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ENCyclopedia of DNA Elements

Tutorial and training materials by OpenHelix

Learn about The ENCODE Project , (ENCyclopedia of DNA Elements), an international consortium of researchers who are moving beyond the basic information of the reference genome sequence. Researchers are using many cutting-edge technologies to learn as much as possible about variations, genes, non-coding transcripts, regulatory elements, and genome structure and more, in extensive detail across the entire genome. The ENCODE project is coordinated by the NHGRI. The UCSC Genome Browser is the designated Data Coordination Center (DCC) , for the ENCODE project, and the official ENCODE data repository. In this tutorial we examine aspects of the ENCODE project and data types, and explore ways for you to access and learn about the ENCODE data available under the UCSC Genome Browser. This tutorial assumes the user has familiarity with the software functionality of the UCSC Genome Browser as described in the Introductory and Advanced Topics tutorials. The focus of this material is on the human ENCODE data at this time. If you are interested in the fly and worm aspects of the project, please visit the modENCODE site for these model organisms.

Note: A second tutorial goes beyond these foundations and explores ways to interact with ENCODE data in 2012. See ENCODE Data Available through the UCSC Genome Browser

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You'll learn:

  • The foundations and background of the ENCODE project
  • Key differences between the pilot phase and the current production phase
  • To identify ENCODE data in the UCSC Genome Browser, and explore the data use policies
  • What types of data are available under ENCODE, and where to find details of the data types and technologies
  • How to interact with the data in the graphical browser, table browser, and by downloading


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This tutorial is a part of the tutorial group UCSC Tutorials. You might find the other tutorials in the group interesting:

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Recent BioMed Central research articles citing this resource

Hu Yang Hai et al., Deep sequencing reveals a novel class of bidirectional promoters associated with neuronal genes Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-457

Yang Hsin-Chou et al., Applying genome-wide gene-based expression quantitative trait locus mapping to study population ancestry and pharmacogenetics Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-319

Wang Lei et al., Exploring the stability of long intergenic non-coding RNA in K562 cells by comparative studies of RNA-Seq datasets Non-coding DNA and RNA. Biology Direct (2014) doi:10.1186/1745-6150-9-15

Mosen-Ansorena David et al., seqCNA: an R package for DNA copy number analysis in cancer using high-throughput sequencing Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-178

Van Bortle Kevin et al., Insulator function and topological domain border strength scale with architectural protein occupancy. Genome Biology (2014) doi:10.1186/gb-2014-15-5-r82

More about the resource:

The UCSC Genome Browser , sometimes referred to as the "Golden Path" browser, offers a well-organized and user-friendly view of the human genome, and dozens of other genomes as well. The data can be accessed with simple text or sequence searches, or probed in depth with customized queries. The ENCODE project represents an international consortium of researchers who are adding depth to our understanding of genomic elements. See the ENCODE site at the National Human Genome Research Institute for background information and important features of the data release and usage policy.


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The materials and slides offered can not be resold or used for profit purposes. Reproduction, distribution and/or use is strictly limited to instructional purposes only and can not be used for for monetary gain or wide distribution.
Copyright 2009, OpenHelix, LLC.

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