ENCODE whole-genome data in the UCSC genome browser (2011 update)

Brian J. Raney, Melissa S. Cline, Kate R. Rosenbloom, Timothy R. Dreszer, Katrina Learned, Galt P. Barber, Laurence R. Meyer, Cricket A. Sloan, Venkat S. Malladi, Krishna M. Roskin, Bernard B. Suh, Angie S. Hinrichs, Hiram Clawson, Ann S. Zweig, Vanessa Kirkup, Pauline A. Fujita, Brooke Rhead, Kayla E. Smith, Andy Pohl, Robert M. KuhnDonna Karolchik, David Haussler, W. James Kent

Research output: Contribution to journalArticle

143 Scopus citations

Abstract

The ENCODE project is an international consortium with a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) at the University of California, Santa Cruz serves as the central repository for ENCODE data. In this role, the DCC offers a collection of high-throughput, genome-wide data generated with technologies such as ChIP-Seq, RNA-Seq, DNA digestion and others. This data helps illuminate transcription factor-binding sites, histone marks, chromatin accessibility, DNA methylation, RNA expression, RNA binding and other cell-state indicators. It includes sequences with quality scores, alignments, signals calculated from the alignments, and in most cases, element or peak calls calculated from the signal data. Each data set is available for visualization and download via the UCSC Genome Browser (http://genome.ucsc.edu/). ENCODE data can also be retrieved using a metadata system that captures the experimental parameters of each assay. The ENCODE web portal at UCSC (http://encodeproject.org/) provides information about the ENCODE data and links for access.

Original languageEnglish (US)
Pages (from-to)D871-D875
JournalNucleic acids research
Volume39
Issue numberSUPPL. 1
DOIs
StatePublished - Jan 1 2011
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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    Raney, B. J., Cline, M. S., Rosenbloom, K. R., Dreszer, T. R., Learned, K., Barber, G. P., Meyer, L. R., Sloan, C. A., Malladi, V. S., Roskin, K. M., Suh, B. B., Hinrichs, A. S., Clawson, H., Zweig, A. S., Kirkup, V., Fujita, P. A., Rhead, B., Smith, K. E., Pohl, A., ... Kent, W. J. (2011). ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic acids research, 39(SUPPL. 1), D871-D875. https://doi.org/10.1093/nar/gkq1017