{"lab": {"correspondence": [{"contact_email": "YW5hLnBvbWJvQG1kYy1iZXJsaW4uZGU=", "@id": "/users/bce4f2b5-9a2a-4db2-9dd6-7d61f19025c1/", "display_title": "Ana Pombo"}], "uuid": "cf5abe29-1cf9-4413-b02e-664b47a6d53d", "status": "current", "display_title": "Ana Pombo, MDC", "@type": ["Lab", "Item"], "title": "Ana Pombo, MDC", "@id": "/labs/ana-pombo-lab/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.cf5abe29-1cf9-4413-b02e-664b47a6d53d"]}}, "award": {"display_title": "SAN DIEGO CENTER FOR 4D NUCLEOME RESEARCH", "status": "current", "name": "1U54DK107977-01", "project": "4DN", "description": "NOFIC: The complete sequencing of the human genome has provided an unprecedented opportunity for the study of the structure and function of the human genome. 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Due to recent advancements in molecular methods based on high-throughput DNA sequencing, single cell analytical approaches, and high-resolution microscopy, the time for breaking through these previous limitations has come. We will establish a highly collaborative, innovative team in order to develop the tools necessary to transform our understanding of chromatin architecture and function in mammalian cells. We will begin by developing datasets that establish gold standards for the study of nuclear structure and function using genetic, biochemical and imaging approaches. We will optimize current existing technologies for mapping genome wide chromatin interactions, while also developing novel, complementary approaches for studying chromatin structure. We will also develop innovative analytical methods to interpret the chromatin structural data, unraveling principles of structural- and temporal- chromatin organization. Our highly collaborative team will draw on the diverse experiences of its members to provide a synergistic environment to push the limits of our understanding of nuclear structure. We expect that the tools and datasets generated through the proposed research will dramatically advance our understanding of the chromatin structure and function in human cells.", "@type": ["Award", "Item"], "uuid": "4871e338-b07d-4665-a00a-357648e5bad6", "@id": "/awards/1U54DK107977-01/", "center_title": "NOFIC - Ren", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "pi": {"error": "no view permissions"}}, "status": "released", "aliases": ["ana-pombo-lab:gam_f123_tier2"], "accession": "4DNESRQDNG61", "documents": [{"uuid": "f9474e25-bf41-4752-85c0-37e496b9ffbe", "@type": ["Document", "Item"], "@id": "/documents/f9474e25-bf41-4752-85c0-37e496b9ffbe/", "status": "released", "display_title": "191120_F123mESC_batch_analysis_metrics.xlsx", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "description": "Replicates of GAM on F123xCAST mouse ES cells", "date_created": "2019-12-13T03:02:45.677187+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-05-28T15:59:16.734596+00:00"}, "public_release": "2021-02-09", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-seq/4DNEX1KG9YVX/", "@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "uuid": "b0fee370-48b1-443d-9163-f97b6af29cd5", "accession": "4DNEX1KG9YVX", "display_title": "GAM on F123-CASTx129 (Tier 2) - 4DNEX1KG9YVX", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-seq/4DNEXOWEU1HW/", "@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "uuid": "2b074ff4-713f-40b3-b2c2-c08a477382b2", "accession": "4DNEXOWEU1HW", "display_title": "GAM on F123-CASTx129 (Tier 2) - 4DNEXOWEU1HW", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_headers": [{"lab": {"status": "current", "@id": "/labs/ana-pombo-lab/", "uuid": "cf5abe29-1cf9-4413-b02e-664b47a6d53d", "@type": ["Lab", "Item"], "display_title": "Ana Pombo, MDC", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.cf5abe29-1cf9-4413-b02e-664b47a6d53d"]}}, "body": "**NOTE** The excel workbook [**downloadable from this page**](https://data.4dnucleome.org/documents/f9474e25-bf41-4752-85c0-37e496b9ffbe/) contains information that can be used to evaluate the quality of the GAM libraries linked to this dataset.\n\nThe workbook consists of 2 sheets. 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NOTE The excel workbook downloadable from this page contains information that can be used to evaluate the quality of the GAM libraries linked to this dataset.

