{"ID": "PMID:31768977", "lab": {"correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "@type": ["Lab", "Item"], "title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "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/31768977", "award": {"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.", "name": "2U01CA200059-06", "status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "project": "4DN", "center_title": "DCIC - Park", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "@type": ["Award", "Item"], "@id": "/awards/2U01CA200059-06/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Determining mRNA Stability by Metabolic RNA Labeling and Chemical Nucleoside  Conversion.", "status": "current", "aliases": ["4dn-dcic-lab:slam_seq_prot_ref_31768977"], "authors": ["Herzog VA", "Fasching N", "Ameres SL"], "journal": "Methods in molecular biology (Clifton, N.J.)", "abstract": "The varying rates at which mRNAs decay are tightly coordinated with  transcriptional changes to shape gene expression during development and disease.  But currently available RNA sequencing approaches lack the temporal information  to determine the relative contribution of RNA biogenesis, processing and turnover  to the establishment of steady-state gene expression profiles.Here, we describe a  protocol that combines metabolic RNA labeling with chemical nucleoside conversion  by thiol-linked alkylation of 4-thiouridine to determine RNA stability in  cultured cells (SLAMseq). When coupled to cost-effective mRNA 3' end sequencing  approaches, SLAMseq determines the half-life of polyadenylated transcripts in a  global and transcript-specific manner using untargeted or targeted cDNA library  preparation protocols.We provide a step-by-step instruction for time-resolved  mRNA 3' end sequencing, which augments traditional RNA-seq approaches to acquire  the temporal resolution necessary to study the molecular principles that control  gene expression.", "date_created": "2024-10-17T16:57:37.508278+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-10-17T16:57:37.793156+00:00"}, "date_published": "2020", "public_release": "2024-10-17", "schema_version": "2", "project_release": "2024-10-17", "@id": "/publications/c9f55e2a-3968-4aed-b995-ce2a8d792df2/", "@type": ["Publication", "Item"], "uuid": "c9f55e2a-3968-4aed-b995-ce2a8d792df2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "Herzog VA et al. (2020) PMID:31768977", "external_references": [], "short_attribution": "Herzog VA et al. (2020)", "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}