{"lab": {"@type": ["Lab", "Item"], "@id": "/labs/jennifer-cremins-lab/", "title": "Jennifer Cremins, UPENN", "correspondence": [{"contact_email": "amNyZW1pbnNAc2Vhcy51cGVubi5lZHU=", "@id": "/users/8773d50c-1716-4153-9a18-d0f5ff2aa5ee/", "display_title": "Jennifer Phillips-Cremins"}], "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "display_title": "Jennifer Cremins, UPENN", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}, "award": {"display_title": "ENGINEERING AND IMAGING 3D GENOME STRUCTURE-FUNCTION DYNAMICS ACROSS TIME SCALES", "@id": "/awards/1U01DK127405-01/", "project": "4DN", "description": "RT-CDF:The mammalian genome folds into tens of thousands of long-range looping interactions. A critical unknown is whether and how chromatin loops control gene expression, and a major unresolved question is how the temporal progression of loops relates to transcription dynamics. One major barrier to answering this question is that loops change on a range of timescales, necessitating the use of tools and model systems amenable to tracking and engineering loops longitudinally and in real time on both short and long timing. Here, we propose to develop and apply new engineering and imaging tools to measure, induce, and perturb loops with precise temporal control in three different biological systems spanning minutes, hours, and weeks. At the shortest timescale (minutes, Aim 1), we will examine loop dynamics in human induced pluripotent stem cell-derived neurons in response to electrical stimulation, revealing how interaction frequency is functionally connected to transcriptional bursting of immediate early and secondary response genes. On the timescale of hours (Aim 3), we will elucidate how the architectural protein YY1 connects enhancer-promoter loops that re-assemble upon the exit from mitosis by erythroid cells. On the timescale of weeks (Aim 2), we will use a cellular \u201cTime Machine\u201d to longitudinally track the rare cells that undergo cellular reprogramming, allowing us to dissect the functionality of loop formation and dissolution with single-cell and subcellular resolution during the reprogramming of somatic cells to pluripotency and transition of melanoma cancer cells to a resistant phenotype. Our team consists of a highly productive and collaborative set of junior and senior investigators with complementary expertise and overlapping interests, including Dr. Gerd Blobel (epigenetics, mitosis, loop engineering), Dr. Eric Joyce (Oligopaints imaging), Dr. Bomyi Lim (nascent transcript live cell imaging), Dr. Jennifer Phillips-Cremins (chromatin architecture, loop engineering, neurobiology), Dr. Stanley Qi (CRISPR genome engineering, live cell imaging), and Dr. Arjun Raj (single cell genomics, RNA imaging, reprogramming). We will develop and apply live and fixed cell imaging techniques for chromatin contacts, and in the same cells image nascent transcription. We will build a cadre of synthetic architectural proteins to engineer loops in a time-dependent inducible manner. Successful application of our engineering and imaging tools across biological systems will yield a comprehensive and rigorous assessment of the cause-and-effect relationship between loops and distinct biological phenotypes across timescales.", "uuid": "b3046311-087c-4141-8e98-a099b96ac6cd", "center_title": "Phillips-Cremins", "name": "1U01DK127405-01", "status": "current", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "pi": {"error": "no view permissions"}}, "study": "Cohesin Protein Function", "status": "released", "aliases": ["cremins-lab:Hi-C-wt-hct116"], "accession": "4DNESNSTBMBY", "condition": "wild-type", "description": "Replicates of in situ Hi-C on untreated HCT116 WAPL-mAID2 cells", "study_group": "Disrupted or Atypical Cells", "date_created": "2021-10-30T01:35:23.212994+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_group": "Hi-C on HCT116 +/- WAPL", "dataset_label": "Hi-C on HCT116", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-07-17T06:46:07.180781+00:00"}, "public_release": "2021-11-10", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"status": "released", "uuid": "f96906f8-4595-4268-b440-ab51bc933e9b", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXN474APC", "@id": "/experiments-hi-c/4DNEXN474APC/", "display_title": "in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G) with Arima - A1, A2 - 4DNEXN474APC", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"status": "released", "uuid": "0906f714-2ee8-4ef4-9e02-b31069af5ea4", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEX7S1OYDN", "@id": "/experiments-hi-c/4DNEX7S1OYDN/", "display_title": "in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G) with Arima - A1, A2 - 4DNEX7S1OYDN", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"award": {"@id": "/awards/1U01DK127405-01/", "@type": ["Award", "Item"], "uuid": "b3046311-087c-4141-8e98-a099b96ac6cd", "display_title": "ENGINEERING AND IMAGING 3D GENOME STRUCTURE-FUNCTION DYNAMICS ACROSS TIME SCALES", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@id": "/labs/jennifer-cremins-lab/", "display_title": "Jennifer Cremins, UPENN", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}, "name": "64c86bb1-e37b-44ff-b829-e27daa49b059", "filetype": "HiglassViewConfig", "description": "4DNESNSTBMBY (Replicates of in situ Hi-C on untreated HCT116 WAPL-mAID2 cells): 4DNFIYKBWW4V, 4DNFIG49IPR6, 4DNFIWTWQ8GQ, 4DNFIPPNYV71", "uuid": "64c86bb1-e37b-44ff-b829-e27daa49b059", "title": "4DNESNSTBMBY - Processed files", "display_title": "4DNESNSTBMBY - Processed files", "contributing_labs": [{"uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "status": "current", "display_title": "David Gilbert, SDBRI", "@type": ["Lab", "Item"], "@id": "/labs/david-gilbert-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/64c86bb1-e37b-44ff-b829-e27daa49b059/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}, "location": "tab:processed-files", "description": "auto_generated_higlass_view_config"}], "static_headers": [{"lab": {"@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "<b>In Situ Hi-C</b>\n\n<p>\n   In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed <i>in situ</i> inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n</p>\n<p>\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n</p>\n<p>\nSee <a href=\"https://www.sciencedirect.com/science/article/pii/S0092867414014974?via%3Dihub\">Rao et al., 2014</a> for more details.\n</p>\n\n<div>\n<img style=\"width: 600px;max-width:100%;\" src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/IsHC_fig1.png\"/>\n  <br/><br/>\n  <em>Image source: Rao et al., 2014, Figure 1A</em>\n</div>", "name": "item-page-headers.ExperimentType.insituhic", "award": {"display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "status": "current", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@id": "/awards/1U01CA200059-01/", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Assay Description", "status": "released", "aliases": ["4dn-dcic-lab:experiment_infobox_hic"], "options": {"filetype": "html", "collapsible": false, "default_open": false, "convert_ext_links": true}, "date_created": "2018-09-07T18:19:43.777198+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-11-09T14:48:01.220007+00:00"}, "schema_version": "2", "@id": "/static-sections/298554ad-20e2-4449-a752-ac190123dab7/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "298554ad-20e2-4449-a752-ac190123dab7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.56c9c683-bb11-471b-b590-c656f7dc03c1"]}, "display_title": "Assay Description", "external_references": [], "content": "<b>In Situ Hi-C</b>\n\n<p>\n   In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed <i>in situ</i> inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n</p>\n<p>\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n</p>\n<p>\nSee <a href=\"https://www.sciencedirect.com/science/article/pii/S0092867414014974?via%3Dihub\">Rao et al., 2014</a> for more details.\n</p>\n\n<div>\n<img style=\"width: 600px;max-width:100%;\" src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/IsHC_fig1.png\"/>\n  <br/><br/>\n  <em>Image source: Rao et al., 2014, Figure 1A</em>\n</div>", "filetype": "html", "content_as_html": "<div class=\"html-container\"><b>In Situ Hi-C</b>\n<p>\n   In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed <i>in situ</i> inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n</p>\n<p>\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n</p>\n<p>\nSee <a href=\"https://www.sciencedirect.com/science/article/pii/S0092867414014974?via%3Dihub\" rel=\"noopener noreferrer\" target=\"_blank\">Rao et al., 2014</a> for more details.\n</p>\n<div>\n<img src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/IsHC_fig1.png\" style=\"width: 600px;max-width:100%;\"/>\n<br/><br/>\n<em>Image source: Rao et al., 2014, Figure 1A</em>\n</div></div>"}], "processed_files": [{"file_classification": "processed file", "display_title": "4DNFIIBWRXMP.pairs.gz", "file_type": "contact list-combined", "md5sum": "0c7eaf1dffb19a3c176469b52e5cd8de", "@id": "/files-processed/4DNFIIBWRXMP/", "file_type_detailed": "contact list-combined (pairs)", "file_size": 7285007461, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/175c0095-2745-4095-bab9-01820a8aaf67/4DNFIIBWRXMP.pairs.gz", "uuid": "175c0095-2745-4095-bab9-01820a8aaf67", "href": "/files-processed/4DNFIIBWRXMP/@@download/4DNFIIBWRXMP.pairs.gz", "accession": "4DNFIIBWRXMP", "status": "released", "genome_assembly": "GRCh38", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "upload_key": "175c0095-2745-4095-bab9-01820a8aaf67/4DNFIIBWRXMP.