{"ID": "PMID:28497783", "lab": {"display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "title": "4DN DCIC, HMS", "status": "current", "correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/28497783", "award": {"name": "2U01CA200059-06", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "project": "4DN", "center_title": "DCIC - Park", "@type": ["Award", "Item"], "status": "current", "@id": "/awards/2U01CA200059-06/", "description": "DCIC: The goals of the 4D Nucleome (4DN) Data Coordination and Integration Center (DCIC) are to collect, store, curate, display, and analyze data generated in the 4DN Network. We have assembled a team of investigators, staff scientists, and developers with a strong track record in analysis of chromatin interaction data, image processing, data visualization, integrative analysis of genomic and epigenomic data, data portal development, large-scale computing, and development of secure and \ufb02exible cloud technologies. In the \ufb01rst phase of the 4DN Project, we have developed the 4DN Data Portal as a central resource with tools for data submission, curation, analysis and quality control, visualization, exploration, and download. The portal provides an easy-to-navigate interface for accessing raw and intermediate data \ufb01les, allows for programmatic access via APIs, and incorporates novel analysis and visualization tools developed by DCIC as well as other Network members. In the second phase of the 4DN Project, we will continue to support the research activities by the 4DN Network, and to lead the creation of a well curated 4DN data resource for the scienti\ufb01c community. At the same time, we propose to enhance the utility of the 4DN Scienti\ufb01c Data and the Data Portal in multiple ways: i. We will create a platform to integrate imaging and sequencing data and support the creating of reference nuclear maps in a common coordinate system; ii. We will provide support for 4DN Projects on Human Health and Disease with customized ontology applications and protected data management; iii. We will develop new cloud platform capabilities to bring user analyses to the 4DN Data Portal, and apply cost-ef\ufb01ciency improvements to support increasing data volumes; iv. We will perform regular outreach activities to raise awareness about the data and tools generated by the Network and DCIC. Overall, we will ensure that the data generated in 4DN will have maximal impact for the scienti\ufb01c community.", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks.", "status": "current", "aliases": ["4dn-dcic-lab:pmid_28497783_bliss_method_pub"], "authors": ["Yan WX", "Mirzazadeh R", "Garnerone S", "Scott D", "Schneider MW", "Kallas T", "Custodio J", "Wernersson E", "Li Y", "Gao L", "Federova Y", "Zetsche B", "Zhang F", "Bienko M", "Crosetto N"], "journal": "Nature communications", "abstract": "Precisely measuring the location and frequency of DNA double-strand breaks (DSBs) along the genome is instrumental to understanding genomic fragility, but current  methods are limited in versatility, sensitivity or practicality. Here we present  Breaks Labeling In Situ and Sequencing (BLISS), featuring the following: (1) direct labelling of DSBs in fixed cells or tissue sections on a solid surface; (2) low-input requirement by linear amplification of tagged DSBs by in vitro transcription; (3) quantification of DSBs through unique molecular identifiers; and (4) easy scalability and multiplexing. We apply BLISS to profile endogenous and exogenous DSBs in low-input samples of cancer cells, embryonic stem cells and liver tissue. We demonstrate the sensitivity of BLISS by assessing the genome-wide off-target activity of two CRISPR-associated RNA-guided endonucleases, Cas9 and Cpf1, observing that Cpf1 has higher specificity than Cas9. Our results establish BLISS as a versatile, sensitive and efficient method  for genome-wide DSB mapping in many applications.", "date_created": "2022-01-19T18:02:30.474889+00:00", "published_by": "External", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-01-19T18:02:30.705537+00:00"}, "date_published": "2017-05-12", "public_release": "2022-01-19", "schema_version": "2", "project_release": "2022-01-19", "@id": "/publications/e98eaf6e-fedd-43a1-8683-113acf22bf3a/", "@type": ["Publication", "Item"], "uuid": "e98eaf6e-fedd-43a1-8683-113acf22bf3a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "Yan WX et al. (2017) PMID:28497783", "external_references": [], "short_attribution": "Yan WX et al. (2017)", "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}