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.
- 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
This tutorial is a part of the tutorial group UCSC Tutorials. You might find the other tutorials in the group interesting:
View additional tutorials for resources in
Recent BioMed Central research articles citing this resource
St. Laurent Georges et al., Dark matter RNA illuminates the puzzle of genome-wide association studies. BMC Medicine (2014) doi:10.1186/1741-7015-12-97
Ansari Daniel et al., The role of quantitative mass spectrometry in the discovery of pancreatic cancer biomarkers for translational science Patient-targeted molecular therapies. Journal of Translational Medicine (2014) doi:10.1186/1479-5876-12-87
Glauser A Dominique et al., The multiplicity of alternative splicing decisions in Caenorhabditis elegans is linked to specific intronic regulatory motifs and minisatellites Multicellular invertebrate genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-364
Jing Zhe et al., A gene-specific non-enhancer sequence is critical for expression from the promoter of the small heat shock protein gene αB-crystallin. Human Genomics (2014) doi:10.1186/1479-7364-8-5
Warton Kristina et al., Methylation-capture and Next-Generation Sequencing of free circulating DNA from human plasma Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-476
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.