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "quality_metric": {"@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "display_title": "QualityMetricPairsqc from 2021-11-02", "@id": "/quality-metrics-pairsqc/4d28db40-79cb-416b-a21f-8525bb5d3c98/", "status": "released", "Total reads": 366311278, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIIBWRXMP/pairsqc_report.html", "uuid": "4d28db40-79cb-416b-a21f-8525bb5d3c98", "quality_metric_summary": [{"title": "Filtered Reads", "value": "366311278", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "61.397", "tooltip": "Percent of filtered reads (=224.9m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "20.379", "tooltip": "Percent of filtered reads (=74.65m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "18.224", "tooltip": "Percent of filtered reads (=66.76m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "extra_files": [{"href": "/files-processed/4DNFIIBWRXMP/@@download/4DNFIIBWRXMP.pairs.gz.px2", "md5sum": "e7efc835ee8729ef073e4499fb94dc85", "file_size": 12739214, "file_format": {"status": "released", "display_title": "pairs_px2", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "file_format": "pairs_px2", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs_px2/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"display_title": "4DN DCIC, HMS", "status": "current", "name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"name": "jennifer-cremins-lab", "@type": ["Lab", "Item"], "@id": "/labs/jennifer-cremins-lab/", "display_title": "Jennifer Cremins, UPENN", "status": "current", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}], "external_references": [], "track_and_facet_info": {"dataset": "Hi-C on HCT116", "condition": "wild-type", "experimental_lab": "Jennifer Cremins, UPENN", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "Arima - A1, A2", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-21T14:36:52.389577+00:00"}}, {"file_classification": "processed file", "display_title": "4DNFIXTAS6EE.hic", "file_type": "contact matrix", "md5sum": "0f742d02bd51084be9a530cb7b2ec4fc", "@id": "/files-processed/4DNFIXTAS6EE/", "file_type_detailed": "contact matrix (hic)", "file_size": 3423011285, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/3768b89a-e124-40eb-8acd-94a4fdd35807/4DNFIXTAS6EE.hic", "uuid": "3768b89a-e124-40eb-8acd-94a4fdd35807", "href": "/files-processed/4DNFIXTAS6EE/@@download/4DNFIXTAS6EE.hic", "accession": "4DNFIXTAS6EE", "status": "released", "genome_assembly": "GRCh38", "file_format": {"status": "released", "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/hic/", "display_title": "hic", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "upload_key": "3768b89a-e124-40eb-8acd-94a4fdd35807/4DNFIXTAS6EE.hic", "@type": ["FileProcessed", "File", "Item"], "lab": {"display_title": "4DN DCIC, HMS", "status": "current", "name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"name": "jennifer-cremins-lab", "@type": ["Lab", "Item"], "@id": "/labs/jennifer-cremins-lab/", "display_title": "Jennifer Cremins, UPENN", "status": "current", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}], "external_references": [], "track_and_facet_info": {"dataset": "Hi-C on HCT116", "condition": "wild-type", "experimental_lab": "Jennifer Cremins, UPENN", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "Arima - A1, A2", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:19:42.701785+00:00"}}, {"file_classification": "processed file", "display_title": "4DNFIYKBWW4V.mcool", "file_type": "contact matrix", "md5sum": "31140a9a16f722c7741dd6a1c55fa2ce", "@id": "/files-processed/4DNFIYKBWW4V/", "file_type_detailed": "contact matrix (mcool)", "file_size": 2266682470, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/60923cb7-1dfa-405f-ae73-06a2e5c141a9/4DNFIYKBWW4V.mcool", "uuid": "60923cb7-1dfa-405f-ae73-06a2e5c141a9", "href": "/files-processed/4DNFIYKBWW4V/@@download/4DNFIYKBWW4V.mcool", "notes_to_tsv": ["WARNING - Due to a bug in the version of cooler (0.8.3) used in the current 4DN standard Hi-C processing pipeline some pixels may occur mulitple times at a single resolution with different counts being reported for each occurence.  This duplication does not affect the higlass display of these files, howevver, downstream analyses using this file may encounter issues due to this pixel duplication.  The counts from the duplicate pixels can be aggregated to determine the correct count value at that location. If this issue is problematic for your needs you should consider regenerating the matrices from the merged pairs file of the associated dataset using a more recent version of cooler.  We are working to update the pipeline but do not yet have a predicted date for when this issue will be resolved."], "accession": "4DNFIYKBWW4V", "status": "released", "higlass_uid": "7fc6f5cf-98c8-4af0-a795-af681e5e695d", "genome_assembly": "GRCh38", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/mcool/", "display_title": "mcool", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "upload_key": "60923cb7-1dfa-405f-ae73-06a2e5c141a9/4DNFIYKBWW4V.mcool", "@type": ["FileProcessed", "File", "Item"], "quality_metric": {"@type": ["QualityMetricMcool", "QualityMetric", "Item"], "overall_quality_status": "PASS", "display_title": "QualityMetricMcool from 2021-11-03", "@id": "/quality-metrics-mcool/f2d1e521-0887-4142-a828-9948efaa8802/", "status": "released", "uuid": "f2d1e521-0887-4142-a828-9948efaa8802", "quality_metric_summary": [{"title": "Failed Balancing", "value": "None", "tooltip": "Resolutions where balancing failed", "numberType": "string"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "4DN DCIC, HMS", "status": "current", "name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"name": "jennifer-cremins-lab", "@type": ["Lab", "Item"], "@id": "/labs/jennifer-cremins-lab/", "display_title": "Jennifer Cremins, UPENN", "status": "current", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}], "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"uuid": "9cccc019-48d3-47ea-be8d-e824050f5fc9", "status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIYKBWW4V - contact matrix for HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G) in situ Hi-C Arima - A1, A2", "@id": "/higlass-view-configs/9cccc019-48d3-47ea-be8d-e824050f5fc9/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "external_references": [], "track_and_facet_info": {"dataset": "Hi-C on HCT116", "condition": "wild-type", "experimental_lab": "Jennifer Cremins, UPENN", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "Arima - A1, A2", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "4DN DCIC, HMS", "track_title": "contact matrix for HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G) in situ Hi-C Arima - A1, A2"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-08-25T17:48:40.218486+00:00"}}, {"file_classification": "processed file", "display_title": "4DNFIG49IPR6.bed.gz", "file_type": "boundaries", "md5sum": "d947aa77b6ace12a8ee615548ad0e831", "@id": "/files-processed/4DNFIG49IPR6/", "file_type_detailed": "boundaries (bed)", "file_size": 136353, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/cdd45ad0-e089-4879-a89a-9a488657dad6/4DNFIG49IPR6.bed.gz", "uuid": "cdd45ad0-e089-4879-a89a-9a488657dad6", "href": "/files-processed/4DNFIG49IPR6/@@download/4DNFIG49IPR6.bed.gz", "accession": "4DNFIG49IPR6", "status": "released", "higlass_uid": "Lw6EY_32TJOL-_4qxi4Gxg", "genome_assembly": "GRCh38", "file_format": {"status": "released", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bed/", "display_title": "bed", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "upload_key": "cdd45ad0-e089-4879-a89a-9a488657dad6/4DNFIG49IPR6.bed.gz", "@type": ["FileProcessed", "File", "Item"], "extra_files": [{"use_for": "visualization", "href": "/files-processed/4DNFIG49IPR6/@@download/4DNFIG49IPR6.beddb", "md5sum": "32a9cd00750204019510c538b60f2ccc", "file_size": 1580032, "file_format": {"status": "released", "display_title": "beddb", "uuid": "76dc8c06-67d8-487b-8fc8-d841752a0b60", "file_format": "beddb", "@type": ["FileFormat", "Item"], "@id": "/file-formats/beddb/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"display_title": "4DN DCIC, HMS", "status": "current", "name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"name": "jennifer-cremins-lab", "@type": ["Lab", "Item"], "@id": "/labs/jennifer-cremins-lab/", "display_title": "Jennifer Cremins, UPENN", "status": "current", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}], "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"uuid": "5a0b9eb4-0f8b-4817-a34d-59df67c5e5b4", "status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIG49IPR6 - boundaries for HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G) in situ Hi-C Arima - A1, A2", "@id": "/higlass-view-configs/5a0b9eb4-0f8b-4817-a34d-59df67c5e5b4/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "external_references": [], "track_and_facet_info": {"dataset": "Hi-C on HCT116", "condition": "wild-type", "experimental_lab": "Jennifer Cremins, UPENN", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "Arima - A1, A2", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "4DN DCIC, HMS", "track_title": "boundaries for HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G) in situ Hi-C Arima - A1, A2"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-21T14:46:23.276982+00:00"}}, {"file_classification": "processed file", "display_title": "4DNFIWTWQ8GQ.bw", "file_type": "insulation score-diamond", "md5sum": "cec41301a03107551ff4af616b70d3bd", "@id": "/files-processed/4DNFIWTWQ8GQ/", "file_type_detailed": "insulation score-diamond (bw)", "file_size": 