{"lab": {"status": "current", "uuid": "c38cf2e8-1129-48e1-b8a4-d42e88258e30", "@type": ["Lab", "Item"], "display_title": "Giacomo Cavalli, UM", "@id": "/labs/giacomo-cavalli-lab/", "title": "Giacomo Cavalli, UM", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c38cf2e8-1129-48e1-b8a4-d42e88258e30"]}}, "award": {"name": "external-award", "status": "current", "@id": "/awards/external-award/", "center": "External", "display_title": "EXTERNAL AWARD", "description": "Funding source is from outside 4DN.", "project": "External", "center_title": "External", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "study": "Gene activation (zfp608 or sox4)", "status": "released", "aliases": ["4dn-dcic-lab:dCas9_sox4gRNA"], "accession": "4DNES68MSHVU", "condition": "control - sox4 gRNA with empty dCas9", "description": "in situ Hi-C on E14Tg2-dCas9 cell line infected by sox4 gRNA", "study_group": "Disrupted or Atypical Cells", "date_created": "2019-08-12T14:59:34.089381+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "Hi-C on E14Tg2 cell line", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-08-12T14:46:17.487517+00:00"}, "public_release": "2019-12-01", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"uuid": "ee84ebfe-db70-4684-9a52-3070620cfdd0", "display_title": "in situ Hi-C on ES-E14TG2a with DpnII - 4DNEXUIOAGJ7", "accession": "4DNEXUIOAGJ7", "@type": ["ExperimentHiC", "Experiment", "Item"], "status": "released", "@id": "/experiments-hi-c/4DNEXUIOAGJ7/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"uuid": "d2507bb9-5fcb-42a6-83bd-d0b6093b7617", "display_title": "in situ Hi-C on ES-E14TG2a with DpnII - 4DNEX5O7D76E", "accession": "4DNEX5O7D76E", "@type": ["ExperimentHiC", "Experiment", "Item"], "status": "released", "@id": "/experiments-hi-c/4DNEX5O7D76E/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"status": "released", "lab": {"@type": ["Lab", "Item"], "uuid": "c38cf2e8-1129-48e1-b8a4-d42e88258e30", "display_title": "Giacomo Cavalli, UM", "@id": "/labs/giacomo-cavalli-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c38cf2e8-1129-48e1-b8a4-d42e88258e30"]}}, "contributing_labs": [], "description": "4DNES68MSHVU (in situ Hi-C on E14Tg2-dCas9 cell line infected by sox4 gRNA): 4DNFIQEYBCFU, 4DNFIJQJ9DS4, 4DNFI8I34GZ4, 4DNFIMB6DOU3", "uuid": "49259f06-a803-4e08-8749-b74dbad72b6d", "@type": ["HiglassViewConfig", "UserContent", "Item"], "award": {"status": "current", "@type": ["Award", "Item"], "display_title": "EXTERNAL AWARD", "@id": "/awards/external-award/", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/higlass-view-configs/49259f06-a803-4e08-8749-b74dbad72b6d/", "display_title": "4DNES68MSHVU - Processed files", "name": "49259f06-a803-4e08-8749-b74dbad72b6d", "filetype": "HiglassViewConfig", "title": "4DNES68MSHVU - Processed files", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}, "location": "tab:processed-files", "description": "auto_generated_higlass_view_config"}], "static_headers": [{"lab": {"@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "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": {"@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "status": "current", "@id": "/awards/1U01CA200059-01/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "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": {"@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "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": {"@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "status": "current", "@id": "/awards/1U01CA200059-01/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "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": [{"file_type": "contact list-combined", "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."], "file_classification": "processed file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/761c5083-b9bd-49be-958d-b6e437ecc288/4DNFIM4EYR7Z.pairs.gz", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "upload_key": "761c5083-b9bd-49be-958d-b6e437ecc288/4DNFIM4EYR7Z.pairs.gz", "genome_assembly": "GRCm38", "href": "/files-processed/4DNFIM4EYR7Z/@@download/4DNFIM4EYR7Z.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIM4EYR7Z", "display_title": "4DNFIM4EYR7Z.pairs.gz", "file_size": 5288712002, "file_type_detailed": "contact list-combined (pairs)", "md5sum": "04012e86bc8e34192b26c9aead2cab13", "uuid": "761c5083-b9bd-49be-958d-b6e437ecc288", "@id": "/files-processed/4DNFIM4EYR7Z/", "status": "released", "quality_metric": {"uuid": "a6bb5bad-99eb-48a0-947a-2e87a6305853", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Total reads": 398828351, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIM4EYR7Z/pairsqc_report.html", "overall_quality_status": "PASS", "@id": "/quality-metrics-pairsqc/a6bb5bad-99eb-48a0-947a-2e87a6305853/", "status": "released", "display_title": "QualityMetricPairsqc from 2019-10-28", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "398828351", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "39.383", "tooltip": "Percent of filtered reads (=157.07m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "49.459", "tooltip": "Percent of filtered reads (=197.26m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "11.158", "tooltip": "Percent of filtered reads (=44.5m)", "numberType": "percent"}]}, "lab": {"@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "@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"]}}, "contributing_labs": [{"display_title": "Giacomo