{"lab": {"status": "current", "title": "Christine Disteche, UW", "display_title": "Christine Disteche, UW", "correspondence": [{"contact_email": "Y2Rpc3RlY2hAdS53YXNoaW5ndG9uLmVkdQ==", "@id": "/users/d89fb49f-f068-43c3-8e3c-6b1c68757a53/", "display_title": "Christine Disteche"}], "uuid": "53f8d746-0c48-4151-92a0-2d24ad28cb5a", "@type": ["Lab", "Item"], "@id": "/labs/christine-disteche-lab/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.53f8d746-0c48-4151-92a0-2d24ad28cb5a"]}}, "award": {"@type": ["Award", "Item"], "@id": "/awards/1U54DK107979-01/", "display_title": "UNIVERSITY OF WASHINGTON CENTER FOR NUCLEAR ORGANIZATION AND FUNCTION", "uuid": "fcc7f634-9252-499f-b79c-380795af2ddd", "description": "NOFIC: A current grand challenge in genomics involves accurately assaying, at all relevant scales, the 3D conformation of DNA in vivo and then linking conformational changes to dynamic processes such as the cell cycle, differentiation and disease. Here we propose to create the University of Washington Center for Nuclear Organization and Function, bringing together an interdisciplinary team of investigators whose diverse areas of expertise - technology development, computational modeling, and mouse and human biology - make them ideally suited to this challenge. Our overall hypothesis is that characterizing and understanding changes in genome architecture over time (the 4D nucleome) will lead to fundamental insights into human biology and disease. We will address this hypothesis by developing a combination of experimental and computational methods development, coupled with their systematic biological validation and application to development- and disease-relevant systems. On the experimental side, we will further optimize our recently developed DNase Hi- C assay, including combinatorial methods for single cells, ultimately aiming to concurrently assay nuclear architecture and gene expression within each of many single cells. On the computational side, we will extend our existing 3D modeling algorithms to account for diploidy, cell-to-cell variabilit, the hierarchical nature of genome architecture, and to explicitly model architectural changes over cell cycle and cell differentiation time scales. We will then employ several complementary computational methods to link our 4D nucleome models to existing, 1D genomics data sets. The outputs of these new experimental and computational technologies will be subjected to orthogonal validation in several well-understood model systems: human cell lines, in vivo tissues from interspecific F1 hybrid mice, mouse embryonic stem cells (ESCs) and skeletal myoblasts. We will also test specific predictions of the models in response to targeted (genome editing) or large-scale (chromosome silencing) perturbations. After initial validation and in parallel with further methods development, we will apply our new tools to the analysis of three biological systems: we will characterize the dynamics of nuclear architecture during the directed differentiation of na\u00efve human ESCs into cardiomyocytes and endothelial cells; we will test the hypothesis that cardiomyopathy-inducing mutations in the nuclear scaffolding protein, lamin A, are associated with derangements in cardiomyocyte nuclear architecture; and we will determine the changes in human cardiomyocyte nuclear architecture induced by trisomy 21. The proposed center will produce new experimental protocols for ascertaining 4D nucleome architecture, two new software toolkits for modeling the 4D nucleome and linking features of the nucleome to other types of genomic data, a variety of publicly available, large-scale 4D nucleome data sets in mouse and human systems, and fundamental insights into human biology and disease. In all of this work, we will work closely and openly with NOFIC and the 4DN Network to maximize the impact of our center and the overall program.", "name": "1U54DK107979-01", "project": "4DN", "center_title": "NOFIC - Shendure", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["disteche_lab:DNaseHiC-WG-F1-brain_repset"], "accession": "4DNESRWDFFF8", "condition": "brain", "description": "Replicates of DNase Hi-C on whole brain from an F1 adult female mouse", "study_group": "Single Time Point and Condition", "date_created": "2018-02-06T23:45:19.946625+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "DNase