8203565, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/df1d1612-3f0c-41aa-a2d7-23405d31bf26/4DNFIWTWQ8GQ.bw", "uuid": "df1d1612-3f0c-41aa-a2d7-23405d31bf26", "href": "/files-processed/4DNFIWTWQ8GQ/@@download/4DNFIWTWQ8GQ.bw", "accession": "4DNFIWTWQ8GQ", "status": "released", "higlass_uid": "622f962a-7c68-451f-9d7c-dbb529615673", "genome_assembly": "GRCh38", "file_format": {"status": "released", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "display_title": "bw", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "upload_key": "df1d1612-3f0c-41aa-a2d7-23405d31bf26/4DNFIWTWQ8GQ.bw", "@type": ["FileProcessed", "File", "Item"], "lab": {"display_title": "4DN DCIC, HMS", "status": "current", "name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"name": "jennifer-cremins-lab", "@type": ["Lab", "Item"], "@id": "/labs/jennifer-cremins-lab/", "display_title": "Jennifer Cremins, UPENN", "status": "current", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}], "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"uuid": "5288ae54-3d5b-4879-bef0-128aa92cdbd3", "status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIWTWQ8GQ - insulation score-diamond for HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G) in situ Hi-C Arima - A1, A2", "@id": "/higlass-view-configs/5288ae54-3d5b-4879-bef0-128aa92cdbd3/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "external_references": [], "track_and_facet_info": {"dataset": "Hi-C on HCT116", "condition": "wild-type", "experimental_lab": "Jennifer Cremins, UPENN", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "Arima - A1, A2", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "4DN DCIC, HMS", "track_title": "insulation score-diamond for HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G) in situ Hi-C Arima - A1, A2"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-21T14:46:28.186994+00:00"}}, {"file_classification": "processed file", "display_title": "4DNFIPPNYV71.bw", "file_type": "compartments", "md5sum": "412e6f7e0f817e25a908428da8a71df8", "@id": "/files-processed/4DNFIPPNYV71/", "file_type_detailed": "compartments (bw)", "file_size": 208910, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/4870a162-3b31-4f86-adca-f323d8b06404/4DNFIPPNYV71.bw", "uuid": "4870a162-3b31-4f86-adca-f323d8b06404", "href": "/files-processed/4DNFIPPNYV71/@@download/4DNFIPPNYV71.bw", "accession": "4DNFIPPNYV71", "status": "released", "higlass_uid": "f2fa7a4d-32b4-44b8-8305-dcbc43769117", "genome_assembly": "GRCh38", "file_format": {"status": "released", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "display_title": "bw", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "upload_key": "4870a162-3b31-4f86-adca-f323d8b06404/4DNFIPPNYV71.bw", "@type": ["FileProcessed", "File", "Item"], "lab": {"display_title": "4DN DCIC, HMS", "status": "current", "name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"name": "jennifer-cremins-lab", "@type": ["Lab", "Item"], "@id": "/labs/jennifer-cremins-lab/", "display_title": "Jennifer Cremins, UPENN", "status": "current", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}], "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"uuid": "b2bf0de6-e251-45e0-9e10-868c357fc95d", "status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIPPNYV71 - compartments for HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G) in situ Hi-C Arima - A1, A2", "@id": "/higlass-view-configs/b2bf0de6-e251-45e0-9e10-868c357fc95d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "external_references": [], "track_and_facet_info": {"dataset": "Hi-C on HCT116", "condition": "wild-type", "experimental_lab": "Jennifer Cremins, UPENN", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "Arima - A1, A2", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "4DN DCIC, HMS", "track_title": "compartments for HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G) in situ Hi-C Arima - A1, A2"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-21T14:46:13.800912+00:00"}}], "project_release": "2021-11-10", "contributing_labs": [{"@type": ["Lab", "Item"], "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "status": "current", "correspondence": [{"contact_email": "Z2lsYmVydEBzZGJyaS5vcmc=", "@id": "/users/1dbb8e49-38e4-4154-a97c-af8176a58c44/", "display_title": "David Gilbert"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "experiments_in_set": [{"display_title": "in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G) with Arima - A1, A2 - 4DNEXN474APC", "files": [{"status": "released", "file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/2886cca3-3f0f-4f71-a642-088f6d6dfe46/4DNFIKZ7ZNRN.fastq.gz", "paired_end": "1", "accession": "4DNFIKZ7ZNRN", "uuid": "2886cca3-3f0f-4f71-a642-088f6d6dfe46", "file_size": 9755176075, "display_title": "4DNFIKZ7ZNRN.fastq.gz", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIKZ7ZNRN/", "upload_key": "2886cca3-3f0f-4f71-a642-088f6d6dfe46/4DNFIKZ7ZNRN.fastq.gz", "md5sum": "94fbb499d69423f53d449b561db04119", "file_type_detailed": "reads (fastq)", "file_type": "reads", "href": "/files-fastq/4DNFIKZ7ZNRN/@@download/4DNFIKZ7ZNRN.fastq.gz", "quality_metric": {"status": "released", "Sequence length": "35-37", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/abe27734-69bd-40cf-84e3-ef8e131baab0/", "Total Sequences": 416370447, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIKZ7ZNRN/fastqc_report.html", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2021-11-01", "uuid": "abe27734-69bd-40cf-84e3-ef8e131baab0", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/jennifer-cremins-lab/", "name": "jennifer-cremins-lab", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "display_title": "Jennifer Cremins, UPENN", "@type": ["Lab", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}, "contributing_labs": [{"name": "david-gilbert-lab", "@id": "/labs/david-gilbert-lab/", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "display_title": "David Gilbert, SDBRI", "@type": ["Lab", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIF2Y5P3F.fastq.gz", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIF2Y5P3F/", "file_type": "reads", "uuid": "5e4e89d6-b3f9-4011-9818-9450c981bd26", "accession": "4DNFIF2Y5P3F", "file_format": {"status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "file_format": "fastq", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Jennifer Cremins, UPENN", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on HCT116", "condition": "wild-type", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "Jennifer Cremins, UPENN"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/5e4e89d6-b3f9-4011-9818-9450c981bd26/4DNFIF2Y5P3F.fastq.gz", "paired_end": "2", "accession": "4DNFIF2Y5P3F", "uuid": "5e4e89d6-b3f9-4011-9818-9450c981bd26", "file_size": 9994373489, "display_title": "4DNFIF2Y5P3F.fastq.gz", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIF2Y5P3F/", "upload_key": "5e4e89d6-b3f9-4011-9818-9450c981bd26/4DNFIF2Y5P3F.fastq.gz", "md5sum": "5448110dec33dbf84f25e19dc0bd014a", "file_type_detailed": "reads (fastq)", "file_type": "reads", "href": "/files-fastq/4DNFIF2Y5P3F/@@download/4DNFIF2Y5P3F.fastq.gz", "quality_metric": {"status": "released", "Sequence length": "35-37", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/7aabf65d-bbe9-4eb1-8816-1b754d87260e/", "Total Sequences": 416370447, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIF2Y5P3F/fastqc_report.html", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2021-11-01", "uuid": "7aabf65d-bbe9-4eb1-8816-1b754d87260e", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/jennifer-cremins-lab/", "name": "jennifer-cremins-lab", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "display_title": "Jennifer Cremins, UPENN", "@type": ["Lab", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}, "contributing_labs": [{"name": "david-gilbert-lab", "@id": "/labs/david-gilbert-lab/", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "display_title": "David Gilbert, SDBRI", "@type": ["Lab", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIKZ7ZNRN.fastq.gz", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFIKZ7ZNRN/", "file_type": "reads", "uuid": "2886cca3-3f0f-4f71-a642-088f6d6dfe46", "accession": "4DNFIKZ7ZNRN", "file_format": {"status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "file_format": "fastq", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Jennifer Cremins, UPENN", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on HCT116", "condition": "wild-type", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "Jennifer Cremins, UPENN"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "accession": "4DNEXN474APC", "@id": "/experiments-hi-c/4DNEXN474APC/", "uuid": "f96906f8-4595-4268-b440-ab51bc933e9b", "crosslinking_method": "1% Formaldehyde", "status": "released", "@type": ["ExperimentHiC", "Experiment", "Item"], "processed_files": [{"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/256a01c7-2aa9-47ec-bcf9-15c93f56aa77/4DNFIFVI5GB4.bam", "file_type_detailed": "alignments (bam)", "file_size": 35311791893, "file_classification": "processed file", "md5sum": "dfd1e0aeeb45acbf093a1d0c03deedd4", "accession": "4DNFIFVI5GB4", "display_title": "4DNFIFVI5GB4.bam", "upload_key": "256a01c7-2aa9-47ec-bcf9-15c93f56aa77/4DNFIFVI5GB4.bam", "@id": "/files-processed/4DNFIFVI5GB4/", "file_type": "alignments", "href": "/files-processed/4DNFIFVI5GB4/@@download/4DNFIFVI5GB4.bam", "@type": ["FileProcessed", "File", "Item"], "genome_assembly": "GRCh38", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "status": "released", "@id": "/file-formats/bam/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "uuid": "256a01c7-2aa9-47ec-bcf9-15c93f56aa77", "quality_metric": {"@id": "/quality-metrics-bamqc/3c345e9e-3cfc-4b8a-a25d-0c08169fb77e/", "display_title": "QualityMetricBamqc