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The replicate 1 specific files have not changed."}, {"type": "supplementary", "files": [{"@id": "/files-processed/4DNFIZCJ4CEY/", "display_title": "4DNFIZCJ4CEY.csv", "genome_assembly": "GRCm38", "accession": "4DNFIZCJ4CEY", "status": "released", "file_type": "segregation table", "href": "/files-processed/4DNFIZCJ4CEY/@@download/4DNFIZCJ4CEY.csv", "file_size": 154930025, "file_type_detailed": "segregation table (csv)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/320cb21e-0d03-4111-a7bf-4c9df68fff93/4DNFIZCJ4CEY.csv", "@type": ["FileProcessed", "File", "Item"], "uuid": "320cb21e-0d03-4111-a7bf-4c9df68fff93", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@id": "/file-formats/csv/", "display_title": "csv", "@type": ["FileFormat", "Item"], "file_format": "csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Ana Pombo, MDC", "experiment_type": "GAM", "experiment_bucket": "Pombo Lab - GAM pipeline output 40 Kb bin - UPDATED Feb 2021", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F123-CASTx129 (Tier 2)", "lab_name": "Ana Pombo, MDC"}, "last_modified": {"date_modified": "2021-02-24T22:09:09.298432+00:00"}}, {"@id": "/files-processed/4DNFIFBSQ1EO/", "display_title": "4DNFIFBSQ1EO.zip", "genome_assembly": "GRCm38", "accession": "4DNFIFBSQ1EO", "status": "released", "file_type": "normalized contact matrix", "href": "/files-processed/4DNFIFBSQ1EO/@@download/4DNFIFBSQ1EO.zip", "file_size": 959528956, "file_type_detailed": "normalized contact matrix (zip)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/4e46203f-cce1-46a5-8e78-23681d8f84a1/4DNFIFBSQ1EO.zip", "@type": ["FileProcessed", "File", "Item"], "uuid": "4e46203f-cce1-46a5-8e78-23681d8f84a1", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-44f0-91f226248b2c", "@id": "/file-formats/zip/", "display_title": "zip", "@type": ["FileFormat", "Item"], "file_format": "zip", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Ana Pombo, MDC", "experiment_type": "GAM", "experiment_bucket": "Pombo Lab - GAM pipeline output 40 Kb bin - UPDATED Feb 2021", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F123-CASTx129 (Tier 2)", "lab_name": "Ana Pombo, MDC"}, "last_modified": {"date_modified": "2021-02-24T22:09:13.278171+00:00"}}], "title": "Pombo Lab - GAM pipeline output 40 Kb bin - UPDATED Feb 2021", "description": "Results of Pombo lab GAM processing - Segregation tables and pairwise contact matrices at 40 Kb resolution. NOTE: the merged replicate files - both segregation tables and contact matrices have been updated to correct a minor processing error that resulted in a dropped column in the segregation tables - this update should not significantly alter the results, however, here we provide the most up to date 'corrected' files.  The previous files can be found in the 'archived' file collectons.  The replicate 1 specific files have not changed."}, {"type": "supplementary", "files": [{"@id": "/files-processed/4DNFIBYPZI1U/", "display_title": "4DNFIBYPZI1U.csv", "genome_assembly": "GRCm38", "accession": "4DNFIBYPZI1U", "status": "released", "file_type": "segregation table", "href": "/files-processed/4DNFIBYPZI1U/@@download/4DNFIBYPZI1U.csv", "file_size": 123973121, "file_type_detailed": "segregation table (csv)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/46972b4d-0545-4ffb-8657-92619f36b859/4DNFIBYPZI1U.csv", "@type": ["FileProcessed", "File", "Item"], "uuid": "46972b4d-0545-4ffb-8657-92619f36b859", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@id": "/file-formats/csv/", "display_title": "csv", "@type": ["FileFormat", "Item"], "file_format": "csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Ana Pombo, MDC", "experiment_type": "GAM", "experiment_bucket": "Pombo Lab - GAM pipeline output 50 Kb bin - UPDATED Feb 2021", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F123-CASTx129 (Tier 2)", "lab_name": "Ana Pombo, MDC"}, "last_modified": {"date_modified": "2021-02-24T22:09:18.370477+00:00"}}, {"@id": "/files-processed/4DNFI6N8M614/", "display_title": "4DNFI6N8M614.zip", "genome_assembly": "GRCm38", "accession": "4DNFI6N8M614", "status": "released", "file_type": "normalized contact matrix", "href": "/files-processed/4DNFI6N8M614/@@download/4DNFI6N8M614.zip", "file_size": 679540290, "file_type_detailed": "normalized contact matrix (zip)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e9e2c77f-4e42-41d8-8f9e-3c0d6f97e12c/4DNFI6N8M614.zip", "@type": ["FileProcessed", "File", "Item"], "uuid": "e9e2c77f-4e42-41d8-8f9e-3c0d6f97e12c", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-44f0-91f226248b2c", "@id": "/file-formats/zip/", "display_title": "zip", "@type": ["FileFormat", "Item"], "file_format": "zip", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Ana Pombo, MDC", "experiment_type": "GAM", "experiment_bucket": "Pombo Lab - GAM pipeline output 50 Kb bin - UPDATED Feb 2021", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F123-CASTx129 (Tier 2)", "lab_name": "Ana Pombo, MDC"}, "last_modified": {"date_modified": "2021-02-24T22:09:22.409105+00:00"}}], "title": "Pombo Lab - GAM pipeline output 50 Kb bin - UPDATED Feb 2021", "description": "Results of Pombo lab GAM processing - Segregation tables and pairwise contact matrices at 50 Kb resolution. NOTE: the merged replicate files - both segregation tables and contact matrices have been updated to correct a minor processing error that resulted in a dropped column in the segregation tables - this update should not significantly alter the results, however, here we provide the most up to date 'corrected' files.  The previous files can be found in the 'archived' file collectons.  The replicate 1 specific files have not changed."}, {"type": "supplementary", "files": [{"@id": "/files-processed/4DNFIY6GWEDR/", "display_title": "4DNFIY6GWEDR.csv", "genome_assembly": "GRCm38", "accession": "4DNFIY6GWEDR", "status": "released", "file_type": "segregation table", "href": "/files-processed/4DNFIY6GWEDR/@@download/4DNFIY6GWEDR.csv", "file_size": 62059172, "file_type_detailed": "segregation table (csv)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ac0d245c-fbad-4d75-a917-8eb8cf1d6b19/4DNFIY6GWEDR.csv", "@type": ["FileProcessed", "File", "Item"], "uuid": "ac0d245c-fbad-4d75-a917-8eb8cf1d6b19", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@id": "/file-formats/csv/", "display_title": "csv", "@type": ["FileFormat", "Item"], "file_format": "csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Ana Pombo, MDC", "experiment_type": "GAM", "experiment_bucket": "Pombo Lab - GAM pipeline output 100 Kb bin - UPDATED Feb 2021", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F123-CASTx129 (Tier 2)", "lab_name": "Ana Pombo, MDC"}, "last_modified": {"date_modified": "2021-02-24T22:09:27.381748+00:00"}}, {"@id": "/files-processed/4DNFI9IUYYF2/", "display_title": "4DNFI9IUYYF2.zip", "genome_assembly": "GRCm38", "accession": "4DNFI9IUYYF2", "status": "released", "file_type": "normalized contact matrix", "href": "/files-processed/4DNFI9IUYYF2/@@download/4DNFI9IUYYF2.zip", "file_size": 223590339, "file_type_detailed": "normalized contact matrix (zip)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/da0cd120-8365-4eff-a6a9-c1037ace6002/4DNFI9IUYYF2.zip", "@type": ["FileProcessed", "File", "Item"], "uuid": "da0cd120-8365-4eff-a6a9-c1037ace6002", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-44f0-91f226248b2c", "@id": "/file-formats/zip/", "display_title": "zip", "@type": ["FileFormat", "Item"], "file_format": "zip", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Ana Pombo, MDC", "experiment_type": "GAM", "experiment_bucket": "Pombo Lab - GAM pipeline output 100 Kb bin - UPDATED Feb 2021", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F123-CASTx129 (Tier 2)", "lab_name": "Ana Pombo, MDC"}, "last_modified": {"date_modified": "2021-02-24T22:09:31.298560+00:00"}}], "title": "Pombo Lab - GAM pipeline output 100 Kb bin - UPDATED Feb 2021", "description": "Results of Pombo lab GAM processing - Segregation tables and pairwise contact matrices at 100 Kb resolution. NOTE: the merged replicate files - both segregation tables and contact matrices have been updated to correct a minor processing error that resulted in a dropped column in the segregation tables - this update should not significantly alter the results, however, here we provide the most up to date 'corrected' files.  The previous files can be found in the 'archived' file collectons.  The replicate 1 specific files have not changed."