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ENCODE Data at UCSC

Tutorial and training materials by OpenHelix

ENCODE (Encyclopedia Of DNA Elements) is a big data consortium project that has for years generated huge amounts of important new data and analyses about various structural features and other aspects of genome organization. In this tutorial we will focus on the human and mouse data flowing into the UCSC Genome Browser via the Data Coordination Center (DCC) during the production phase of the project. Well describe the ENCODE portal that provides access to many project topics, and then move to exploring numerous data types in the Genome Browser. We will emphasize how to identify and locate data relevant to your research, and explore the data in the browser and other UCSC interfaces. Well examine visualization strategies and important track control features and track details. This tutorial assumes that the viewer has foundational knowledge of the UCSC Genome Browser and Table Browser tools. We also encourage viewers to access the consortiums publication: The ENCODE Project Consortium (2011) A User's Guide to the Encyclopedia of DNA Elements (ENCODE). PLoS Biol 9(4): e1001046. doi:10.1371/journal.pbio.1001046.

New: Explore the massive publication collection available on September 5 2012 via the ENCODE Explorer at Nature.

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You'll learn:

  • Aspects of ENCODE project organization
  • Where to access the ENCODE portal for key project documentation and data collections
  • Ways to find data of interest for your research
  • To visualize and explore ENCODE project results
  • Alternative ways to query or download the data


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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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Renganathan Arun et al., GAS5 long non-coding RNA in malignant pleural mesothelioma. Molecular Cancer (2014) doi:10.1186/1476-4598-13-119

Yamanaka Soichiro et al., piRNA clusters and open chromatin structure. Mobile DNA (2014) doi:10.1186/1759-8753-5-22

Worsley Hunt Rebecca et al., Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment Comparative and evolutionary genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-472

Blanc Valerie et al., Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver. Genome Biology (2014) doi:10.1186/gb-2014-15-6-r79


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