Hi-C on tissues", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-03-20T19:47:13.099903+00:00"}, "public_release": "2018-02-16", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-hi-c/4DNEX8EW839G/", "uuid": "25a28a99-c2c1-4de2-9158-a9bd80d5fc17", "status": "released", "display_title": "DNase Hi-C on brain with DNaseI - 4DNEX8EW839G", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEX8EW839G", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-hi-c/4DNEXB8HHA81/", "uuid": "8d56ff09-b65a-47b3-868e-b5fd976dd138", "status": "released", "display_title": "DNase Hi-C on brain with DNaseI - 4DNEXB8HHA81", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXB8HHA81", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"@id": "/higlass-view-configs/a692b717-832a-419f-9223-6dd03bfdabe1/", "status": "released", "display_title": "4DNESRWDFFF8 - Processed files", "award": {"@type": ["Award", "Item"], "display_title": "UNIVERSITY OF WASHINGTON CENTER FOR NUCLEAR ORGANIZATION AND FUNCTION", "status": "current", "@id": "/awards/1U54DK107979-01/", "uuid": "fcc7f634-9252-499f-b79c-380795af2ddd", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "display_title": "William Noble, UW", "@id": "/labs/william-noble-lab/", "uuid": "a0812d8f-a4cc-4dbe-bd22-76e6e573b5ed", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.a0812d8f-a4cc-4dbe-bd22-76e6e573b5ed"]}}], "title": "4DNESRWDFFF8 - Processed files", "lab": {"display_title": "Christine Disteche, UW", "@id": "/labs/christine-disteche-lab/", "@type": ["Lab", "Item"], "status": "current", "uuid": "53f8d746-0c48-4151-92a0-2d24ad28cb5a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.53f8d746-0c48-4151-92a0-2d24ad28cb5a"]}}, "@type": ["HiglassViewConfig", "UserContent", "Item"], "name": "a692b717-832a-419f-9223-6dd03bfdabe1", "uuid": "a692b717-832a-419f-9223-6dd03bfdabe1", "description": "4DNESRWDFFF8 (Replicates of DNase Hi-C on whole brain from an F1 adult female mouse): 4DNFIM38DJNE, 4DNFIU7YQPGZ, 4DNFIIXOHAUW, 4DNFI6WD32I8", "filetype": "HiglassViewConfig", "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": {"display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "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": "**DNase Hi-C**\n\nDNase Hi-C is a method to detect and quantify pairwise interactions between chromosome regions across the entire genome. DNase Hi-C was designed to overcome the limitations associated with restriction enzyme-based Hi-C approaches. Advances in molecular techniques led to the development of an improved version of this technique known as in situ DNase Hi-C that is dramatically simplified and easy to use.\n\nThe in situ DNase Hi-C 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. Chromatin is then randomly fragmented by DNase I. The resulting chromatin fragments are end-repaired and dA-tailed, then marked with a biotinylated internal adaptor, and proximity ligation is carried out in the intact nucleus to favor ligation events between the cross-linked DNA fragments. The resulting DNA sample contains ligation products consisting of chimeric DNA fragments that were originally in close spatial proximity in the nucleus, marked with biotin at the junction. A whole-genome chromatin interaction library is constructed by shearing the DNA, selecting the biotin-containing fragments with streptavidin magnetic beads and PCR amplification. After high throughput sequencing, analysis of the resulting paired-end sequences produces a matrix that quantitatively characterizes the whole-genome chromatin contacts.\n\nSee [Ramani et al 2016](https://www.ncbi.nlm.nih.gov/pubmed/27685100) for more details on in situ DNase Hi-C.\n\n<dl> <img style=\"width:600px;\" src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/DNAse_HIC.png\" />\n  <br/><br/>\n  <em>Image source: Ramani et. al. Nature Protocols 2016, Figure 1 </em>\n</dl>   ", "name": "item-page-headers.ExperimentType.DNasehic", "award": {"@type": ["Award", "Item"], "status": "current", "@id": "/awards/1U01CA200059-01/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Assay