More and more we are seeing questions about ways to access Epigenomics data in the workshops we do. This often comes up in the workshop we do that focuses on the ENCODE data, because ENCODE is providing several epigenomics data sets that researchers are interested in. [The workshop we do is based on the materials you can find from the UCSC-sponsored freely available ENCODE tutorial.] But there are other browsers and data collections, and researchers want to be sure they are finding as much as possible.
Beside the data that is flowing into the UCSC Genome Browser ENCODE portal, we’ve talked in the past about the NCBI Epigenomics resource, including this tip. We have also explored DAnCER in the past as a tip-of-the-week.
I’m still recovering from my vacation this week, so I’m going to point you to a very nice SciVee example I found on another resource, the Human Epigenomics Visualization Hub from WashU, which can be accessed at this link: http://vizhub.wustl.edu/ It’s longer than our usual tips–about 20 minutes. But if you want to begin to explore the data available on that browser, it’s worth your time.
Based on a UCSC Genome Browser framework, this resource focuses on epigenomics data. Familiarity with basic vocabulary and functional features of the UCSC Genome Browser is something I’d recommend. Check out our freely-available UCSC sponsored tutorials for this which cover features of tracks and displays, including things like bigWig, Sessions, etc.
The project is associated with the Roadmap Epigenomics Project, which you can explore in detail at the project site, and learn more about in the reference below.
In case the embed isn’t working, here is the link to the SciVee page: http://www.scivee.tv/node/31122
Quick link to Vizhub: http://vizhub.wustl.edu/
Follow them on Twitter for news and announcements: @WashUGBrowser
Bernstein, B., Stamatoyannopoulos, J., Costello, J., Ren, B., Milosavljevic, A., Meissner, A., Kellis, M., Marra, M., Beaudet, A., Ecker, J., Farnham, P., Hirst, M., Lander, E., Mikkelsen, T., & Thomson, J. (2010). The NIH Roadmap Epigenomics Mapping Consortium Nature Biotechnology, 28 (10), 1045-1048 DOI: 10.1038/nbt1010-1045