{"ID": "PMID:31351925", "lab": {"display_title": "4DN DCIC, HMS", "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/31351925", "award": {"uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "project": "4DN", "@type": ["Award", "Item"], "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "status": "current", "name": "2U01CA200059-06", "@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.", "center_title": "DCIC - Park", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "4C-seq from beginning to end: A detailed protocol for sample preparation and data  analysis.", "status": "current", "aliases": ["4dn-dcic-lab:4c-seq-exptype-pub"], "authors": ["Krijger PHL", "Geeven G", "Bianchi V", "Hilvering CRE", "de Laat W"], "journal": "Methods (San Diego, Calif.)", "abstract": "Chromosome conformation capture (3C) methods measure DNA contact frequencies  based on nuclear proximity ligation, to uncover in vivo genomic folding patterns.  4C-seq is a derivative 3C method, designed to search the genome for sequences  contacting a selected genomic site of interest. 4C-seq employs inverse PCR and  next generation sequencing to amplify, identify and quantify its proximity  ligated DNA fragments. It generates high-resolution contact profiles for selected  genomic sites based on limited amounts of sequencing reads. 4C-seq can be used to  study multiple aspects of genome organization. It primarily serves to identify  specific long-range DNA contacts between individual regulatory DNA modules,  forming for example regulatory chromatin loops between enhancers and promoters,  or architectural chromatin loops between cohesin- and CTCF- associated domain  boundaries. Additionally, 4C-seq contact profiles can reveal the contours of  contact domains and can identify the structural domains that co-occupy the same  nuclear compartment. Here, we present an improved step-by-step protocol for  sample preparation and the generation of 4C-seq sequencing libraries, including  an optimized PCR and 4C template purification strategy. In addition, a data  processing pipeline is provided which processes multiplexed 4C-seq reads directly  from FASTQ files and generates files compatible with standard genome browsers for  visualization and further statistical analysis of the data such as peak calling  using peakC. The protocols and the pipeline presented should readily allow anyone  to generate, visualize and interpret their own high resolution 4C contact  datasets.", "categories": ["key publication"], "date_created": "2023-10-18T13:55:50.575954+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-10-18T13:55:50.810618+00:00"}, "date_published": "2020-01-01", "public_release": "2023-10-18", "schema_version": "2", "project_release": "2023-10-18", "@id": "/publications/d80a1c3d-d260-4fa2-9b67-a1e33750659d/", "@type": ["Publication", "Item"], "uuid": "d80a1c3d-d260-4fa2-9b67-a1e33750659d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "Krijger PHL et al. (2020) PMID:31351925", "external_references": [], "short_attribution": "Krijger PHL et al. (2020)", "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}