Description", "status": "released", "aliases": ["4dn-dcic-lab:experiment_infobox_DNase_HiC"], "options": {"filetype": "md", "collapsible": false, "default_open": false}, "date_created": "2018-10-10T14:46:27.255283+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-04-22T14:18:40.446552+00:00"}, "schema_version": "2", "@id": "/static-sections/84448fd6-ccf0-45a7-86c8-673b5686c059/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "84448fd6-ccf0-45a7-86c8-673b5686c059", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.56c9c683-bb11-471b-b590-c656f7dc03c1"]}, "display_title": "Assay Description", "external_references": [], "content": "**DNase Hi-C**\n\nDNase Hi-C is a method to detect and quantify pairwise interactions between chromosome regions across the entire genome. DNase Hi-C was designed to overcome the limitations associated with restriction enzyme-based Hi-C approaches. Advances in molecular techniques led to the development of an improved version of this technique known as in situ DNase Hi-C that is dramatically simplified and easy to use.\n\nThe in situ DNase Hi-C 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. Chromatin is then randomly fragmented by DNase I. The resulting chromatin fragments are end-repaired and dA-tailed, then marked with a biotinylated internal adaptor, and proximity ligation is carried out in the intact nucleus to favor ligation events between the cross-linked DNA fragments. The resulting DNA sample contains ligation products consisting of chimeric DNA fragments that were originally in close spatial proximity in the nucleus, marked with biotin at the junction. A whole-genome chromatin interaction library is constructed by shearing the DNA, selecting the biotin-containing fragments with streptavidin magnetic beads and PCR amplification. After high throughput sequencing, analysis of the resulting paired-end sequences produces a matrix that quantitatively characterizes the whole-genome chromatin contacts.\n\nSee [Ramani et al 2016](https://www.ncbi.nlm.nih.gov/pubmed/27685100) for more details on in situ DNase Hi-C.\n\n<dl> <img style=\"width:600px;\" src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/DNAse_HIC.png\" />\n  <br/><br/>\n  <em>Image source: Ramani et. al. Nature Protocols 2016, Figure 1 </em>\n</dl>   ", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p><strong>DNase Hi-C</strong></p>\n<p>DNase Hi-C is a method to detect and quantify pairwise interactions between chromosome regions across the entire genome. DNase Hi-C was designed to overcome the limitations associated with restriction enzyme-based Hi-C approaches. Advances in molecular techniques led to the development of an improved version of this technique known as in situ DNase Hi-C that is dramatically simplified and easy to use.</p>\n<p>The in situ DNase Hi-C 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. Chromatin is then randomly fragmented by DNase I. The resulting chromatin fragments are end-repaired and dA-tailed, then marked with a biotinylated internal adaptor, and proximity ligation is carried out in the intact nucleus to favor ligation events between the cross-linked DNA fragments. The resulting DNA sample contains ligation products consisting of chimeric DNA fragments that were originally in close spatial proximity in the nucleus, marked with biotin at the junction. A whole-genome chromatin interaction library is constructed by shearing the DNA, selecting the biotin-containing fragments with streptavidin magnetic beads and PCR amplification. After high throughput sequencing, analysis of the resulting paired-end sequences produces a matrix that quantitatively characterizes the whole-genome chromatin contacts.</p>\n<p>See <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/27685100\" rel=\"noopener noreferrer\" target=\"_blank\">Ramani et al 2016</a> for more details on in situ DNase Hi-C.</p>\n<dl> <img src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/DNAse_HIC.png\" style=\"width:600px;\"/>\n<br/><br/>\n<em>Image source: Ramani et. al. Nature Protocols 2016, Figure 1 </em>\n</dl></div>"}, {"lab": {"display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "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": "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"], "status": "current", "@id": "/awards/1U01CA200059-01/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "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", "file_type_detailed": "contact list-combined (pairs)", "@type": ["FileProcessed", "File", "Item"], "genome_assembly": "GRCm38", "accession": "4DNFIZ3RDODA", "display_title": "4DNFIZ3RDODA.pairs.gz", "uuid": "d5ed474c-b3f4-4967-8d2d-9f3f5680e093", "href": "/files-processed/4DNFIZ3RDODA/@@download/4DNFIZ3RDODA.pairs.gz", "upload_key": "d5ed474c-b3f4-4967-8d2d-9f3f5680e093/4DNFIZ3RDODA.pairs.gz", "@id": "/files-processed/4DNFIZ3RDODA/", "md5sum": "de361555ce61760d1153ae57ee6f2417", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/d5ed474c-b3f4-4967-8d2d-9f3f5680e093/4DNFIZ3RDODA.pairs.gz", "file_classification": "processed file", "status": "released", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 8382829705, "lab": {"status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "quality_metric": {"display_title": "QualityMetricPairsqc from 2018-06-22", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Total reads": 447409210, "status": "released", "@id": "/quality-metrics-pairsqc/e7d373d9-e9d7-4060-9456-52643c48f6f2/", "uuid": "e7d373d9-e9d7-4060-9456-52643c48f6f2", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIZ3RDODA/pairsqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "447409210", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "26.013", "tooltip": "Percent of filtered reads (=116.38m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "63.928", "tooltip": "Percent of filtered reads (=286.02m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "10.06", "tooltip": "Percent of filtered reads (=45.01m)", "numberType": "percent"}]}, "extra_files": [{"md5sum": "69008ba2b1bc80a2c3299bc5f1671275", "href": "/files-processed/4DNFIZ3RDODA/@@download/4DNFIZ3RDODA.pairs.gz.px2", "file_size": 17698282, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "pairs_px2", "status": "released", "@id": "/file-formats/pairs_px2/", "file_format": "pairs_px2", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "last_modified": {"date_modified": "2021-12-16T16:54:11.052124+00:00"}, "contributing_labs": [{"@type": ["Lab", "Item"], "name": "william-noble-lab", "@id": "/labs/william-noble-lab/", "display_title": "William Noble, UW", "status": "current", "uuid": "a0812d8f-a4cc-4dbe-bd22-76e6e573b5ed", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.a0812d8f-a4cc-4dbe-bd22-76e6e573b5ed"]}}, {"@type": ["Lab", "Item"], "name": "christine-disteche-lab", "@id": "/labs/christine-disteche-lab/", "display_title": "Christine Disteche, UW", "status": "current", "uuid": "53f8d746-0c48-4151-92a0-2d24ad28cb5a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.53f8d746-0c48-4151-92a0-2d24ad28cb5a"]}}], "track_and_facet_info": {"dataset": "DNase Hi-C on tissues", "condition": "brain", "experimental_lab": "Christine Disteche, UW", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "DNase Hi-C", "assay_info": "DNaseI", "biosource_name": "brain", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_type": "contact matrix", "file_type_detailed": "contact matrix (hic)", "@type": ["FileProcessed", "File", "Item"], "genome_assembly": "GRCm38", "accession": "4DNFIQ48NYOW", "display_title": "4DNFIQ48NYOW.hic", "uuid": "60d98cc6-4583-4ebe-9c5a-77fc421ef560", "href": "/files-processed/4DNFIQ48NYOW/@@download/4DNFIQ48NYOW.hic", "upload_key": "60d98cc6-4583-4ebe-9c5a-77fc421ef560/4DNFIQ48NYOW.hic", "@id": "/files-processed/4DNFIQ48NYOW/", "md5sum": "917ae52d07f3a54611b5565e3afa1040", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/60d98cc6-4583-4ebe-9c5a-77fc421ef560/4DNFIQ48NYOW.hic", "file_classification": "processed file", "status": "released", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/hic/", "display_title": "hic", "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 2246759663, "lab": {"status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "name": "4dn-dcic-lab", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "last_modified": {"date_modified": "2021-03-28T16:15:18.449645+00:00"}, "contributing_labs": [{"@type": ["Lab", "Item"], "name": "william-noble-lab", "@id": "/labs/william-noble-lab/", "display_title": "William Noble, UW", "status": "current", "uuid": "a0812d8f-a4cc-4dbe-bd22-76e6e573b5ed", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.a0812d8f-a4cc-4dbe-bd22-76e6e573b5ed"]}}, {"@type": ["Lab", "Item"], "name": "christine-disteche-lab", "@id": "/labs/christine-disteche-lab/", "display_title": "Christine Disteche, UW", "status": "current", "uuid": "53f8d746-0c48-4151-92a0-2d24ad28cb5a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.53f8d746-0c48-4151-92a0-2d24ad28cb5a"]}}], "track_and_facet_info": {"dataset": "DNase Hi-C on tissues", "condition": "brain", "experimental_lab": "Christine Disteche, UW", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "DNase Hi-C", "assay_info": "DNaseI", "biosource_name": "brain", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_type": "contact matrix", "file_type_detailed": "contact matrix (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.  