}, {"type": "supplementary", "files": [{"@id": "/files-processed/4DNFIJU76V2U/", "display_title": "4DNFIJU76V2U.csv", "genome_assembly": "GRCm38", "accession": "4DNFIJU76V2U", "status": "released", "file_type": "segregation table", "href": "/files-processed/4DNFIJU76V2U/@@download/4DNFIJU76V2U.csv", "file_size": 24897589, "file_type_detailed": "segregation table (csv)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/316f21e6-6a95-4b07-999c-45782f1e3f22/4DNFIJU76V2U.csv", "@type": ["FileProcessed", "File", "Item"], "uuid": "316f21e6-6a95-4b07-999c-45782f1e3f22", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@id": "/file-formats/csv/", "display_title": "csv", "@type": ["FileFormat", "Item"], "file_format": "csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Ana Pombo, MDC", "experiment_type": "GAM", "experiment_bucket": "Pombo Lab - GAM pipeline output 250 Kb bin - UPDATED Feb 2021", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F123-CASTx129 (Tier 2)", "lab_name": "Ana Pombo, MDC"}, "last_modified": {"date_modified": "2021-02-24T22:09:36.215583+00:00"}}, {"@id": "/files-processed/4DNFILSM5WRT/", "display_title": "4DNFILSM5WRT.zip", "genome_assembly": "GRCm38", "accession": "4DNFILSM5WRT", "status": "released", "file_type": "normalized contact matrix", "href": "/files-processed/4DNFILSM5WRT/@@download/4DNFILSM5WRT.zip", "file_size": 43871745, "file_type_detailed": "normalized contact matrix (zip)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/179d789c-4812-44b8-9f37-b04dc252347e/4DNFILSM5WRT.zip", "@type": ["FileProcessed", "File", "Item"], "uuid": "179d789c-4812-44b8-9f37-b04dc252347e", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-44f0-91f226248b2c", "@id": "/file-formats/zip/", "display_title": "zip", "@type": ["FileFormat", "Item"], "file_format": "zip", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Ana Pombo, MDC", "experiment_type": "GAM", "experiment_bucket": "Pombo Lab - GAM pipeline output 250 Kb bin - UPDATED Feb 2021", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F123-CASTx129 (Tier 2)", "lab_name": "Ana Pombo, MDC"}, "last_modified": {"date_modified": "2021-02-24T22:09:40.317978+00:00"}}], "title": "Pombo Lab - GAM pipeline output 250 Kb bin - UPDATED Feb 2021", "description": "Results of Pombo lab GAM processing - Segregation tables and pairwise contact matrices at 250 Kb resolution. NOTE: the merged replicate files - both segregation tables and contact matrices have been updated to correct a minor processing error that resulted in a dropped column in the segregation tables - this update should not significantly alter the results, however, here we provide the most up to date 'corrected' files.  The previous files can be found in the 'archived' file collectons.  The replicate 1 specific files have not changed."}, {"type": "supplementary", "files": [{"@id": "/files-processed/4DNFIMU2M7H6/", "display_title": "4DNFIMU2M7H6.csv", "genome_assembly": "GRCm38", "accession": "4DNFIMU2M7H6", "status": "released", "file_type": "segregation table", "href": "/files-processed/4DNFIMU2M7H6/@@download/4DNFIMU2M7H6.csv", "file_size": 12531628, "file_type_detailed": "segregation table (csv)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/0fcee52d-c56f-49e3-bec8-23f40a4c01b2/4DNFIMU2M7H6.csv", "@type": ["FileProcessed", "File", "Item"], "uuid": "0fcee52d-c56f-49e3-bec8-23f40a4c01b2", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@id": "/file-formats/csv/", "display_title": "csv", "@type": ["FileFormat", "Item"], "file_format": "csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Ana Pombo, MDC", "experiment_type": "GAM", "experiment_bucket": "Pombo Lab - GAM pipeline output 500 Kb bin - UPDATED Feb 2021", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F123-CASTx129 (Tier 2)", "lab_name": "Ana Pombo, MDC"}, "last_modified": {"date_modified": "2021-02-24T22:09:44.712248+00:00"}}, {"@id": "/files-processed/4DNFISHKFB5Z/", "display_title": "4DNFISHKFB5Z.zip", "genome_assembly": "GRCm38", "accession": "4DNFISHKFB5Z", "status": "released", "file_type": "normalized contact matrix", "href": "/files-processed/4DNFISHKFB5Z/@@download/4DNFISHKFB5Z.zip", "file_size": 11645405, "file_type_detailed": "normalized contact matrix (zip)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f88f7f57-d709-4d61-8db4-fcd839b8a070/4DNFISHKFB5Z.zip", "@type": ["FileProcessed", "File", "Item"], "uuid": "f88f7f57-d709-4d61-8db4-fcd839b8a070", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-44f0-91f226248b2c", "@id": "/file-formats/zip/", "display_title": "zip", "@type": ["FileFormat", "Item"], "file_format": "zip", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Ana