Cavalli, UM", "name": "giacomo-cavalli-lab", "@id": "/labs/giacomo-cavalli-lab/", "@type": ["Lab", "Item"], "uuid": "c38cf2e8-1129-48e1-b8a4-d42e88258e30", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c38cf2e8-1129-48e1-b8a4-d42e88258e30"]}}], "extra_files": [{"md5sum": "d5fbeae16d5e7e43dbac5b307adf7723", "file_size": 9069142, "href": "/files-processed/4DNFIM4EYR7Z/@@download/4DNFIM4EYR7Z.pairs.gz.px2", "file_format": {"file_format": "pairs_px2", "display_title": "pairs_px2", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "@id": "/file-formats/pairs_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-04-06T20:26:26.731472+00:00"}, "external_references": [], "track_and_facet_info": {"dataset": "Hi-C on E14Tg2 cell line", "condition": "control - 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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."], "higlass_uid": "095b960b-51ef-4cd6-9537-08851bdaf4c0", "file_classification": "processed file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/71c94fce-2c66-4a7a-9204-1a6eaafd2bec/4DNFIQEYBCFU.mcool", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/mcool/", "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "status": "released", "display_title": "mcool", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "upload_key": "71c94fce-2c66-4a7a-9204-1a6eaafd2bec/4DNFIQEYBCFU.mcool", "genome_assembly": "GRCm38", "href": "/files-processed/4DNFIQEYBCFU/@@download/4DNFIQEYBCFU.mcool", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIQEYBCFU", "display_title": "4DNFIQEYBCFU.mcool", "file_size": 1625818246, "file_type_detailed": "contact matrix (mcool)", "md5sum": 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(2017) PMID:29053968", "@type": ["Publication", "Item"], "short_attribution": "Bonev B et al. (2017)", "uuid": "1c0ab106-2afe-4cda-bbbd-ceaea2627f37", "status": "current", "date_published": "2017-10-19", "abstract": "Chromosome conformation capture technologies have revealed important insights into genome folding. Yet, how spatial genome architecture is related to gene expression and cell fate remains unclear. We comprehensively mapped 3D chromatin  organization during mouse neural differentiation in vitro and in vivo, generating the highest-resolution Hi-C maps available to date. We found that transcription is correlated with chromatin insulation and long-range interactions, but dCas9-mediated activation is insufficient for creating TAD boundaries de novo. Additionally, we discovered long-range contacts between gene bodies of exon-rich, active genes in all cell types. During neural differentiation, contacts between active TADs become less pronounced while inactive TADs interact more strongly. An extensive Polycomb network in stem cells is disrupted, while dynamic interactions between neural transcription factors appear in vivo. Finally, cell type-specific  enhancer-promoter contacts are established concomitant to gene expression. This work shows that multiple factors influence the dynamics of chromatin interactions in development.", "url": "https://www.ncbi.nlm.nih.gov/pubmed/29053968", "authors": ["Bonev B", "Mendelson Cohen N", "Szabo Q", "Fritsch L", "Papadopoulos GL", "Lubling Y", "Xu X", "Lv X", "Hugnot JP", "Tanay A", "Cavalli G"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"status": "current", "uuid": "1c0ab106-2afe-4cda-bbbd-ceaea2627f37", "@type": ["Publication", "Item"], "ID": "PMID:29053968", "abstract": "Chromosome conformation capture technologies have revealed important insights into genome folding. Yet, how spatial genome architecture is related to gene expression and cell fate remains unclear. We comprehensively mapped 3D chromatin  organization during mouse neural differentiation in vitro and in vivo, generating the highest-resolution Hi-C maps available to date. We found that transcription is correlated with chromatin insulation and long-range interactions, but dCas9-mediated activation is insufficient for creating TAD boundaries de novo. Additionally, we discovered long-range contacts between gene bodies of exon-rich, active genes in all cell types. During neural differentiation, contacts between active TADs become less pronounced while inactive TADs interact more strongly. An extensive Polycomb network in stem cells is disrupted, while dynamic interactions between neural transcription factors appear in vivo. Finally, cell type-specific  enhancer-promoter contacts are established concomitant to gene expression. This work shows that multiple factors influence the dynamics of chromatin interactions in development.", "journal": "Cell", "authors": ["Bonev B", "Mendelson Cohen N", "Szabo Q", "Fritsch L", "Papadopoulos GL", "Lubling Y", "Xu X", "Lv X", "Hugnot JP", "Tanay A", "Cavalli G"], "@id": "/publications/1c0ab106-2afe-4cda-bbbd-ceaea2627f37/", "date_published": "2017-10-19", "display_title": "Bonev B et al. (2017) PMID:29053968", "title": "Multiscale 3D Genome Rewiring during Mouse Neural Development.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 2, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSPNCVY1Y/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing Cell Culture Details"], "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/4DNBSQV58OA8/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing Cell Culture Details"], "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": []}