": "4DNFI9WBQ8NU", "file_type": "compartments", "higlass_uid": "eb691385-8b0e-49cc-afcb-438377670c70", "status": "released", "md5sum": "e68499dddbb59d178eaf321a59013a88", "@id": "/files-processed/4DNFI9WBQ8NU/", "@type": ["FileProcessed", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/6452dbe7-d2c7-40ba-a4b2-7b87c5a9fcd8/4DNFI9WBQ8NU.bw", "genome_assembly": "GRCm38", "file_format": {"uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "display_title": "bw", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "file_size": 5040425, "lab": {"@id": "/labs/david-zarkower-lab/", "display_title": "David Zarkower, UMN", "@type": ["Lab", "Item"], "status": "current", "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "name": "david-zarkower-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"uuid": "8b0ec8cd-054d-42f5-8712-e1412cf2d5d7", "status": "released", "@id": "/higlass-view-configs/8b0ec8cd-054d-42f5-8712-e1412cf2d5d7/", "display_title": "4DNFI9WBQ8NU - compartments for Sertoli cell in situ Hi-C Arima - A1, A2", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "track_and_facet_info": {"dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "experimental_lab": "David Zarkower, UMN", "replicate_info": "merged replicates", "experiment_bucket": "Derived data file provided by the Zarkower Lab", "experiment_type": "in situ Hi-C", "assay_info": "Arima - A1, A2", "biosource_name": "Sertoli cell", "lab_name": "David Zarkower, UMN", "track_title": "compartments for Sertoli cell in situ Hi-C Arima - A1, A2"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-12-16T07:00:32.951177+00:00"}}], "title": "Derived data file provided by the Zarkower Lab", "description": "The associated files contain balanced normalized contact matrices, dot calls and A/B compartments generated for this dataset and provided by the experimental lab.", "higlass_view_config": {"@id": "/higlass-view-configs/df074829-7167-42d9-ae75-605201d8f6b2/", "description": "Supplementary Files (Derived data file provided by the Zarkower Lab) for 4DNES265ETYQ (in situ Hi-C on primary mouse Sertoli cells from 7 day old males): 4DNFI82S5W3G, 4DNFI9WBQ8NU", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "display_title": "4DNES265ETYQ - Derived data file provided by the Zarkower Lab", "uuid": "df074829-7167-42d9-ae75-605201d8f6b2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}, "last_modified": {"date_modified": "2024-07-18T06:02:43.692902+00:00"}}}, {"type": "preliminary", "files": [{"file_type_detailed": "contact list-combined (pairs)", "display_title": "4DNFI45ST7L8.pairs.gz", "href": "/files-processed/4DNFI45ST7L8/@@download/4DNFI45ST7L8.pairs.gz", "uuid": "c31e368d-2c71-480c-bf3a-7fb33d30a3b4", "accession": "4DNFI45ST7L8", "file_type": "contact list-combined", "status": "released", "md5sum": "a1e2ca7fa12b2a90bfda3fcd39997a3c", "@id": "/files-processed/4DNFI45ST7L8/", "@type": ["FileProcessed", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c31e368d-2c71-480c-bf3a-7fb33d30a3b4/4DNFI45ST7L8.pairs.gz", "genome_assembly": "GRCm38", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 11564481361, "contributing_labs": [{"@type": ["Lab", "Item"], "@id": "/labs/david-zarkower-lab/", "display_title": "David Zarkower, UMN", "name": "david-zarkower-lab", "status": "current", "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}], "lab": {"@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "quality_metric": {"display_title": "QualityMetricPairsqc from 2024-07-09", "@id": "/quality-metrics-pairsqc/d3d0921c-b75a-4f11-a129-7ef70aa119e8/", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI45ST7L8/pairsqc_report.html", "uuid": "d3d0921c-b75a-4f11-a129-7ef70aa119e8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "631310043", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "52.72", "tooltip": "Percent of filtered reads (=332.83m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "30.713", "tooltip": "Percent of filtered reads (=193.9m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "16.567", "tooltip": "Percent of filtered reads (=104.59m)", "numberType": "percent"}]}, "track_and_facet_info": {"dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "experimental_lab": "David Zarkower, UMN", "replicate_info": "merged replicates", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "experiment_type": "in situ Hi-C", "assay_info": "Arima - A1, A2", "biosource_name": "Sertoli