from 2021-11-02", "uuid": "3c345e9e-3cfc-4b8a-a25d-0c08169fb77e", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "status": "released", "quality_metric_summary": [{"title": "Total Reads", "value": "416370447", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "21.87", "tooltip": "Percent of total reads (=91.06m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "21.583", "tooltip": "Percent of total reads (=89.87m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "7.448", "tooltip": "Percent of total reads (=31.01m)", "numberType": "percent"}, {"title": "Walks", "value": "0.0", "tooltip": "Percent of total reads (=0.0m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.145", "tooltip": "Percent of total reads (=0.6m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"status": "current", "@type": ["Lab", "Item"], "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "display_title": "Jennifer Cremins, UPENN", "name": "jennifer-cremins-lab", "@id": "/labs/jennifer-cremins-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Jennifer Cremins, UPENN", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on HCT116", "condition": "wild-type", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "last_modified": {"date_modified": "2023-04-14T15:19:21.508170+00:00"}}, {"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/60978ae1-0a61-49f3-92d7-9ed75d428a16/4DNFIKWG53DQ.pairs.gz", "file_type_detailed": "contact list-replicate (pairs)", "file_size": 4429670507, "file_classification": "processed file", "md5sum": "a2047a65200afd97ab4a5397a01ae64c", "accession": "4DNFIKWG53DQ", "display_title": "4DNFIKWG53DQ.pairs.gz", "upload_key": "60978ae1-0a61-49f3-92d7-9ed75d428a16/4DNFIKWG53DQ.pairs.gz", "@id": "/files-processed/4DNFIKWG53DQ/", "file_type": "contact list-replicate", "href": "/files-processed/4DNFIKWG53DQ/@@download/4DNFIKWG53DQ.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "genome_assembly": "GRCh38", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "pairs", "status": "released", "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "uuid": "60978ae1-0a61-49f3-92d7-9ed75d428a16", "quality_metric": {"@id": "/quality-metrics-pairsqc/87d68e56-79a8-413c-9ab7-7847999189e5/", "display_title": "QualityMetricPairsqc from 2021-11-02", "uuid": "87d68e56-79a8-413c-9ab7-7847999189e5", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "status": "released", "Total reads": 204432068, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIKWG53DQ/pairsqc_report.html", "quality_metric_summary": [{"title": "Filtered Reads", "value": "204432068", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "60.704", "tooltip": "Percent of filtered reads (=124.1m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "20.542", "tooltip": "Percent of filtered reads (=41.99m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "18.755", "tooltip": "Percent of filtered reads (=38.34m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"status": "current", "@type": ["Lab", "Item"], "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "display_title": "Jennifer Cremins, UPENN", "name": "jennifer-cremins-lab", "@id": "/labs/jennifer-cremins-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}], "extra_files": [{"md5sum": "365d4149911e5fa71dcbb37888d5bc8f", "file_size": 25475089, "href": "/files-processed/4DNFIKWG53DQ/@@download/4DNFIKWG53DQ.pairs.gz.px2", "file_format": {"file_format": "pairs_px2", "@id": "/file-formats/pairs_px2/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "display_title": "pairs_px2", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Jennifer Cremins, UPENN", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on HCT116", "condition": "wild-type", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "last_modified": {"date_modified": "2023-04-21T14:37:04.232130+00:00"}}], "other_processed_files": [{"type": "preliminary", "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.", "files": [{"@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIS3EFVO2/", "file_size": 35050433308, "file_type": "alignments", "status": "released", "file_type_detailed": "alignments (bam)", "accession": "4DNFIS3EFVO2", "genome_assembly": "GRCh38", "md5sum": "c5c9016c883661507cda2a84fe342864", "href": "/files-processed/4DNFIS3EFVO2/@@download/4DNFIS3EFVO2.bam", "uuid": "2d59bec0-c8df-4266-ba4d-5ad299da1f3b", "display_title": "4DNFIS3EFVO2.bam", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/2d59bec0-c8df-4266-ba4d-5ad299da1f3b/4DNFIS3EFVO2.bam", "file_format": {"@type": ["FileFormat", "Item"], "file_format": "bam", "status": "released", "display_title": "bam", "@id": "/file-formats/bam/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "contributing_labs": [{"status": "current", "display_title": "Jennifer Cremins, UPENN", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "name": "jennifer-cremins-lab", "@type": ["Lab", "Item"], "@id": "/labs/jennifer-cremins-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}], "last_modified": {"date_modified": "2024-08-08T00:19:11.572126+00:00"}, "track_and_facet_info": {"experimental_lab": "Jennifer Cremins, UPENN", "experiment_type": "in situ Hi-C", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on HCT116", "condition": "wild-type", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "4DN DCIC, HMS"}}, {"@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIHHZ62B4/", "file_size": 4106062396, "file_type": "contact list-replicate", "status": "released", "file_type_detailed": "contact list-replicate (pairs)", "accession": "4DNFIHHZ62B4", "genome_assembly": "GRCh38", "md5sum": "fb8b7278b15342acd5d74583ccb8e838", "href": "/files-processed/4DNFIHHZ62B4/@@download/4DNFIHHZ62B4.pairs.gz", "uuid": "74641890-deb6-4941-915d-d163413a6636", "display_title": "4DNFIHHZ62B4.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/74641890-deb6-4941-915d-d163413a6636/4DNFIHHZ62B4.pairs.gz", "file_format": {"@type": ["FileFormat", "Item"], "file_format": "pairs", "status": "released", "display_title": "pairs", "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "quality_metric": {"status": "released", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIHHZ62B4/pairsqc_report.html", "uuid": "9d4715ee-1002-41b0-8e95-c73724a36b55", "display_title": "QualityMetricPairsqc from 2024-07-04", "overall_quality_status": "PASS", "@id": "/quality-metrics-pairsqc/9d4715ee-1002-41b0-8e95-c73724a36b55/", "quality_metric_summary": [{"title": "Filtered Reads", "value": "204430265", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "60.704", "tooltip": "Percent of filtered reads (=124.1m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "20.541", "tooltip": "Percent of filtered reads (=41.99m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "18.755", "tooltip": "Percent of filtered reads (=38.34m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "contributing_labs": [{"status": "current", "display_title": "Jennifer Cremins, UPENN", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "name": "jennifer-cremins-lab", "@type": ["Lab", "Item"], "@id": "/labs/jennifer-cremins-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}], "last_modified": {"date_modified": "2024-08-08T00:14:45.384379+00:00"}, "track_and_facet_info": {"experimental_lab": "Jennifer Cremins, UPENN", "experiment_type": "in situ Hi-C", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on HCT116", "condition": "wild-type", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "4DN DCIC, HMS"}}]}], "digestion_enzyme": {"uuid": "1b967af3-f275-4480-93d7-c6ce62a908c6", "status": "released", "name": "Arima - A1, A2", "@id": "/enzymes/Arima%20-%20A1,%20A2/", "display_title": "Arima - A1, A2", "@type": ["Enzyme", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "biosample": {"modifications_summary": "None", "treatments_summary": "None", "@type": ["Biosample", "Item"], "uuid": "331b4805-e5fa-4407-bd0c-c5166a93651d", "biosample_category": ["Tier 2"], "biosource_summary": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "@id": "/biosamples/4DNBSJY6PP9M/", "display_title": "4DNBSJY6PP9M", "accession": "4DNBSJY6PP9M", "biosample_type": "immortalized cells", "status": "released", "biosource": [{"display_title": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G) - 4DNSRJ3TG8FL", "@type": ["Biosource", "Item"], "biosource_type": "immortalized cell line", "@id": "/biosources/4DNSRJ3TG8FL/", "status": "released", "cell_line_tier": "Unclassified", "accession": "4DNSRJ3TG8FL", "uuid": "9b648444-2b84-449a-b6ca-c879d518866c", "organism": {"status": "released", "name": "human", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "scientific_name": "Homo sapiens", "@id": "/organisms/9606/", "@type": ["Organism", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"uuid": "49d090b2-5326-40ce-9c19-7a214c682272", "status": "released", "preferred_name": "HCT116", "term_name": "HCT116", "@id": "/ontology-terms/EFO:0002824/", "synonyms": ["HCT-116 cell", "HCT116 cell"], "display_title": "HCT116", "@type": ["OntologyTerm", "Item"], "term_id": "EFO:0002824", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "display_title": "cell", "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "display_title": "cell", "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["large bowel", "posterior intestine"], "@type": ["OntologyTerm", "Item"], "uuid": "3e39f551-bc0b-4bee-b932-29d71956fb94", "@id": "/ontology-terms/UBERON:0001155/", "status": "released", "term_name": "colon", "preferred_name": "colon", "display_title": "colon", "term_id": "UBERON:0001155", "slim_terms": [{"display_title": "large