Pombo, MDC", "experiment_type": "GAM", "experiment_bucket": "Pombo Lab - GAM pipeline output 500 Kb bin - UPDATED Feb 2021", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F123-CASTx129 (Tier 2)", "lab_name": "Ana Pombo, MDC"}, "last_modified": {"date_modified": "2021-02-24T22:09:48.759636+00:00"}}], "title": "Pombo Lab - GAM pipeline output 500 Kb bin - UPDATED Feb 2021", "description": "Results of Pombo lab GAM processing - Segregation tables and pairwise contact matrices at 500 Kb resolution. NOTE: the merged replicate files - both segregation tables and contact matrices have been updated to correct a minor processing error that resulted in a dropped column in the segregation tables - this update should not significantly alter the results, however, here we provide the most up to date 'corrected' files.  The previous files can be found in the 'archived' file collectons.  The replicate 1 specific files have not changed."}, {"type": "supplementary", "files": [{"@id": "/files-processed/4DNFINOD31UQ/", "display_title": "4DNFINOD31UQ.csv", "genome_assembly": "GRCm38", "accession": "4DNFINOD31UQ", "status": "released", "file_type": "segregation table", "href": "/files-processed/4DNFINOD31UQ/@@download/4DNFINOD31UQ.csv", "file_size": 6349793, "file_type_detailed": "segregation table (csv)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/fa1b8367-8cd6-44e1-8e4d-b778ef382b8c/4DNFINOD31UQ.csv", "@type": ["FileProcessed", "File", "Item"], "uuid": "fa1b8367-8cd6-44e1-8e4d-b778ef382b8c", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@id": "/file-formats/csv/", "display_title": "csv", "@type": ["FileFormat", "Item"], "file_format": "csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Ana Pombo, MDC", "experiment_type": "GAM", "experiment_bucket": "Pombo Lab - GAM pipeline output 1 Mb bin - UPDATED Feb 2021", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F123-CASTx129 (Tier 2)", "lab_name": "Ana Pombo, MDC"}, "last_modified": {"date_modified": "2021-02-24T22:09:53.283739+00:00"}}, {"@id": "/files-processed/4DNFIJRX16EK/", "display_title": "4DNFIJRX16EK.zip", "genome_assembly": "GRCm38", "accession": "4DNFIJRX16EK", "status": "released", "file_type": "normalized contact matrix", "href": "/files-processed/4DNFIJRX16EK/@@download/4DNFIJRX16EK.zip", "file_size": 2927075, "file_type_detailed": "normalized contact matrix (zip)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/6db7f5e0-be22-476e-a306-c782de725e44/4DNFIJRX16EK.zip", "@type": ["FileProcessed", "File", "Item"], "uuid": "6db7f5e0-be22-476e-a306-c782de725e44", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-44f0-91f226248b2c", "@id": "/file-formats/zip/", "display_title": "zip", "@type": ["FileFormat", "Item"], "file_format": "zip", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Ana Pombo, MDC", "experiment_type": "GAM", "experiment_bucket": "Pombo Lab - GAM pipeline output 1 Mb bin - UPDATED Feb 2021", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F123-CASTx129 (Tier 2)", "lab_name": "Ana Pombo, MDC"}, "last_modified": {"date_modified": "2021-02-24T22:09:57.514478+00:00"}}], "title": "Pombo Lab - GAM pipeline output 1 Mb bin - UPDATED Feb 2021", "description": "Results of Pombo lab GAM processing - Segregation tables and pairwise contact matrices at 1 Mb resolution. NOTE: the merged replicate files - both segregation tables and contact matrices have been updated to correct a minor processing error that resulted in a dropped column in the segregation tables - this update should not significantly alter the results, however, here we provide the most up to date 'corrected' files.  The previous files can be found in the 'archived' file collectons.  The replicate 1 specific files have not changed."}], "@id": "/experiments-seq/4DNEX1KG9YVX/", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "b0fee370-48b1-443d-9163-f97b6af29cd5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "GAM on F123-CASTx129 (Tier 2) - 4DNEX1KG9YVX", "external_references": [], "experiment_sets": [{"uuid": "01b4333b-8008-4aac-b966-591b8aa98c9a", "experimentset_type": "replicate", "display_title": "4DNESRQDNG61", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "status": "released", "@id": "/experiment-set-replicates/4DNESRQDNG61/", "accession": "4DNESRQDNG61", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"display_title": "Irastorza-Azcarate I et al. (2024) PMID:38766012", "title": "Extensive folding variability between homologous chromosomes in mammalian cells.", "uuid": "cf26b7d2-d57e-467f-8509-d873abdad0bc", "@id": "/publications/cf26b7d2-d57e-467f-8509-d873abdad0bc/", "ID": "PMID:38766012", "@type": ["Publication", "Item"], "status": "current", "abstract": "Genetic variation and 3D chromatin structure have major roles in gene regulation.  