{"lab": {"status": "current", "@id": "/labs/benjamin-rowland-lab/", "@type": ["Lab", "Item"], "title": "Benjamin Rowland, NKI", "display_title": "Benjamin Rowland, NKI", "uuid": "6e1ac73e-bdb7-4995-b003-2c31f538049a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6e1ac73e-bdb7-4995-b003-2c31f538049a"]}}, "award": {"center": "External", "@type": ["Award", "Item"], "center_title": "External", "project": "External", "description": "Funding source is from outside 4DN.", "display_title": "EXTERNAL AWARD", "status": "current", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@id": "/awards/external-award/", "name": "external-award", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "study": "Cohesin Protein Function", "badges": [{"badge": {"title": "Replicate Numbers", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "display_title": "Replicate Numbers", "badge_classification": "Warning", "warning": "Replicate Numbers", "@type": ["Badge", "Item"], "status": "released", "@id": "/badges/replicate-numbers/", "description": "Issues with replicate numbers", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Replicate set contains only a single biological replicate"]}], "status": "released", "aliases": ["4dn-dcic-lab:GSE95014_hap1_wt"], "accession": "4DNESIU6F8HF", "condition": "WT", "description": "Hi-C on Hap1 wt cells", "study_group": "Disrupted or Atypical Cells", "date_created": "2018-10-17T20:57:16.589222+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "Hi-C on HAP-1 +/- WAPL or SCC4 KO", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-07-31T14:46:09.800159+00:00"}, "public_release": "2018-12-06", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "98297166-92ef-495d-bbdf-44ae7e640b49", "@id": "/experiments-hi-c/4DNEXMF4CO8O/", "accession": "4DNEXMF4CO8O", "display_title": "in situ Hi-C on HAP-1 with MboI - 4DNEXMF4CO8O", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 1, "tec_rep_no": 2, "replicate_exp": {"@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "63d20613-cb03-4548-a18b-e3b9454cf016", "@id": "/experiments-hi-c/4DNEXZPB8C7E/", "accession": "4DNEXZPB8C7E", "display_title": "in situ Hi-C on HAP-1 with MboI - 4DNEXZPB8C7E", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 1, "tec_rep_no": 3, "replicate_exp": {"@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "081ba0dd-f92a-4885-ae1e-0aa4527e25d7", "@id": "/experiments-hi-c/4DNEX25INNTK/", "accession": "4DNEX25INNTK", "display_title": "in situ Hi-C on HAP-1 with MboI - 4DNEX25INNTK", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"award": {"uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@id": "/awards/external-award/", "status": "current", "@type": ["Award", "Item"], "display_title": "EXTERNAL AWARD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "50f52072-735c-4a0f-82c8-4fc2581deebd", "title": "4DNESIU6F8HF - Processed files", "contributing_labs": [], "name": "50f52072-735c-4a0f-82c8-4fc2581deebd", "@id": "/higlass-view-configs/50f52072-735c-4a0f-82c8-4fc2581deebd/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "display_title": "4DNESIU6F8HF - Processed files", "description": "4DNESIU6F8HF (Hi-C on Hap1 wt cells): 4DNFIT64Q7A3, 4DNFIG6JAVAH, 4DNFIXU91ODD, 4DNFI2DJ2HNF", "filetype": "HiglassViewConfig", "lab": {"status": "current", "uuid": "6e1ac73e-bdb7-4995-b003-2c31f538049a", "display_title": "Benjamin Rowland, NKI", "@type": ["Lab", "Item"], "@id": "/labs/benjamin-rowland-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6e1ac73e-bdb7-4995-b003-2c31f538049a"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}, "location": "tab:processed-files", "description": "auto_generated_higlass_view_config"}], "static_headers": [{"lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "<b>In Situ Hi-C</b>\n\n<p>\n   In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed <i>in situ</i> inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n</p>\n<p>\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n</p>\n<p>\nSee <a href=\"https://www.sciencedirect.com/science/article/pii/S0092867414014974?via%3Dihub\">Rao et al., 2014</a> for more details.\n</p>\n\n<div>\n<img style=\"width: 600px;max-width:100%;\" src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/IsHC_fig1.png\"/>\n  <br/><br/>\n  <em>Image source: Rao et al., 2014, Figure 1A</em>\n</div>", "name": "item-page-headers.ExperimentType.insituhic", "award": {"status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@type": ["Award", "Item"], "@id": "/awards/1U01CA200059-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Assay Description", "status": "released", "aliases": ["4dn-dcic-lab:experiment_infobox_hic"], "options": {"filetype": "html", "collapsible": false, "default_open": false, "convert_ext_links": true}, "date_created": "2018-09-07T18:19:43.777198+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-11-09T14:48:01.220007+00:00"}, "schema_version": "2", "@id": "/static-sections/298554ad-20e2-4449-a752-ac190123dab7/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "298554ad-20e2-4449-a752-ac190123dab7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.56c9c683-bb11-471b-b590-c656f7dc03c1"]}, "display_title": "Assay Description", "external_references": [], "content": "<b>In Situ Hi-C</b>\n\n<p>\n   In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed <i>in situ</i> inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n</p>\n<p>\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n</p>\n<p>\nSee <a href=\"https://www.sciencedirect.com/science/article/pii/S0092867414014974?via%3Dihub\">Rao et al., 2014</a> for more details.\n</p>\n\n<div>\n<img style=\"width: 600px;max-width:100%;\" src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/IsHC_fig1.png\"/>\n  <br/><br/>\n  <em>Image source: Rao et al., 2014, Figure 1A</em>\n</div>", "filetype": "html", "content_as_html": "<div class=\"html-container\"><b>In Situ Hi-C</b>\n<p>\n   In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed <i>in situ</i> inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n</p>\n<p>\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n</p>\n<p>\nSee <a href=\"https://www.sciencedirect.com/science/article/pii/S0092867414014974?via%3Dihub\" rel=\"noopener noreferrer\" target=\"_blank\">Rao et al., 2014</a> for more details.