intestine", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "111174bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0000059/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "digestive system", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "111129bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0001007/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"status": "released", "@id": "/biosample-cell-cultures/9d0448d0-ff0e-47d3-a6d7-47d44151ff38/", "in_vitro_differentiated": "No", "uuid": "9d0448d0-ff0e-47d3-a6d7-47d44151ff38", "@type": ["BiosampleCellCulture", "Item"], "display_title": "BiosampleCellCulture from 2021-10-30", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing morphology_image"], "badge": {"title": "Biosample Metadata Incomplete", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "@id": "/badges/biosample-metadata-incomplete/", "badge_classification": "Warning", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "display_title": "Biosample Metadata Incomplete", "warning": "Biosample Metadata Incomplete", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-icon.svg", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "tissue_organ_info": {"organ_system": ["large intestine", "digestive system"], "tissue_source": "colon"}}, "experiment_type": {"assay_subclass_short": "Hi-C", "status": "released", "@id": "/experiment-types/in-situ-hi-c/", "assay_classification": "3C via Ligation", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "@type": ["ExperimentType", "Item"], "title": "in situ Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "display_title": "in situ Hi-C", "experiment_category": "Sequencing", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "experiment_categorizer": {"combined": "Enzyme: Arima - A1, A2", "value": "Arima - A1, A2", "field": "Enzyme"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2024-07-16T15:02:01.281754+00:00"}}, {"display_title": "in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G) with Arima - A1, A2 - 4DNEX7S1OYDN", "files": [{"status": "released", "file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/0e88b43c-5c49-40a2-b28d-2bfb6d854639/4DNFI1ME4II4.fastq.gz", "paired_end": "1", "accession": "4DNFI1ME4II4", "uuid": "0e88b43c-5c49-40a2-b28d-2bfb6d854639", "file_size": 7546143107, "display_title": "4DNFI1ME4II4.fastq.gz", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI1ME4II4/", "upload_key": "0e88b43c-5c49-40a2-b28d-2bfb6d854639/4DNFI1ME4II4.fastq.gz", "md5sum": "2bc1b0eb9f85f0aff01566614efbb65c", "file_type_detailed": "reads (fastq)", "file_type": "reads", "href": "/files-fastq/4DNFI1ME4II4/@@download/4DNFI1ME4II4.fastq.gz", "quality_metric": {"status": "released", "Sequence length": "35-37", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/913e94b3-42b9-4022-9c5d-7715956afc93/", "Total Sequences": 320410322, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI1ME4II4/fastqc_report.html", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2021-11-01", "uuid": "913e94b3-42b9-4022-9c5d-7715956afc93", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/jennifer-cremins-lab/", "name": "jennifer-cremins-lab", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "display_title": "Jennifer Cremins, UPENN", "@type": ["Lab", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}, "contributing_labs": [{"name": "david-gilbert-lab", "@id": "/labs/david-gilbert-lab/", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "display_title": "David Gilbert, SDBRI", "@type": ["Lab", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFITA6W68I.fastq.gz", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFITA6W68I/", "file_type": "reads", "uuid": "b1260ea3-c879-4403-a37d-3b3bbc7a5855", "accession": "4DNFITA6W68I", "file_format": {"status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "file_format": "fastq", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Jennifer Cremins, UPENN", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on HCT116", "condition": "wild-type", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "Jennifer Cremins, UPENN"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "file_classification": "raw file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/b1260ea3-c879-4403-a37d-3b3bbc7a5855/4DNFITA6W68I.fastq.gz", "paired_end": "2", "accession": "4DNFITA6W68I", "uuid": "b1260ea3-c879-4403-a37d-3b3bbc7a5855", "file_size": 7711266054, "display_title": "4DNFITA6W68I.fastq.gz", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFITA6W68I/", "upload_key": "b1260ea3-c879-4403-a37d-3b3bbc7a5855/4DNFITA6W68I.fastq.gz", "md5sum": "e3fed0789ef8e3bb883b6ce49493dd69", "file_type_detailed": "reads (fastq)", "file_type": "reads", "href": "/files-fastq/4DNFITA6W68I/@@download/4DNFITA6W68I.fastq.gz", "quality_metric": {"status": "released", "Sequence length": "35-37", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/be27876f-305d-4408-bd60-93772868f4b4/", "Total Sequences": 320410322, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFITA6W68I/fastqc_report.html", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2021-11-01", "uuid": "be27876f-305d-4408-bd60-93772868f4b4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@id": "/labs/jennifer-cremins-lab/", "name": "jennifer-cremins-lab", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "display_title": "Jennifer Cremins, UPENN", "@type": ["Lab", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}, "contributing_labs": [{"name": "david-gilbert-lab", "@id": "/labs/david-gilbert-lab/", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "display_title": "David Gilbert, SDBRI", "@type": ["Lab", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFI1ME4II4.fastq.gz", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "status": "released", "@id": "/files-fastq/4DNFI1ME4II4/", "file_type": "reads", "uuid": "0e88b43c-5c49-40a2-b28d-2bfb6d854639", "accession": "4DNFI1ME4II4", "file_format": {"status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "file_format": "fastq", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Jennifer Cremins, UPENN", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on HCT116", "condition": "wild-type", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "Jennifer Cremins, UPENN"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "accession": "4DNEX7S1OYDN", "@id": "/experiments-hi-c/4DNEX7S1OYDN/", "uuid": "0906f714-2ee8-4ef4-9e02-b31069af5ea4", "crosslinking_method": "1% Formaldehyde", "status": "released", "@type": ["ExperimentHiC", "Experiment", "Item"], "processed_files": [{"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/4b1d2893-ac4e-44b9-a3d5-b042d683c76d/4DNFIKE3VGTU.bam", "file_type_detailed": "alignments (bam)", "file_size": 27644287001, "file_classification": "processed file", "md5sum": "f67b42408559b29908a46f7cf8853260", "accession": "4DNFIKE3VGTU", "display_title": "4DNFIKE3VGTU.bam", "upload_key": "4b1d2893-ac4e-44b9-a3d5-b042d683c76d/4DNFIKE3VGTU.bam", "@id": "/files-processed/4DNFIKE3VGTU/", "file_type": "alignments", "href": "/files-processed/4DNFIKE3VGTU/@@download/4DNFIKE3VGTU.bam", "@type": ["FileProcessed", "File", "Item"], "genome_assembly": "GRCh38", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "status": "released", "@id": "/file-formats/bam/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "uuid": "4b1d2893-ac4e-44b9-a3d5-b042d683c76d", "quality_metric": {"@id": "/quality-metrics-bamqc/5065e7cd-d7a4-4653-be3f-a2c7217b7841/", "display_title": "QualityMetricBamqc from 2021-11-02", "uuid": "5065e7cd-d7a4-4653-be3f-a2c7217b7841", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "status": "released", "quality_metric_summary": [{"title": "Total Reads", "value": "320410322", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "21.961", "tooltip": "Percent of total reads (=70.37m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "21.696", "tooltip": "Percent of total reads (=69.52m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "5.821", "tooltip": "Percent of total reads (=18.65m)", "numberType": "percent"}, {"title": "Walks", "value": "0.0", "tooltip": "Percent of total reads (=0.0m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.13", "tooltip": "Percent of total reads (=0.42m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"status": "current", "@type": ["Lab", "Item"], "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "display_title": "Jennifer Cremins, UPENN", "name": "jennifer-cremins-lab", "@id": "/labs/jennifer-cremins-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Jennifer Cremins, UPENN", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on HCT116", "condition": "wild-type", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "last_modified": {"date_modified": "2023-04-14T15:19:34.083136+00:00"}}, {"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f58f046d-38c0-4352-8e24-65c8922dd431/4DNFI3ZLYLK8.pairs.gz", "file_type_detailed": "contact list-replicate (pairs)", "file_size": 3517913243, "file_classification": "processed file", "md5sum": "9692b64c7b0a3e66ff2dc7fa49376ae7", "accession": "4DNFI3ZLYLK8", "display_title": "4DNFI3ZLYLK8.pairs.gz", "upload_key": "f58f046d-38c0-4352-8e24-65c8922dd431/4DNFI3ZLYLK8.pairs.gz", "@id": "/files-processed/4DNFI3ZLYLK8/", "file_type": "contact list-replicate", "href": "/files-processed/4DNFI3ZLYLK8/@@download/4DNFI3ZLYLK8.