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  1. ENCODE Project
    Full Name of the Resource : Encyclopedia of DNA Elements, all functional elements in the human genome
    Resource Category : Databases -> Human and Other Vertebrate Genomes -> Model Organisms, Comparative Genomics

    Brief Description : The Encyclopedia of DNA Elements (ENCODE) project is an international consortium of investigators funded to analyze the human genome with the goal of producing a comprehensive catalog of functional elements. Initially a pilot project focused on 1% of the human genome sequence, ENCODE was scaled up in September 2007 to cover the entire genome. The ENCODE Data Coordination Center (DCC) at The University of California, Santa Cruz (UCSC) is the primary repository for experimental results generated by ENCODE investigators. These results are captured in the UCSC Genome Bioinformatics database and download server for visualization and data mining via the UCSC Genome Browser and companion tools (Rhead et al. The UCSC Genome Browser Database: update 2010, in this issue). To support the breadth and volume of ENCODE data, new features for organizing and selecting datasets have been added to the browser. Additionally, metadata describing the experiments is now captured more formally via controlled vocabularies which are associated with browser tracks and download files. The ENCODE web portal at UCSC (http://encodeproject.org or http://genome.ucsc.edu/ENCODE) provides information about the ENCODE data and convenient links for access. As of September 2009, the ENCODE investigators have completed four production-level data freezes, consisting of 341 experiments submitted to the ENCODE DCC, with 207 of these released in a total of 18 tracks on the UCSC Genome Browser. These experiments represent a major methodology shift from microarray to high-throughput sequencing assays, and include a broad range of experiment types (e.g. ChIP-seq, RNA-seq, Methyl-seq) in 7 designated common cell types, and 51 additional human cell lines and tissues.

    Institute/s :
    Center for Biomolecular Science and Engineering, School of Engineering,USA
    Address of Institute/s :
    Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA,
    Country : United States

    Associated Institutes :

    • Centre for Genomic Regulation (CRG), Barcelona, Spain and 3Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA

    Associated Country : USA


    Authors/Contributors : Kate R. Rosenbloom; Timothy R. Dreszer; Jeffrey C. Long; Venkat S. Malladi; Cricket A. Sloan; Brian J. Raney; Melissa S. Cline; Donna Karolchik; Galt P. Barber; Hiram Clawson; Mark Diekhans; Pauline A. Fujita; Mary Goldman; Robert C. Gravell; Rachel A. Harte; Angie S. Hinrichs; Vanessa M. Kirkup; Robert M. Kuhn; Katrina Learned; Morgan Maddren; Laurence R. Meyer; Andy Pohl; Brooke Rhead; Matthew C. Wong; Ann S. Zweig; David Haussler ;W. James Kent
    Contact Email : kate@soe.ucsc.edu
    Year : 2011