Due to challenges in mapping chromatin conformation with haplotype-specific  resolution, the effects of genetic sequence variation on 3D genome structure and  gene expression imbalance remain understudied. Here, we applied Genome  Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (mESC) line with  high density of single nucleotide polymorphisms (SNPs). GAM resolved  haplotype-specific 3D genome structures with high sensitivity, revealing  extensive allelic differences in chromatin compartments, topologically  associating domains (TADs), long-range enhancer-promoter contacts, and CTCF  loops. Architectural differences often coincide with allele-specific differences  in gene expression, mediated by Polycomb repression. We show that histone genes  are expressed with allelic imbalance in mESCs, are involved in haplotype-specific  chromatin contact marked by H3K27me3, and are targets of Polycomb repression  through conditional knockouts of Ezh2 or Ring1b. Our work reveals highly distinct  3D folding structures between homologous chromosomes, and highlights their  intricate connections with allelic gene expression.", "journal": "bioRxiv : the preprint server for biology", "authors": ["Irastorza-Azcarate I", "Kukalev A", "Kempfer R", "Thieme CJ", "Mastrobuoni G", "Markowski J", "Loof G", "Sparks TM", "Brookes E", "Natarajan KN", "Sauer S", "Fisher AG", "Nicodemi M", "Ren B", "Schwarz RF", "Kempa S", "Pombo A"], "short_attribution": "Irastorza-Azcarate I et al. (2024)", "date_published": "2024-05-10", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"authors": ["Irastorza-Azcarate I", "Kukalev A", "Kempfer R", "Thieme CJ", "Mastrobuoni G", "Markowski J", "Loof G", "Sparks TM", "Brookes E", "Natarajan KN", "Sauer S", "Fisher AG", "Nicodemi M", "Ren B", "Schwarz RF", "Kempa S", "Pombo A"], "abstract": "Genetic variation and 3D chromatin structure have major roles in gene regulation.  Due to challenges in mapping chromatin conformation with haplotype-specific  resolution, the effects of genetic sequence variation on 3D genome structure and  gene expression imbalance remain understudied. Here, we applied Genome  Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (mESC) line with  high density of single nucleotide polymorphisms (SNPs). GAM resolved  haplotype-specific 3D genome structures with high sensitivity, revealing  extensive allelic differences in chromatin compartments, topologically  associating domains (TADs), long-range enhancer-promoter contacts, and CTCF  loops. Architectural differences often coincide with allele-specific differences  in gene expression, mediated by Polycomb repression. We show that histone genes  are expressed with allelic imbalance in mESCs, are involved in haplotype-specific  chromatin contact marked by H3K27me3, and are targets of Polycomb repression  through conditional knockouts of Ezh2 or Ring1b. Our work reveals highly distinct  3D folding structures between homologous chromosomes, and highlights their  intricate connections with allelic gene expression.", "date_published": "2024-05-10", "display_title": "Irastorza-Azcarate I et al. (2024) PMID:38766012", "uuid": "cf26b7d2-d57e-467f-8509-d873abdad0bc", "journal": "bioRxiv : the preprint server for biology", "ID": "PMID:38766012", "@id": "/publications/cf26b7d2-d57e-467f-8509-d873abdad0bc/", "short_attribution": "Irastorza-Azcarate I et al. (2024)", "status": "current", "@type": ["Publication", "Item"], "title": "Extensive folding variability between homologous chromosomes in mammalian cells.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Default", "value": null}, "experiment_summary": "GAM on F123-CASTx129 (Tier 2)", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSTO156AZ/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample missing doubling_number", "Biosample is a stem cell line over 10 passages but missing karyotype"], "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": []}