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "genome_assembly": "GRCh38", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "pairs", "status": "released", "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "uuid": "f58f046d-38c0-4352-8e24-65c8922dd431", "quality_metric": {"@id": "/quality-metrics-pairsqc/d96c716f-b9f3-4267-aac9-ad4936d6ee4c/", "display_title": "QualityMetricPairsqc from 2021-11-02", "uuid": "d96c716f-b9f3-4267-aac9-ad4936d6ee4c", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "status": "released", "Total reads": 161879210, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI3ZLYLK8/pairsqc_report.html", "quality_metric_summary": [{"title": "Filtered Reads", "value": "161879210", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "62.272", "tooltip": "Percent of filtered reads (=100.81m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "20.173", "tooltip": "Percent of filtered reads (=32.66m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "17.555", "tooltip": "Percent of filtered reads (=28.42m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"status": "current", "@type": ["Lab", "Item"], "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "display_title": "Jennifer Cremins, UPENN", "name": "jennifer-cremins-lab", "@id": "/labs/jennifer-cremins-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}], "extra_files": [{"md5sum": "5a170f6348fcd73f7f5ce805e1c938e2", "file_size": 24647331, "href": "/files-processed/4DNFI3ZLYLK8/@@download/4DNFI3ZLYLK8.pairs.gz.px2", "file_format": {"file_format": "pairs_px2", "@id": "/file-formats/pairs_px2/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "display_title": "pairs_px2", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Jennifer Cremins, UPENN", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on HCT116", "condition": "wild-type", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "last_modified": {"date_modified": "2023-04-21T14:37:00.242111+00:00"}}], "other_processed_files": [{"type": "preliminary", "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.", "files": [{"@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFILQ6V5K1/", "file_size": 27481379696, "file_type": "alignments", "status": "released", "file_type_detailed": "alignments (bam)", "accession": "4DNFILQ6V5K1", "genome_assembly": "GRCh38", "md5sum": "ad790acf248e9c1df05123ceb14cd34c", "href": "/files-processed/4DNFILQ6V5K1/@@download/4DNFILQ6V5K1.bam", "uuid": "8ec436e3-c1eb-4615-a4b9-f869ad35eb4d", "display_title": "4DNFILQ6V5K1.bam", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8ec436e3-c1eb-4615-a4b9-f869ad35eb4d/4DNFILQ6V5K1.bam", "file_format": {"@type": ["FileFormat", "Item"], "file_format": "bam", "status": "released", "display_title": "bam", "@id": "/file-formats/bam/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "contributing_labs": [{"status": "current", "display_title": "Jennifer Cremins, UPENN", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "name": "jennifer-cremins-lab", "@type": ["Lab", "Item"], "@id": "/labs/jennifer-cremins-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}], "last_modified": {"date_modified": "2024-08-08T00:14:12.797979+00:00"}, "track_and_facet_info": {"experimental_lab": "Jennifer Cremins, UPENN", "experiment_type": "in situ Hi-C", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on HCT116", "condition": "wild-type", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "4DN DCIC, HMS"}}, {"@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIJSXL9CH/", "file_size": 3261157700, "file_type": "contact list-replicate", "status": "released", "file_type_detailed": "contact list-replicate (pairs)", "accession": "4DNFIJSXL9CH", "genome_assembly": "GRCh38", "md5sum": "aa9df2ded5fd8d2b8ee1cb96cf9341a6", "href": "/files-processed/4DNFIJSXL9CH/@@download/4DNFIJSXL9CH.pairs.gz", "uuid": "91399e17-ec47-45df-81f2-44b37ae2f5ab", "display_title": "4DNFIJSXL9CH.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/91399e17-ec47-45df-81f2-44b37ae2f5ab/4DNFIJSXL9CH.pairs.gz", "file_format": {"@type": ["FileFormat", "Item"], "file_format": "pairs", "status": "released", "display_title": "pairs", "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "quality_metric": {"status": "released", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJSXL9CH/pairsqc_report.html", "uuid": "9458b097-2375-4606-9721-5108e18fb83b", "display_title": "QualityMetricPairsqc from 2024-07-04", "overall_quality_status": "PASS", "@id": "/quality-metrics-pairsqc/9458b097-2375-4606-9721-5108e18fb83b/", "quality_metric_summary": [{"title": "Filtered Reads", "value": "161878591", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "62.272", "tooltip": "Percent of filtered reads (=100.8m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "20.173", "tooltip": "Percent of filtered reads (=32.66m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "17.555", "tooltip": "Percent of filtered reads (=28.42m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "contributing_labs": [{"status": "current", "display_title": "Jennifer Cremins, UPENN", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "name": "jennifer-cremins-lab", "@type": ["Lab", "Item"], "@id": "/labs/jennifer-cremins-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}], "last_modified": {"date_modified": "2024-08-08T00:10:38.847755+00:00"}, "track_and_facet_info": {"experimental_lab": "Jennifer Cremins, UPENN", "experiment_type": "in situ Hi-C", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on HCT116", "condition": "wild-type", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "4DN DCIC, HMS"}}]}], "digestion_enzyme": {"uuid": "1b967af3-f275-4480-93d7-c6ce62a908c6", "status": "released", "name": "Arima - A1, A2", "@id": "/enzymes/Arima%20-%20A1,%20A2/", "display_title": "Arima - A1, A2", "@type": ["Enzyme", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "biosample": {"modifications_summary": "None", "treatments_summary": "None", "@type": ["Biosample", "Item"], "uuid": "78b4a084-8a6f-4480-88a4-5261701a8660", "biosample_category": ["Tier 2"], "biosource_summary": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "@id": "/biosamples/4DNBSUG4SBQQ/", "display_title": "4DNBSUG4SBQQ", "accession": "4DNBSUG4SBQQ", "biosample_type": "immortalized cells", "status": "released", "biosource": [{"display_title": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G) - 4DNSRJ3TG8FL", "@type": ["Biosource", "Item"], "biosource_type": "immortalized cell line", "@id": "/biosources/4DNSRJ3TG8FL/", "status": "released", "cell_line_tier": "Unclassified", "accession": "4DNSRJ3TG8FL", "uuid": "9b648444-2b84-449a-b6ca-c879d518866c", "organism": {"status": "released", "name": "human", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "scientific_name": "Homo sapiens", "@id": "/organisms/9606/", "@type": ["Organism", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"uuid": "49d090b2-5326-40ce-9c19-7a214c682272", "status": "released", "preferred_name": "HCT116", "term_name": "HCT116", "@id": "/ontology-terms/EFO:0002824/", "synonyms": ["HCT-116 cell", "HCT116 cell"], "display_title": "HCT116", "@type": ["OntologyTerm", "Item"], "term_id": "EFO:0002824", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "display_title": "cell", "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "display_title": "cell", "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["large bowel", "posterior intestine"], "@type": ["OntologyTerm", "Item"], "uuid": "3e39f551-bc0b-4bee-b932-29d71956fb94", "@id": "/ontology-terms/UBERON:0001155/", "status": "released", "term_name": "colon", "preferred_name": "colon", "display_title": "colon", "term_id": "UBERON:0001155", "slim_terms": [{"display_title": "large intestine", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "111174bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0000059/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "digestive system", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "111129bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0001007/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"status": "released", "@id": "/biosample-cell-cultures/342119bf-989b-458d-9328-73d4b6c1ee9e/", "in_vitro_differentiated": "No", "uuid": "342119bf-989b-458d-9328-73d4b6c1ee9e", "@type": ["BiosampleCellCulture", "Item"], "display_title": "BiosampleCellCulture from 2021-10-30", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing morphology_image"], "badge": {"title": "Biosample Metadata Incomplete", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "@id": "/badges/biosample-metadata-incomplete/", "badge_classification": "Warning", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "display_title": "Biosample Metadata Incomplete", "warning": "Biosample Metadata Incomplete", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-icon.svg", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "tissue_organ_info": {"organ_system": ["large intestine", "digestive system"], "tissue_source": "colon"}}, "experiment_type": {"assay_subclass_short": "Hi-C", "status": "released", "@id": "/experiment-types/in-situ-hi-c/", "assay_classification": "3C via Ligation", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "@type": ["ExperimentType", "Item"], "title": "in situ Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "display_title": "in situ Hi-C", "experiment_category": "Sequencing", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "experiment_categorizer": {"combined": "Enzyme: Arima - A1, A2", "value": "Arima - A1, A2", "field": "Enzyme"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2024-07-16T15:02:02.403432+00:00"}}], "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": "raw contact matrix (matrix)", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIA8L9WF6.matrix", "href": "/files-processed/4DNFIA8L9WF6/@@download/4DNFIA8L9WF6.matrix", "accession": "4DNFIA8L9WF6", "file_type": "raw