ENCODE whole-genome data in the UCSC Genome Browser: Update 2012

Kate R. Rosenbloom, Timothy R. Dreszer, Jeffrey C. Long, Venkat S. Malladi, Cricket A. Sloan, Brian J. Raney, Melissa S. Cline, Donna Karolchik, Galt P. Barber, Hiram Clawson, Mark Diekhans, Pauline A. Fujita, Mary Goldman, Robert C. Gravell, Rachel A. Harte, Angie S. Hinrichs, Vanessa M. Kirkup, Robert M. Kuhn, Katrina Learned, Morgan MaddrenLaurence R. Meyer, Andy Pohl, Brooke Rhead, Matthew C. Wong, Ann S. Zweig, David Haussler, W. James Kent

Research output: Contribution to journalArticle

176 Scopus citations

Abstract

The Encyclopedia of DNA Elements (ENCODE) Consortium is entering its 5th year of productionlevel effort generating high-quality whole-genome functional annotations of the human genome. The past year has brought the ENCODE compendium of functional elements to critical mass, with a diverse set of 27 biochemical assays now covering 200 distinct human cell types. Within the mouse genome, which has been under study by ENCODE groups for the past 2 years, 37 cell types have been assayed. Over 2000 individual experiments have been completed and submitted to the Data Coordination Center for public use. UCSC makes this data available on the quality-reviewed public Genome Browser (http://genome.ucsc.edu) and on an early-access Preview Browser (http://genomepreview. ucsc.edu). Visual browsing, data mining and download of raw and processed data files are all supported. An ENCODE portal (http:// encodeproject.org) provides specialized tools and information about the ENCODE data sets.

Original languageEnglish (US)
Pages (from-to)D912-D917
JournalNucleic acids research
Volume40
Issue numberD1
DOIs
StatePublished - Jan 1 2012
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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    Rosenbloom, K. R., Dreszer, T. R., Long, J. C., Malladi, V. S., Sloan, C. A., Raney, B. J., Cline, M. S., Karolchik, D., Barber, G. P., Clawson, H., Diekhans, M., Fujita, P. A., Goldman, M., Gravell, R. C., Harte, R. A., Hinrichs, A. S., Kirkup, V. M., Kuhn, R. M., Learned, K., ... Kent, W. J. (2012). ENCODE whole-genome data in the UCSC Genome Browser: Update 2012. Nucleic acids research, 40(D1), D912-D917. https://doi.org/10.1093/nar/gkr1012