\n

The workbook consists of 2 sheets. The first provides descriptions and terms used in the second and highlights those that may be used to evaluate quality of the libraries.\nThe second sheet provides information on each individual GAM library linked to this dataset.
\nEach library corresponds to a single FastQ file that can be identified using the provided Sample_ID in the first column.

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The replicate 1 specific files have not changed."}, {"type": "supplementary", "files": [{"file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@id": "/file-formats/csv/", "display_title": "csv", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/files-processed/4DNFI2XW5X8W/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/9f12e8f3-1841-4dc3-9f01-8ef6fe02b2f9/4DNFI2XW5X8W.csv", "file_type": "segregation table", "uuid": "9f12e8f3-1841-4dc3-9f01-8ef6fe02b2f9", "href": "/files-processed/4DNFI2XW5X8W/@@download/4DNFI2XW5X8W.csv", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "segregation table (csv)", "status": "released", "accession": "4DNFI2XW5X8W", "md5sum": "85fcccde06de7156bef33fcf415e2660", "file_size": 68344829, "display_title": "4DNFI2XW5X8W.csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-02-24T22:07:22.319374+00:00"}, "lab": {"status": "current", "display_title": "Ana Pombo, MDC", "uuid": "cf5abe29-1cf9-4413-b02e-664b47a6d53d", "@type": ["Lab", "Item"], "name": "ana-pombo-lab", "@id": "/labs/ana-pombo-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.cf5abe29-1cf9-4413-b02e-664b47a6d53d"]}}, "track_and_facet_info": {"experimental_lab": "Ana Pombo, MDC", "replicate_info": "merged replicates", "experiment_bucket": "Pombo Lab - GAM pipeline output 100 Kb bin - UPDATED Feb 2021", "experiment_type": "GAM", "biosource_name": "F123-CASTx129 (Tier 2)", "lab_name": "Ana Pombo, MDC"}}, {"file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-44f0-91f226248b2c", "@id": "/file-formats/zip/", "display_title": "zip", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/files-processed/4DNFIYCSTJIZ/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/7686f501-6d6e-4f69-87df-db7ff0657571/4DNFIYCSTJIZ.zip", "file_type": "normalized contact matrix", "uuid": "7686f501-6d6e-4f69-87df-db7ff0657571", "href": "/files-processed/4DNFIYCSTJIZ/@@download/4DNFIYCSTJIZ.zip", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "normalized contact matrix (zip)", "status": "released", "accession": "4DNFIYCSTJIZ", "md5sum": "89813943019c51b5355abae2c64ad3a9", "file_size": 279606917, "display_title": "4DNFIYCSTJIZ.zip", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-02-24T22:07:26.377546+00:00"}, "lab": {"status": "current", "display_title": "Ana Pombo, MDC", "uuid": "cf5abe29-1cf9-4413-b02e-664b47a6d53d", "@type": ["Lab", "Item"], "name": "ana-pombo-lab", "@id": "/labs/ana-pombo-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.cf5abe29-1cf9-4413-b02e-664b47a6d53d"]}}, "track_and_facet_info": {"experimental_lab": "Ana Pombo, MDC", "replicate_info": "merged replicates", "experiment_bucket": "Pombo Lab - GAM pipeline output 100 Kb bin - UPDATED Feb 2021", "experiment_type": "GAM", "biosource_name": "F123-CASTx129 (Tier 2)", "lab_name": "Ana Pombo, MDC"}}], "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": [{"file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@id": "/file-formats/csv/", "display_title": "csv", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/files-processed/4DNFIHP7GI1T/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/25e5a286-f61f-4b78-a36d-471db409c217/4DNFIHP7GI1T.csv", "file_type": "segregation table", "uuid": "25e5a286-f61f-4b78-a36d-471db409c217", "href": "/files-processed/4DNFIHP7GI1T/@@download/4DNFIHP7GI1T.csv", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "segregation table (csv)", "status": "released", "accession": "4DNFIHP7GI1T", "md5sum": "1f1b047e41d6ef1c7e30ec39783de18a", "file_size": 