ENCyclopedia of DNA Elements
Free Tutorial Suite Sponsored By UCSC ENCODE
| 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 | Sponsored by: 
| |||||
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
| | | | |
Related tutorialsThis tutorial is a part of the tutorial group UCSC Tutorials. You might find the other tutorials in the group interesting:
CategoriesView additional tutorials for resources in
| Recent BioMed Central research articles citing this resourceShen Shih Pei et al., Identifying targets of the Sox domain protein Dichaete in the Drosophila CNS via targeted expression of dominant negative proteins Neural development. BMC Developmental Biology (2013) doi:10.1186/1471-213X-13-1 Malueka Ghazali Rusdy et al., Categorization of 77 dystrophin exons into 5 groups by a decision tree using indexes of splicing regulatory factors as decision markers. BMC Genetics (2012) doi:10.1186/1471-2156-13-23 Akalin Altuna et al., methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biology (2012) doi:10.1186/gb-2012-13-10-r87 Ni Yunyun et al., Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data. BMC Genetics (2012) doi:10.1186/1471-2156-13-46 Ritz Justin et al., Evaluating our ability to predict the structural disruption of RNA by SNPs SNP-SIG 2011: Identification and annotation of SNPs in the context of structure, function and disease SNP-SIG 2011: Identification and annotation of SNPs in the context of structure, function and disease. BMC Genomics (2012) doi:10.1186/1471-2164-13-S4-S6 |
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.
Click here for technical information on using OpenHelix tutorial and training materials
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.