ENCODE Project Common Cell Types

National Human Genome Research Institute

National Institutes of Health
U.S. Department of Health and Human Services

ENCODE Project Common Cell Types

The Encyclopedia of DNA Elements (ENCODE) Project seeks to identify functional elements in the human genome. To aid in the integration and comparison of data produced using different technologies and platforms, the ENCODE Consortium has designated cell types that will be used by all investigators. These common cell types include both cell lines and primary cell types, and plans are being made to explore the use of primary tissues and embryonic stem (ES) cells.

Cell types were selected largely for practical reasons, including their wide availability, the ability to grow them easily, and their capacity to produce sufficient numbers of cells for use in all technologies being used by ENCODE investigators. Secondary considerations were the diversity in tissue source of the cells, germ layer lineage representation, the availability of existing data generated using the cell type, and coordination with other ongoing projects. Effort was also made to select at least some cell types that have a relatively normal karyotype.

The cell types and rationales for their selection are described below:

Tier 1:

Tier 2:

Tier 2.5:

Additional information about the ENCODE common cell types, including cell growth protocols being used by ENCODE investigators, is available at http://genome.ucsc.edu/ENCODE/cellTypes.html.

Information on Common Resources used by the ENCODE pilot project, including the pilot project target sequences, BAC Clones for ENCODE targets, cell lines and antibodies to DNA-binding proteins can be found at www.genome.gov/12513455.

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Last Updated: March 9, 2012