cell", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2024-08-08T01:58:09.762500+00:00"}}, {"file_type_detailed": "contact matrix (hic)", "display_title": "4DNFILYYUCB3.hic", "href": "/files-processed/4DNFILYYUCB3/@@download/4DNFILYYUCB3.hic", "uuid": "931f33c5-4ec3-4108-a60d-9d613df295c0", "accession": "4DNFILYYUCB3", "file_type": "contact matrix", "status": "released", "md5sum": "b806e851c689c6e1f087891205855f61", "@id": "/files-processed/4DNFILYYUCB3/", "@type": ["FileProcessed", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/931f33c5-4ec3-4108-a60d-9d613df295c0/4DNFILYYUCB3.hic", "genome_assembly": "GRCm38", "file_format": {"uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/hic/", "display_title": "hic", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 4318898424, "contributing_labs": [{"@type": ["Lab", "Item"], "@id": "/labs/david-zarkower-lab/", "display_title": "David Zarkower, UMN", "name": "david-zarkower-lab", "status": "current", "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}], "lab": {"@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "track_and_facet_info": {"dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "experimental_lab": "David Zarkower, UMN", "replicate_info": "merged replicates", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "experiment_type": "in situ Hi-C", "assay_info": "Arima - A1, A2", "biosource_name": "Sertoli cell", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2024-08-08T01:56:30.287218+00:00"}}, {"file_type_detailed": "contact matrix (mcool)", "display_title": "4DNFIA6NMC6G.mcool", "href": "/files-processed/4DNFIA6NMC6G/@@download/4DNFIA6NMC6G.mcool", "uuid": "25f40094-98ef-426e-afd1-64b70a79fd63", "accession": "4DNFIA6NMC6G", "file_type": "contact matrix", "higlass_uid": "3519ee30-8092-4333-b286-f73f8b631409", "status": "released", "md5sum": "cfc2712fea96e27b3951d7efc8623a54", "@id": "/files-processed/4DNFIA6NMC6G/", "@type": ["FileProcessed", "File", "Item"], "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/25f40094-98ef-426e-afd1-64b70a79fd63/4DNFIA6NMC6G.mcool", "genome_assembly": "GRCm38", "file_format": {"uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/mcool/", "display_title": "mcool", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 2965561676, "contributing_labs": [{"@type": ["Lab", "Item"], "@id": "/labs/david-zarkower-lab/", "display_title": "David Zarkower, UMN", "name": "david-zarkower-lab", "status": "current", "uuid": "0b568aa3-cb33-45d9-8b92-39912efcc97d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0b568aa3-cb33-45d9-8b92-39912efcc97d"]}}], "lab": {"@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "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": {"uuid": "81b19c2a-b4f4-432b-ac92-0e943c4d8a58", "status": "released", "@id": "/higlass-view-configs/81b19c2a-b4f4-432b-ac92-0e943c4d8a58/", "display_title": "4DNFIA6NMC6G - contact matrix for Sertoli cell in situ Hi-C Arima - A1, A2", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "quality_metric": {"display_title": "QualityMetricMcool from 2024-07-09", "@id": "/quality-metrics-mcool/de7c4723-172b-4d74-b35a-a8043afea5f5/", "@type": ["QualityMetricMcool", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "uuid": "de7c4723-172b-4d74-b35a-a8043afea5f5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Failed Balancing", "value": "None", "tooltip": "Resolutions where balancing failed", "numberType": "string"}]}, "track_and_facet_info": {"dataset": "Hi-C on mouse somatic gonadal cells", "condition": "male Sertoli cells", "experimental_lab": "David Zarkower, UMN", "replicate_info": "merged replicates", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "experiment_type": "in situ Hi-C", "assay_info": "Arima - A1, A2", "biosource_name": "Sertoli cell", "lab_name": "4DN DCIC, HMS", "track_title": "contact matrix for Sertoli cell in situ Hi-C Arima - A1, A2"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2024-08-08T02:46:11.504861+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": {"@id": "/higlass-view-configs/00d55baf-915e-4c03-b1e8-db7cc944abca/", "description": "Supplementary Files (HiC Processing Pipeline - v0.3.0) for 4DNES265ETYQ (in situ Hi-C on primary mouse Sertoli cells from 7 day old males): 4DNFIA6NMC6G", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "display_title": "4DNES265ETYQ - HiC Processing Pipeline - v0.3.0", "uuid": "00d55baf-915e-4c03-b1e8-db7cc944abca", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}, "last_modified": {"date_modified": "2024-07-17T19:32:52.916786+00:00"}}}], "@id": "/experiment-set-replicates/4DNES265ETYQ/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "c80a1a65-0ac0-4ba0-bed4-1886a49ac4ce", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNES265ETYQ", "external_references": [], "produced_in_pub": {"abstract": "Mammalian sexual development commences when fetal bipotential progenitor cells adopt male Sertoli (in XY) or female granulosa (in XX) gonadal cell fates. Differentiation of these cells involves extensive divergence in chromatin state and gene expression, reflecting distinct roles in sexual differentiation and gametogenesis. Surprisingly, differentiated gonadal cell fates require active maintenance through postnatal life to prevent sexual transdifferentiation and female cell fate can be reprogrammed by ectopic expression of the sex regulator DMRT1. Here we examine how DMRT1 reprograms granulosa cells to Sertoli-like cells in vivo and in culture. We define postnatal sex-biased gene expression programs and identify three-dimensional chromatin contacts and differentially accessible chromatin regions (DARs) associated with differentially expressed genes. Using a  conditional transgene we find DMRT1 only partially reprograms the ovarian transcriptome in the absence of SOX9 and its paralog SOX8, indicating that these  factors functionally cooperate with DMRT1. ATAC-seq and ChIP-seq show that DMRT1  induces formation of many DARs that it binds with SOX9, and DMRT1 is required for binding of SOX9 at most of these. We suggest that DMRT1 can act as a pioneer factor to open chromatin and allow binding of SOX9, which then cooperates with DMRT1 to reprogram sexual cell fate.", "display_title": "Lindeman RE et al. (2021) PMID:34096593", "journal": "Nucleic acids research", "authors": ["Lindeman RE", "Murphy MW", "Agrimson KS", "Gewiss RL", "Bardwell VJ", "Gearhart MD", "Zarkower D"], "title": "The conserved sex regulator DMRT1 recruits SOX9 in sexual cell fate reprogramming.", "date_published": "2021-06-07", "@type": ["Publication", "Item"], "short_attribution": "Lindeman RE et al. (2021)", "url": "https://www.ncbi.nlm.nih.gov/pubmed/34096593", "ID": "PMID:34096593", "status": "current", "@id": "/publications/9a3e1015-b41e-4bdc-8eea-419f536815ec/", "uuid": "9a3e1015-b41e-4bdc-8eea-419f536815ec", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"uuid": "9a3e1015-b41e-4bdc-8eea-419f536815ec", "@type": ["Publication", "Item"], "@id": "/publications/9a3e1015-b41e-4bdc-8eea-419f536815ec/", "abstract": "Mammalian sexual development commences when fetal bipotential progenitor cells adopt male Sertoli (in XY) or female granulosa (in XX) gonadal cell fates. Differentiation of these cells involves extensive divergence in chromatin state and gene expression, reflecting distinct roles in sexual differentiation and gametogenesis. Surprisingly, differentiated gonadal cell fates require active maintenance through postnatal life to prevent sexual transdifferentiation and female cell fate can be reprogrammed by ectopic expression of the sex regulator DMRT1. Here we examine how DMRT1 reprograms granulosa cells to Sertoli-like cells in vivo and in culture. We define postnatal sex-biased gene expression programs and identify three-dimensional chromatin contacts and differentially accessible chromatin regions (DARs) associated with differentially expressed genes. Using a  conditional transgene we find DMRT1 only partially reprograms the ovarian transcriptome in the absence of SOX9 and its paralog SOX8, indicating that these  factors functionally cooperate with DMRT1. ATAC-seq and ChIP-seq show that DMRT1  induces formation of many DARs that it binds with SOX9, and DMRT1 is required for binding of SOX9 at most of these. We suggest that DMRT1 can act as a pioneer factor to open chromatin and allow binding of SOX9, which then cooperates with DMRT1 to reprogram sexual cell fate.", "journal": "Nucleic acids research", "date_published": "2021-06-07", "status": "current", "display_title": "Lindeman RE et al. (2021) PMID:34096593", "authors": ["Lindeman RE", "Murphy MW", "Agrimson KS", "Gewiss RL", "Bardwell VJ", "Gearhart MD", "Zarkower D"], "ID": "PMID:34096593", "title": "The conserved sex regulator DMRT1 recruits SOX9 in sexual cell fate reprogramming.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 2, "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}