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 Maddren; Laurence R. Meyer; Andy Pohl; Brooke Rhead; Matthew C. Wong; Ann S. Zweig; David Haussler; W. James Kent

doi:10.1093/nar/gkr1012

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

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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 language	English (US)
Pages (from-to)	D912-D917
Journal	Nucleic acids research
Volume	40
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkr1012
State	Published - Jan 2012
Externally published	Yes

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

Rosenbloom, KR, Dreszer, TR, Long, JC, Malladi, VS, Sloan, CA, Raney, BJ, Cline, MS, Karolchik, D, Barber, GP, Clawson, H, Diekhans, M, Fujita, PA, Goldman, M, Gravell, RC, Harte, RA, Hinrichs, AS, Kirkup, VM, Kuhn, RM, Learned, K, Maddren, M, Meyer, LR, Pohl, A, Rhead, B, Wong, MC, Zweig, AS, Haussler, D & Kent, WJ 2012, 'ENCODE whole-genome data in the UCSC Genome Browser: Update 2012', Nucleic acids research, vol. 40, no. D1, pp. D912-D917. https://doi.org/10.1093/nar/gkr1012

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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.",

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

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AU - Learned, Katrina

AU - Maddren, Morgan

AU - Meyer, Laurence R.

AU - Pohl, Andy

AU - Rhead, Brooke

AU - Wong, Matthew C.

AU - Zweig, Ann S.

AU - Haussler, David

AU - Kent, W. James

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

Abstract

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