27414236, "display_title": "4DNFIHP7GI1T.csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-02-24T22:07:31.469900+00:00"}, "lab": {"status": "current", "display_title": "Ana Pombo, MDC", "uuid": "cf5abe29-1cf9-4413-b02e-664b47a6d53d", "@type": ["Lab", "Item"], "name": "ana-pombo-lab", "@id": "/labs/ana-pombo-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.cf5abe29-1cf9-4413-b02e-664b47a6d53d"]}}, "track_and_facet_info": {"experimental_lab": "Ana Pombo, MDC", "replicate_info": "merged replicates", "experiment_bucket": "Pombo Lab - GAM pipeline output 250 Kb bin - UPDATED Feb 2021", "experiment_type": "GAM", "biosource_name": "F123-CASTx129 (Tier 2)", "lab_name": "Ana Pombo, MDC"}}, {"file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-44f0-91f226248b2c", "@id": "/file-formats/zip/", "display_title": "zip", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/files-processed/4DNFI4BA43KR/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/fe7ab34e-0493-43cc-9ab9-25285684d439/4DNFI4BA43KR.zip", "file_type": "normalized contact matrix", "uuid": "fe7ab34e-0493-43cc-9ab9-25285684d439", "href": "/files-processed/4DNFI4BA43KR/@@download/4DNFI4BA43KR.zip", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "normalized contact matrix (zip)", "status": "released", "accession": "4DNFI4BA43KR", "md5sum": "390f7a42d4ae2b277004967ee508b27f", "file_size": 47769799, "display_title": "4DNFI4BA43KR.zip", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-02-24T22:07:35.692412+00:00"}, "lab": {"status": "current", "display_title": "Ana Pombo, MDC", "uuid": "cf5abe29-1cf9-4413-b02e-664b47a6d53d", "@type": ["Lab", "Item"], "name": "ana-pombo-lab", "@id": "/labs/ana-pombo-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.cf5abe29-1cf9-4413-b02e-664b47a6d53d"]}}, "track_and_facet_info": {"experimental_lab": "Ana Pombo, MDC", "replicate_info": "merged replicates", "experiment_bucket": "Pombo Lab - GAM pipeline output 250 Kb bin - UPDATED Feb 2021", "experiment_type": "GAM", "biosource_name": "F123-CASTx129 (Tier 2)", "lab_name": "Ana Pombo, MDC"}}], "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": [{"file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@id": "/file-formats/csv/", "display_title": "csv", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/files-processed/4DNFIWMZMPZR/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/d0773636-e135-4769-befb-3c7ef6ddd609/4DNFIWMZMPZR.csv", "file_type": "segregation table", "uuid": "d0773636-e135-4769-befb-3c7ef6ddd609", "href": "/files-processed/4DNFIWMZMPZR/@@download/4DNFIWMZMPZR.csv", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "segregation table (csv)", "status": "released", "accession": "4DNFIWMZMPZR", "md5sum": "abcc243ccd192d6844710f04d36f9545", "file_size": 13794085, "display_title": "4DNFIWMZMPZR.csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-02-24T22:07:40.462919+00:00"}, "lab": {"status": "current", "display_title": "Ana Pombo, MDC", "uuid": "cf5abe29-1cf9-4413-b02e-664b47a6d53d", "@type": ["Lab", "Item"], "name": "ana-pombo-lab", "@id": "/labs/ana-pombo-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.cf5abe29-1cf9-4413-b02e-664b47a6d53d"]}}, "track_and_facet_info": {"experimental_lab": "Ana Pombo, MDC", "replicate_info": "merged replicates", "experiment_bucket": "Pombo Lab - GAM pipeline output 500 Kb bin - UPDATED Feb 2021", "experiment_type": "GAM", "biosource_name": "F123-CASTx129 (Tier 2)", "lab_name": "Ana Pombo, MDC"}}, {"file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-44f0-91f226248b2c", "@id": "/file-formats/zip/", "display_title": "zip", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/files-processed/4DNFIJ7L3YVM/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/13e38469-851a-46c8-b725-2793ec11481e/4DNFIJ7L3YVM.zip", "file_type": "normalized contact matrix", "uuid": "13e38469-851a-46c8-b725-2793ec11481e", "href": "/files-processed/4DNFIJ7L3YVM/@@download/4DNFIJ7L3YVM.zip", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "normalized