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(2015)", "title": "Bipartite structure of the inactive mouse X chromosome.", "@type": ["Publication", "Item"], "uuid": "8aeb7ef2-26e2-4458-99df-64d57e97cde8", "display_title": "Deng X et al. (2015) doi:10.1186/s13059-015-0728-8", "ID": "doi:10.1186/s13059-015-0728-8", "date_published": "2015-08-07", "status": "current", "authors": ["Deng X", "Ma W", "Ramani V", "Hill A", "Yang F", "Ay F", "Berletch JB", "Blau CA", "Shendure J", "Duan Z", "Noble WS", "Disteche CM"], "@id": "/publications/8aeb7ef2-26e2-4458-99df-64d57e97cde8/", "url": "https://www.ncbi.nlm.nih.gov/pubmed/26248554", "abstract": "BACKGROUND: In mammals, one of the female X chromosomes and all imprinted genes are expressed exclusively from a single allele in somatic cells. To evaluate structural changes associated with allelic silencing, we have applied a recently  developed Hi-C assay that uses DNase I for chromatin fragmentation to mouse F1 hybrid systems. RESULTS: We find radically different conformations for the two female mouse X chromosomes. The inactive X has two superdomains of frequent intrachromosomal contacts separated by a boundary region. Comparison with the recently reported two-superdomain structure of the human inactive X shows that the genomic content of the superdomains differs between species, but part of the  boundary region is conserved and located near the Dxz4/DXZ4 locus. In mouse, the  boundary region also contains a minisatellite, Ds-TR, and both Dxz4 and Ds-TR appear to be anchored to the nucleolus. Genes that escape X inactivation do not cluster but are located near the periphery of the 3D structure, as are regions enriched in CTCF or RNA polymerase. Fewer short-range intrachromosomal contacts are detected for the inactive alleles of genes subject to X inactivation compared with the active alleles and with genes that escape X inactivation. This pattern is also evident for imprinted genes, in which more chromatin contacts are detected for the expressed allele. CONCLUSIONS: By applying a novel Hi-C method to map allelic chromatin contacts, we discover a specific bipartite organization  of the mouse inactive X chromosome that probably plays an important role in maintenance of gene silencing.", "journal": "Genome biology", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"authors": ["Deng X", "Ma W", "Ramani V", "Hill A", "Yang F", "Ay F", "Berletch JB", "Blau CA", "Shendure J", "Duan Z", "Noble WS", "Disteche CM"], "date_published": "2015-08-07", "@type": ["Publication", "Item"], "title": "Bipartite structure of the inactive mouse X chromosome.", "display_title": "Deng X et al. 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Comparison with the recently reported two-superdomain structure of the human inactive X shows that the genomic content of the superdomains differs between species, but part of the  boundary region is conserved and located near the Dxz4/DXZ4 locus. In mouse, the  boundary region also contains a minisatellite, Ds-TR, and both Dxz4 and Ds-TR appear to be anchored to the nucleolus. Genes that escape X inactivation do not cluster but are located near the periphery of the 3D structure, as are regions enriched in CTCF or RNA polymerase. Fewer short-range intrachromosomal contacts are detected for the inactive alleles of genes subject to X inactivation compared with the active alleles and with genes that escape X inactivation. This pattern is also evident for imprinted genes, in which more chromatin contacts are detected for the expressed allele. CONCLUSIONS: By applying a novel Hi-C method to map allelic chromatin contacts, we discover a specific bipartite organization  of the mouse inactive X chromosome that probably plays an important role in maintenance of gene silencing.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 2, "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}