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

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 ( ENCODE data can also be retrieved using a metadata system that captures the experimental parameters of each assay. The ENCODE web portal at UCSC ( provides information about the ENCODE data and links for access.

Pubmed ID: 21037257


  • Raney BJ
  • Cline MS
  • Rosenbloom KR
  • Dreszer TR
  • Learned K
  • Barber GP
  • Meyer LR
  • Sloan CA
  • Malladi VS
  • Roskin KM
  • Suh BB
  • Hinrichs AS
  • Clawson H
  • Zweig AS
  • Kirkup V
  • Fujita PA
  • Rhead B
  • Smith KE
  • Pohl A
  • Kuhn RM
  • Karolchik D
  • Haussler D
  • Kent WJ


Nucleic acids research

Publication Data

January 23, 2011

Associated Grants

  • Agency: NHGRI NIH HHS, Id: 5P41HG002371-09
  • Agency: NHGRI NIH HHS, Id: 5U41HG004568-02
  • Agency: Howard Hughes Medical Institute, Id:

Mesh Terms

  • Databases, Genetic
  • Gene Expression Regulation
  • Genome, Human
  • Genomics
  • Humans
  • Internet
  • Software
  • User-Computer Interface