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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."], "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFILRZL2GF", "higlass_uid": "b'Ojumdp5NSOOyG5DOkSCEUg'", "genome_assembly": "GRCh38", "file_size": 761573346, "md5sum": "eeac4ffc3314a7be5a06e3532c0ab5ad", "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFILRZL2GF - contact matrix for IMR-90 TCC HindIII", "status": "released", "@id": "/higlass-view-configs/f091363e-82e8-4b61-b9be-0217ba51369e/", "uuid": "f091363e-82e8-4b61-b9be-0217ba51369e", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "track_and_facet_info": {"dataset": "TCC on IMR90 +/- Adenovirus", "condition": "24h control", "experimental_lab": "Lin Chen, USC", "replicate_info": "unreplicated", "experiment_bucket": "HiC Processing Pipeline - Preliminary Files", "experiment_type": "TCC", "assay_info": "HindIII", "biosource_name": "IMR-90", "lab_name": "4DN DCIC, HMS", "track_title": "contact matrix for IMR-90 TCC HindIII"}, "contributing_labs": [{"display_title": "Frank Alber, UCLA", "status": "current", "uuid": "b3ffd506-c343-4e0f-85e2-f6ba93dff336", "name": "frank-alber-lab", "@type": ["Lab", "Item"], "@id": "/labs/frank-alber-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b3ffd506-c343-4e0f-85e2-f6ba93dff336"]}}, {"display_title": "Lin Chen, USC", "status": "current", "uuid": "542b0e82-094f-4914-b04f-0cdbe994f936", "name": "lin-chen-lab", "@type": ["Lab", "Item"], "@id": "/labs/lin-chen-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.542b0e82-094f-4914-b04f-0cdbe994f936"]}}], "quality_metric": {"@type": ["QualityMetricMcool", "QualityMetric", "Item"], "@id": "/quality-metrics-mcool/f81af8cc-9024-4687-9898-632c053ad257/", "display_title": "QualityMetricMcool from 2021-05-21", "status": "released", "overall_quality_status": "PASS", "uuid": "f81af8cc-9024-4687-9898-632c053ad257", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Failed Balancing", "value": "None", "tooltip": "Resolutions where balancing failed", "numberType": "string"}]}, "lab": {"display_title": "4DN DCIC, HMS", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "name": "4dn-dcic-lab", "@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": "2023-08-25T17:52:41.208706+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "title": "HiC Processing Pipeline - Preliminary Files", "description": "The 4DN Hi-C pipeline was run as is, using only the human genome. For processed results including the virus, see the attached publication.", "higlass_view_config": {"description": "Supplementary Files (HiC Processing Pipeline - Preliminary Files) for 4DNES9M5YSX6 (TCC on IMR90 cells 24h after mock infection): 4DNFILRZL2GF", "display_title": "4DNES9M5YSX6 - HiC Processing Pipeline - Preliminary Files", "@id": "/higlass-view-configs/53e84da0-2720-4cb4-8afe-631ce715db60/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "53e84da0-2720-4cb4-8afe-631ce715db60", "status": "released", "last_modified": {"date_modified": "2020-10-30T16:57:24.214565+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "@id": "/experiment-set-replicates/4DNES9M5YSX6/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "004ea156-9291-48e2-82be-4a2af8f4e105", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNES9M5YSX6", "external_references": [], "produced_in_pub": {"authors": ["Li H", "Kalhor R", "Li B", "Su T", "Berk A", "Kurdistani S", "Alber F", "Chen L"], "display_title": "Li H et al. (2017) doi:10.1101/142604", "title": "Specific Virus-Host Genome Interactions Revealed By Tethered Chromosome Conformation Capture", "@type": ["Publication", "Item"], "date_published": "2017-05-26", "short_attribution": "Li H et al. (2017)", "@id": "/publications/a12cdabd-b6cf-42c7-b68e-3ca20b1475fe/", "url": "http://biorxiv.org/lookup/doi/10.1101/142604", "abstract": "Viruses have evolved a variety of mechanisms to interact with host cells for their adaptive benefits, including subverting host immune responses and hijacking host DNA replication/transcription machineries [1-3]. Although interactions between viral and host proteins have been studied extensively, little is known about how the vial genome may interact with the host genome and how such interactions could affect the activities of both the virus and the host cell. Since the three-dimensional organization of a genome can have significant impact on genomic activities such as transcription and replication, we hypothesize that such structure-based regulation of genomic functions also applies to viral genomes depending on their association with host genomic regions and their spatial locations inside the nucleus. Here, we used Tethered Chromosome Conformation Capture (TCC) to investigate viral-host genome interactions between the adenovirus and human lung fibroblast cells. We found viral-host genome interactions were enriched in certain active chromatin regions and chromatin domains marked by H3K27me3. The contacts by viral DNA seems to impact the structure and function of the host genome, leading to remodeling of the fibroblast epigenome. Our study represents the first comprehensive analysis of viral-host interactions at the genome structure level, revealing unexpectedly specific virus-host genome interactions. The non-random nature of such interactions indicates a deliberate but poorly understood mechanism for targeting of host DNA by foreign genomes.", "uuid": "a12cdabd-b6cf-42c7-b68e-3ca20b1475fe", "status": "current", "ID": "doi:10.1101/142604", "journal": "bioRxiv", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"status": "current", "@id": "/publications/a12cdabd-b6cf-42c7-b68e-3ca20b1475fe/", "title": "Specific Virus-Host Genome Interactions Revealed By Tethered Chromosome Conformation Capture", "ID": "doi:10.1101/142604", "abstract": "Viruses have evolved a variety of mechanisms to interact with host cells for their adaptive benefits, including subverting host immune responses and hijacking host DNA replication/transcription machineries [1-3]. Although interactions between viral and host proteins have been studied extensively, little is known about how the vial genome may interact with the host genome and how such interactions could affect the activities of both the virus and the host cell. Since the three-dimensional organization of a genome can have significant impact on genomic activities such as transcription and replication, we hypothesize that such structure-based regulation of genomic functions also applies to viral genomes depending on their association with host genomic regions and their spatial locations inside the nucleus. Here, we used Tethered Chromosome Conformation Capture (TCC) to investigate viral-host genome interactions between the adenovirus and human lung fibroblast cells. We found viral-host genome interactions were enriched in certain active chromatin regions and chromatin domains marked by H3K27me3. The contacts by viral DNA seems to impact the structure and function of the host genome, leading to remodeling of the fibroblast epigenome. Our study represents the first comprehensive analysis of viral-host interactions at the genome structure level, revealing unexpectedly specific virus-host genome interactions. The non-random nature of such interactions indicates a deliberate but poorly understood mechanism for targeting of host DNA by foreign genomes.", "uuid": "a12cdabd-b6cf-42c7-b68e-3ca20b1475fe", "display_title": "Li H et al. (2017) doi:10.1101/142604", "journal": "bioRxiv", "authors": ["Li H", "Kalhor R", "Li B", "Su T", "Berk A", "Kurdistani S", "Alber F", "Chen L"], "date_published": "2017-05-26", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 1, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSE4YUHFO/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing doubling_number", "Biosample missing morphology_image"], "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": "/experiment-set-replicates/4DNES9M5YSX6/", "embedded_path": "badges", "item": {"messages": ["Replicate set contains only a single biological replicate"], "badge": {"commendation": null, "warning": "Replicate Numbers", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "@id": "/badges/replicate-numbers/", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "description": "Issues with replicate numbers"}}}]}, "validation-errors": []}