ENCODE Project at NHGRI    ENCODE Data Coordination Center at UCSC
ENCODE at UCSC (2003-2012) - Downloads - Help
ENCODE investigators employ a variety of assays and methods to identify functional elements. The discovery and annotation of gene elements is accomplished primarily by sequencing RNA from a diverse range of sources, comparative genomics, integrative bioinformatic methods, and human curation. Regulatory elements are typically investigated through DNA hypersensitivity assays, assays of DNA methylation, and chromatin immunoprecipitation (ChIP) of proteins that interact with DNA, including modified histones and transcription factors, followed by sequencing (ChIP-Seq).

Credits: Darryl Leja (NHGRI), Ian Dunham (EBI), Michael Pazin (NHGRI)

To visualise human ENCODE data at UCSC, open the Genome Browser, select the February 2009 assembly (GRCh37/hg19) or the March 2006 assembly (NCBI36/hg18) of the human genome, and go to your region of interest. The bulk of the ENCODE data can be found in the Expression and Regulation track groups, with a few in the Mapping, Genes, and Variation groups. Although most participating research groups have provided several tracks, generally only selected data from each research group are displayed by default. Click the hyperlinked name of a particular track to display a page containing configuration options and details about the methods used to generate the data. See the Genome Browser User's Guide for further information about displaying tracks and navigating in the Genome Browser.

Data from the earlier ENCODE project pilot phase, which covered approximately 1% of the genome,  are available on the March 2006 (NCBI36/hg18), May 2004 (NCBI35/hg17), and July 2003 (NCBI34/hg16) human genome assemblies. The ENCODE Pilot Project web pages provide convenient browser access to these regions.