contact matrix (zip)", "status": "released", "accession": "4DNFIJ7L3YVM", "md5sum": "b2e2e046d04073992b55b0df960bc4ce", "file_size": 12116710, "display_title": "4DNFIJ7L3YVM.zip", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-02-24T22:07:44.484643+00:00"}, "lab": {"status": "current", "display_title": "Ana Pombo, MDC", "uuid": "cf5abe29-1cf9-4413-b02e-664b47a6d53d", "@type": ["Lab", "Item"], "name": "ana-pombo-lab", "@id": "/labs/ana-pombo-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.cf5abe29-1cf9-4413-b02e-664b47a6d53d"]}}, "track_and_facet_info": {"experimental_lab": "Ana Pombo, MDC", "replicate_info": "merged replicates", "experiment_bucket": "Pombo Lab - GAM pipeline output 500 Kb bin - UPDATED Feb 2021", "experiment_type": "GAM", "biosource_name": "F123-CASTx129 (Tier 2)", "lab_name": "Ana Pombo, MDC"}}], "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. 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The replicate 1 specific files have not changed."}, {"type": "supplementary", "files": [{"file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-94f336118b2c", "@id": "/file-formats/csv/", "display_title": "csv", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/files-processed/4DNFIDRE98XN/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/33390669-59df-4ef5-9d2c-2e3effd87119/4DNFIDRE98XN.csv", "file_type": "segregation table", "uuid": "33390669-59df-4ef5-9d2c-2e3effd87119", "href": "/files-processed/4DNFIDRE98XN/@@download/4DNFIDRE98XN.csv", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "segregation table (csv)", "status": "released", "accession": "4DNFIDRE98XN", "md5sum": "3a20980644a913cb187a8ec1df29c7b7", "file_size": 6985270, "display_title": "4DNFIDRE98XN.csv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-02-24T22:07:49.637664+00:00"}, "lab": {"status": "current", "display_title": "Ana Pombo, MDC", "uuid": "cf5abe29-1cf9-4413-b02e-664b47a6d53d", "@type": ["Lab", "Item"], "name": "ana-pombo-lab", "@id": "/labs/ana-pombo-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.cf5abe29-1cf9-4413-b02e-664b47a6d53d"]}}, "track_and_facet_info": {"experimental_lab": "Ana Pombo, MDC", "replicate_info": "merged replicates", "experiment_bucket": "Pombo Lab - GAM pipeline output 1 Mb bin - UPDATED Feb 2021", "experiment_type": "GAM", "biosource_name": "F123-CASTx129 (Tier 2)", "lab_name": "Ana Pombo, MDC"}}, {"file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-44f0-91f226248b2c", "@id": "/file-formats/zip/", "display_title": "zip", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/files-processed/4DNFIA1WXCRO/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/47279789-ad47-4154-877e-91041e741f51/4DNFIA1WXCRO.zip", "file_type": "normalized contact matrix", "uuid": "47279789-ad47-4154-877e-91041e741f51", "href": "/files-processed/4DNFIA1WXCRO/@@download/4DNFIA1WXCRO.zip", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "normalized contact matrix (zip)", "status": "released", "accession": "4DNFIA1WXCRO", "md5sum": "651248404398d0c8daedce57b8f68d28", "file_size": 2992760, "display_title": "4DNFIA1WXCRO.zip", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2021-02-24T22:07:53.916290+00:00"}, "lab": {"status": "current", "display_title": "Ana Pombo, MDC", "uuid": "cf5abe29-1cf9-4413-b02e-664b47a6d53d", "@type": ["Lab", "Item"], "name": "ana-pombo-lab", "@id": "/labs/ana-pombo-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.cf5abe29-1cf9-4413-b02e-664b47a6d53d"]}}, "track_and_facet_info": {"experimental_lab": "Ana Pombo, MDC", "replicate_info": "merged replicates", "experiment_bucket": "Pombo Lab - GAM pipeline output 1 Mb bin - UPDATED Feb 2021", "experiment_type": "GAM", "biosource_name": "F123-CASTx129 (Tier 2)", "lab_name": "Ana Pombo, MDC"}}], "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. 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