\n</p>\n<div>\n<img src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/IsHC_fig1.png\" style=\"width: 600px;max-width:100%;\"/>\n<br/><br/>\n<em>Image source: Rao et al., 2014, Figure 1A</em>\n</div></div>"}, {"lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "Some annotated bam and pairs files generated in this Experiment Set may contain distinct reads that share the same identifier. This was caused by merging fastq files with integer identifiers (eg. @1, @2) during processing.", "name": "item-page-header.ES_files_with_integer_id_issue_warning_hic", "award": {"status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@type": ["Award", "Item"], "@id": "/awards/1U01CA200059-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Note on Processed Files", "status": "released", "aliases": ["4dn-dcic-lab:files_with_integer_id_issue_warning_hic_ES"], "options": {"filetype": "md", "collapsible": true, "default_open": true}, "date_created": "2020-04-06T19:36:49.278997+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-04-19T23:58:37.106537+00:00"}, "schema_version": "2", "@id": "/static-sections/a16d9553-7158-4121-80f7-d1342213b3fa/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "a16d9553-7158-4121-80f7-d1342213b3fa", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.56c9c683-bb11-471b-b590-c656f7dc03c1"]}, "display_title": "Note on Processed Files", "external_references": [], "content": "Some annotated bam and pairs files generated in this Experiment Set may contain distinct reads that share the same identifier. This was caused by merging fastq files with integer identifiers (eg. @1, @2) during processing.", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p>Some annotated bam and pairs files generated in this Experiment Set may contain distinct reads that share the same identifier. This was caused by merging fastq files with integer identifiers (eg. @1, @2) during processing.</p></div>"}], "processed_files": [{"accession": "4DNFIOI2TOQB", "@type": ["FileProcessed", "File", "Item"], "genome_assembly": "GRCh38", "file_type_detailed": "contact list-combined (pairs)", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "display_title": "pairs", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFIOI2TOQB.pairs.gz", "notes_to_tsv": ["WARNING: some distinct reads in this file may share the same identifier because the file was generated after merging fastq files with integer identifiers (eg. @1, @2) during processing."], "md5sum": "d3c7ac88f471dae7809f4b8e9fc64fe9", "file_type": "contact list-combined", "file_classification": "processed file", "file_size": 6394621051, "upload_key": "0dee9da2-f3c1-4802-8504-d46169b0de95/4DNFIOI2TOQB.pairs.gz", "@id": "/files-processed/4DNFIOI2TOQB/", "href": "/files-processed/4DNFIOI2TOQB/@@download/4DNFIOI2TOQB.pairs.gz", "uuid": "0dee9da2-f3c1-4802-8504-d46169b0de95", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/0dee9da2-f3c1-4802-8504-d46169b0de95/4DNFIOI2TOQB.pairs.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "extra_files": [{"href": "/files-processed/4DNFIOI2TOQB/@@download/4DNFIOI2TOQB.pairs.gz.px2", "file_size": 24346248, "md5sum": "5cfc5f44f1bf587ad0270c08236c5809", "file_format": {"@id": "/file-formats/pairs_px2/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "display_title": "pairs_px2", "file_format": "pairs_px2", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"Total reads": 423311879, "status": "released", "display_title": "QualityMetricPairsqc from 2018-11-28", "uuid": "0309203f-8d41-4a7c-ad07-97d781bd2d8f", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "@id": "/quality-metrics-pairsqc/0309203f-8d41-4a7c-ad07-97d781bd2d8f/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIOI2TOQB/pairsqc_report.html", "overall_quality_status": "PASS", "quality_metric_summary": [{"title": "Filtered Reads", "value": "423311879", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "63.972", "tooltip": "Percent of filtered reads (=270.8m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "21.546", "tooltip": "Percent of filtered reads (=91.21m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "14.482", "tooltip": "Percent of filtered reads (=61.3m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"display_title": "Benjamin Rowland, NKI", "uuid": "6e1ac73e-bdb7-4995-b003-2c31f538049a", "name": "benjamin-rowland-lab", "@type": ["Lab", "Item"], "@id": "/labs/benjamin-rowland-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6e1ac73e-bdb7-4995-b003-2c31f538049a"]}}], "external_references": [], "track_and_facet_info": {"dataset": "Hi-C on HAP-1 +/- WAPL or SCC4 KO", "condition": "WT", "experimental_lab": "Benjamin Rowland, NKI", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "MboI", "biosource_name": "HAP-1", "lab_name": "4DN DCIC, HMS"}, "last_modified": {"date_modified": "2021-05-17T21:53:29.639960+00:00"}}, {"accession": "4DNFIK61ILGM", "@type": ["FileProcessed", "File", "Item"], "genome_assembly": "GRCh38", "file_type_detailed": "contact matrix (hic)", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/hic/", "display_title": "hic", "status": "released", "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFIK61ILGM.hic", "md5sum": "1f9a3f4eba4dbc381a30b1ba75cd8739", "file_type": "contact matrix", "file_classification": "processed file", "file_size": 3463571678, "upload_key": "70c0f730-5da1-4863-9b7a-6cdd31066cff/4DNFIK61ILGM.hic", "@id": "/files-processed/4DNFIK61ILGM/", "href": "/files-processed/4DNFIK61ILGM/@@download/4DNFIK61ILGM.hic", "uuid": "70c0f730-5da1-4863-9b7a-6cdd31066cff", "status": "released", "open_data_url": 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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.  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