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
Ebert Grit et al., Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7 Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-537
Werner Andreas et al., Contribution of natural antisense transcription to an endogenous siRNA signature in human cells Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-19
Taudien Stefan et al., Narrowing down the distal border of the copy number variable beta-defensin gene cluster on human 8p23. BMC Research Notes (2014) doi:10.1186/1756-0500-7-93
Zhang Xianghong et al., 8p23 beta-defensin copy number determination by single-locus pseudogene-based paralog ratio tests risk bias due to low-frequency sequence variations Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-64
Levitsky G Victor et al., Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data Transcriptomic methods. BMC Genomics (2014) doi:10.1186/1471-2164-15-80
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.