contact matrix", "genome_assembly": "GRCh38", "status": "released", "file_size": 1068049030, "uuid": "355399bf-38bc-498c-b568-b7453081bf9e", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/355399bf-38bc-498c-b568-b7453081bf9e/4DNFIA8L9WF6.matrix", "@id": "/files-processed/4DNFIA8L9WF6/", "file_format": {"uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce2", "display_title": "matrix", "@id": "/file-formats/matrix/", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "f0e5ca864b6680938fc8fedb8591b51d", "lab": {"status": "current", "@type": ["Lab", "Item"], "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "name": "jennifer-cremins-lab", "@id": "/labs/jennifer-cremins-lab/", "display_title": "Jennifer Cremins, UPENN", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "Hi-C on HCT116", "condition": "wild-type", "experimental_lab": "Jennifer Cremins, UPENN", "replicate_info": "merged replicates", "experiment_bucket": "Matrices and Dot Calls - Cremins lab", "experiment_type": "in situ Hi-C", "assay_info": "Arima - A1, A2", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "Jennifer Cremins, UPENN"}, "contributing_labs": [{"status": "current", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "name": "david-gilbert-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "last_modified": {"date_modified": "2022-03-09T21:56:43.752855+00:00"}}, {"file_type_detailed": "normalized contact matrix (matrix)", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFISM6BTBO.matrix", "href": "/files-processed/4DNFISM6BTBO/@@download/4DNFISM6BTBO.matrix", "accession": "4DNFISM6BTBO", "file_type": "normalized contact matrix", "genome_assembly": "GRCh38", "status": "released", "file_size": 1066378031, "uuid": "2d62544c-416e-470b-92d3-0f3f86d1e04b", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/2d62544c-416e-470b-92d3-0f3f86d1e04b/4DNFISM6BTBO.matrix", "@id": "/files-processed/4DNFISM6BTBO/", "file_format": {"uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce2", "display_title": "matrix", "@id": "/file-formats/matrix/", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "f3a4a26fa7f455efae89336d860ab006", "lab": {"status": "current", "@type": ["Lab", "Item"], "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "name": "jennifer-cremins-lab", "@id": "/labs/jennifer-cremins-lab/", "display_title": "Jennifer Cremins, UPENN", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "Hi-C on HCT116", "condition": "wild-type", "experimental_lab": "Jennifer Cremins, UPENN", "replicate_info": "merged replicates", "experiment_bucket": "Matrices and Dot Calls - Cremins lab", "experiment_type": "in situ Hi-C", "assay_info": "Arima - A1, A2", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "Jennifer Cremins, UPENN"}, "contributing_labs": [{"status": "current", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "name": "david-gilbert-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "last_modified": {"date_modified": "2022-03-09T21:56:35.437199+00:00"}}, {"file_type_detailed": "balanced normalized contact matrix (matrix)", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI5MR78O6.matrix", "href": "/files-processed/4DNFI5MR78O6/@@download/4DNFI5MR78O6.matrix", "accession": "4DNFI5MR78O6", "file_type": "balanced normalized contact matrix", "genome_assembly": "GRCh38", "status": "released", "file_size": 1063711358, "uuid": "7ad173b4-0ba1-4ff0-b745-6349afd1247d", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/7ad173b4-0ba1-4ff0-b745-6349afd1247d/4DNFI5MR78O6.matrix", "@id": "/files-processed/4DNFI5MR78O6/", "file_format": {"uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce2", "display_title": "matrix", "@id": "/file-formats/matrix/", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "4ef184b5f8937acbfabed7a14fe126b4", "lab": {"status": "current", "@type": ["Lab", "Item"], "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "name": "jennifer-cremins-lab", "@id": "/labs/jennifer-cremins-lab/", "display_title": "Jennifer Cremins, UPENN", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "Hi-C on HCT116", "condition": "wild-type", "experimental_lab": "Jennifer Cremins, UPENN", "replicate_info": "merged replicates", "experiment_bucket": "Matrices and Dot Calls - Cremins lab", "experiment_type": "in situ Hi-C", "assay_info": "Arima - A1, A2", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "Jennifer Cremins, UPENN"}, "contributing_labs": [{"status": "current", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "name": "david-gilbert-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "last_modified": {"date_modified": "2022-03-09T21:56:28.531456+00:00"}}, {"file_type_detailed": "coordinates (bed)", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFID193V8K.bed.gz", "href": "/files-processed/4DNFID193V8K/@@download/4DNFID193V8K.bed.gz", "accession": "4DNFID193V8K", "file_type": "coordinates", "genome_assembly": "GRCh38", "status": "released", "file_size": 952599, "uuid": "0443a3a7-d90d-49b6-93cf-36d2b9ced087", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/0443a3a7-d90d-49b6-93cf-36d2b9ced087/4DNFID193V8K.bed.gz", "@id": "/files-processed/4DNFID193V8K/", "file_format": {"uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "display_title": "bed", "@id": "/file-formats/bed/", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "3b2b8f5d10cd05a7a61621b30fd6189d", "lab": {"status": "current", "@type": ["Lab", "Item"], "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "name": "jennifer-cremins-lab", "@id": "/labs/jennifer-cremins-lab/", "display_title": "Jennifer Cremins, UPENN", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experiment_type": "in situ Hi-C", "replicate_info": "4DNESNSTBMBY, 4DNES1JP4KZ1", "experiment_bucket": "reference file", "lab_name": "Jennifer Cremins, UPENN"}, "contributing_labs": [{"status": "current", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "name": "david-gilbert-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "last_modified": {"date_modified": "2022-03-09T21:56:22.227400+00:00"}}, {"file_type_detailed": "dot calls (txt)", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIOQLL854.txt", "href": "/files-processed/4DNFIOQLL854/@@download/4DNFIOQLL854.txt", "accession": "4DNFIOQLL854", "file_type": "dot calls", "genome_assembly": "GRCh38", "status": "released", "file_size": 3049554, "uuid": "e76429ac-54e1-4db4-9c67-3cb7c8442565", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e76429ac-54e1-4db4-9c67-3cb7c8442565/4DNFIOQLL854.txt", "@id": "/files-processed/4DNFIOQLL854/", "file_format": {"uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "display_title": "txt", "@id": "/file-formats/txt/", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "814c3eece7d7a47b2485f71860deaed8", "lab": {"status": "current", "@type": ["Lab", "Item"], "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "name": "jennifer-cremins-lab", "@id": "/labs/jennifer-cremins-lab/", "display_title": "Jennifer Cremins, UPENN", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "Hi-C on HCT116", "condition": "wild-type", "experimental_lab": "Jennifer Cremins, UPENN", "replicate_info": "merged replicates", "experiment_bucket": "Matrices and Dot Calls - Cremins lab", "experiment_type": "in situ Hi-C", "assay_info": "Arima - A1, A2", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "Jennifer Cremins, UPENN"}, "contributing_labs": [{"status": "current", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "name": "david-gilbert-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "last_modified": {"date_modified": "2022-03-09T21:56:20.030898+00:00"}}], "title": "Matrices and Dot Calls - Cremins lab", "description": "Contact matrices were generated and normalized by the data and used to generate dot calls for this replicate set."}, {"type": "preliminary", "files": [{"file_type_detailed": "contact list-combined (pairs)", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIEZHVNGF.pairs.gz", "href": "/files-processed/4DNFIEZHVNGF/@@download/4DNFIEZHVNGF.pairs.gz", "accession": "4DNFIEZHVNGF", "file_type": "contact list-combined", "genome_assembly": "GRCh38", "status": "released", "file_size": 6203848875, "uuid": "09508a1f-73f0-4c0e-93fb-4ea6d12aabb0", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/09508a1f-73f0-4c0e-93fb-4ea6d12aabb0/4DNFIEZHVNGF.pairs.gz", "@id": "/files-processed/4DNFIEZHVNGF/", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "6741751cef915e83bf5f3488213474ca", "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIEZHVNGF/pairsqc_report.html", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "uuid": "f34c34d0-451e-4d24-acc4-fe939b7a7e6b", "status": "released", "overall_quality_status": "PASS", "display_title": "QualityMetricPairsqc from 2024-07-08", "@id": "/quality-metrics-pairsqc/f34c34d0-451e-4d24-acc4-fe939b7a7e6b/", "quality_metric_summary": [{"title": "Filtered Reads", "value": "317073989", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "61.715", "tooltip": "Percent of filtered reads (=195.68m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "20.701", "tooltip": "Percent of filtered reads (=65.64m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "17.583", "tooltip": "Percent of filtered reads (=55.75m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "Hi-C on HCT116", "condition": "wild-type", "experimental_lab": "Jennifer Cremins, UPENN", "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": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "4DN DCIC, HMS"}, "contributing_labs": [{"status": "current", "display_title": "Jennifer Cremins, UPENN", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "@id": "/labs/jennifer-cremins-lab/", "name": "jennifer-cremins-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}], "last_modified": {"date_modified": "2024-08-08T01:59:20.796809+00:00"}}, {"file_type_detailed": "contact matrix (hic)", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI5Q92UVL.hic", "href": "/files-processed/4DNFI5Q92UVL/@@download/4DNFI5Q92UVL.hic", "accession": "4DNFI5Q92UVL", "file_type": "contact matrix", "genome_assembly": "GRCh38", "status": "released", "file_size": 3036043314, "uuid": "2b1b0dcd-996a-40b1-bf09-f2fed27c399f", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/2b1b0dcd-996a-40b1-bf09-f2fed27c399f/4DNFI5Q92UVL.hic", "@id": "/files-processed/4DNFI5Q92UVL/", "file_format": {"uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "display_title": "hic", "@id": "/file-formats/hic/", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "c434204ffb49cfec9a9f2eb356b8882d", "lab": {"status": "current", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "Hi-C on HCT116", "condition": "wild-type", "experimental_lab": "Jennifer Cremins, UPENN", "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": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "4DN DCIC, HMS"}, "contributing_labs": [{"status": "current", "display_title": "Jennifer Cremins, UPENN", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "@id": "/labs/jennifer-cremins-lab/", "name": "jennifer-cremins-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}], "last_modified": {"date_modified": "2024-08-08T01:58:36.327227+00:00"}}, {"higlass_uid": "b24c286e-4a89-4ad3-8cbe-802cc1d6c77b", "file_type_detailed": "contact matrix (mcool)", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIGKQMDWV.mcool", "href": "/files-processed/4DNFIGKQMDWV/@@download/4DNFIGKQMDWV.mcool", "accession": "4DNFIGKQMDWV", "file_type": "contact matrix", "genome_assembly": "GRCh38", "status": "released", "file_size": 2000634292, "uuid": "9e0b3232-57de-4a3d-b125-f5f396ea3968", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/9e0b3232-57de-4a3d-b125-f5f396ea3968/4DNFIGKQMDWV.mcool", "@id": "/files-processed/4DNFIGKQMDWV/", "file_format": {"uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "display_title": "mcool", "@id": "/file-formats/mcool/", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "3cd43bbfb005fb6ed5c69077aedf8a3d", "quality_metric": {"@type": ["QualityMetricMcool", "QualityMetric", "Item"], "uuid": "fbe841c9-8aea-441e-b3b9-6f76239c6c5a", "status": "released", "overall_quality_status": "PASS", "display_title": "QualityMetricMcool from 2024-07-09", "@id": "/quality-metrics-mcool/fbe841c9-8aea-441e-b3b9-6f76239c6c5a/", "quality_metric_summary": [{"title": "Failed Balancing", "value": "None", "tooltip": "Resolutions where balancing failed", "numberType": "string"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "52a633c6-3318-413c-b4bb-8f6b355ce92f", "@id": "/higlass-view-configs/52a633c6-3318-413c-b4bb-8f6b355ce92f/", "display_title": "4DNFIGKQMDWV - contact matrix for HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G) in situ Hi-C Arima - A1, A2", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "Hi-C on HCT116", "condition": "wild-type", "experimental_lab": "Jennifer Cremins, UPENN", "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": "HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G)", "lab_name": "4DN DCIC, HMS", "track_title": "contact matrix for HCT116 with Crispr generated mClover and AID-tagged WAPL, AAVS1-OsTIR1(F74G) in situ Hi-C Arima - A1, A2"}, "contributing_labs": [{"status": "current", "display_title": "Jennifer Cremins, UPENN", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "@id": "/labs/jennifer-cremins-lab/", "name": "jennifer-cremins-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}], "last_modified": {"date_modified": "2024-08-08T02:46:14.770708+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": {"status": "released", "display_title": "4DNESNSTBMBY - HiC Processing Pipeline - v0.3.0", "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "763e2528-c49a-46ff-97b4-863fab455bfe", "@id": "/higlass-view-configs/763e2528-c49a-46ff-97b4-863fab455bfe/", "description": "Supplementary Files (HiC Processing Pipeline - v0.3.0) for 4DNESNSTBMBY (Replicates of in situ Hi-C on untreated HCT116 WAPL-mAID2 cells): 4DNFIGKQMDWV", "last_modified": {"date_modified": "2024-07-17T19:32:52.712168+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "@id": "/experiment-set-replicates/4DNESNSTBMBY/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "e90460c1-69ab-499a-9c1d-589b7725f7c2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESNSTBMBY", "external_references": [], "produced_in_pub": {"@id": "/publications/ee8db237-9a92-4b72-8292-a66028a95b5b/", "short_attribution": "Emerson DJ et al. (2022)", "title": "Cohesin-mediated loop anchors confine the locations of human replication origins.", "journal": "Nature", "display_title": "Emerson DJ et al. (2022) PMID:35676475", "ID": "PMID:35676475", "date_published": "2022-06-08", "abstract": "DNA replication occurs through an intricately regulated series of molecular events and is fundamental for genome stability(1,2). At present, it is unknown how the locations of replication origins are determined in the human genome. Here we dissect the role of topologically associating domains (TADs)(3-6), subTADs(7)  and loops(8) in the positioning of replication initiation zones (IZs). We stratify TADs and subTADs by the presence of corner-dots indicative of loops and  the orientation of CTCF motifs. We find that high-efficiency, early replicating IZs localize to boundaries between adjacent corner-dot TADs anchored by high-density arrays of divergently and convergently oriented CTCF motifs. By contrast, low-efficiency IZs localize to weaker dotless boundaries. Following ablation of cohesin-mediated loop extrusion during G1, high-efficiency IZs become diffuse and delocalized at boundaries with complex CTCF motif orientations. Moreover, G1 knockdown of the cohesin unloading factor WAPL results in gained long-range loops and narrowed localization of IZs at the same boundaries. Finally, targeted deletion or insertion of specific boundaries causes local replication timing shifts consistent with IZ loss or gain, respectively. Our data support a model in which cohesin-mediated loop extrusion and stalling at a subset of genetically encoded TAD and subTAD boundaries is an essential determinant of the locations of replication origins in human S phase.", "url": "https://www.ncbi.nlm.nih.gov/pubmed/35676475", "authors": ["Emerson DJ", "Zhao PA", "Cook AL", "Barnett RJ", "Klein KN", "Saulebekova D", "Ge C", "Zhou L", "Simandi Z", "Minsk MK", "Titus KR", "Wang W", "Gong W", "Zhang D", "Yang L", "Venev SV", "Gibcus JH", "Yang H", "Sasaki T", "Kanemaki MT", "Yue F", "Dekker J", "Chen CL", "Gilbert DM", "Phillips-Cremins JE"], "@type": ["Publication", "Item"], "status": "current", "uuid": "ee8db237-9a92-4b72-8292-a66028a95b5b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"abstract": "DNA replication occurs through an intricately regulated series of molecular events and is fundamental for genome stability(1,2). At present, it is unknown how the locations of replication origins are determined in the human genome. Here we dissect the role of topologically associating domains (TADs)(3-6), subTADs(7)  and loops(8) in the positioning of replication initiation zones (IZs). We stratify TADs and subTADs by the presence of corner-dots indicative of loops and  the orientation of CTCF motifs. We find that high-efficiency, early replicating IZs localize to boundaries between adjacent corner-dot TADs anchored by high-density arrays of divergently and convergently oriented CTCF motifs. By contrast, low-efficiency IZs localize to weaker dotless boundaries. Following ablation of cohesin-mediated loop extrusion during G1, high-efficiency IZs become diffuse and delocalized at boundaries with complex CTCF motif orientations. Moreover, G1 knockdown of the cohesin unloading factor WAPL results in gained long-range loops and narrowed localization of IZs at the same boundaries. Finally, targeted deletion or insertion of specific boundaries causes local replication timing shifts consistent with IZ loss or gain, respectively. Our data support a model in which cohesin-mediated loop extrusion and stalling at a subset of genetically encoded TAD and subTAD boundaries is an essential determinant of the locations of replication origins in human S phase.", "title": "Cohesin-mediated loop anchors confine the locations of human replication origins.", "journal": "Nature", "ID": "PMID:35676475", "@type": ["Publication", "Item"], "date_published": "2022-06-08", "display_title": "Emerson DJ et al. (2022) PMID:35676475", "status": "current", "uuid": "ee8db237-9a92-4b72-8292-a66028a95b5b", "@id": "/publications/ee8db237-9a92-4b72-8292-a66028a95b5b/", "authors": ["Emerson DJ", "Zhao PA", "Cook AL", "Barnett RJ", "Klein KN", "Saulebekova D", "Ge C", "Zhou L", "Simandi Z", "Minsk MK", "Titus KR", "Wang W", "Gong W", "Zhang D", "Yang L", "Venev SV", "Gibcus JH", "Yang H", "Sasaki T", "Kanemaki MT", "Yue F", "Dekker J", "Chen CL", "Gilbert DM", "Phillips-Cremins JE"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 2, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSJY6PP9M/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing morphology_image"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}, {"parent": "/biosamples/4DNBSUG4SBQQ/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing morphology_image"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}]}, "validation-errors": []}