ENCODE Project Common Cell Types The Encyclopedia of DNA Elements (ENCODE) Project seeks to identify functional e lements

in the human genome. To aid in the integration and comparison of data pr oduced using different technologies and platforms, the ENCODE Consortium has des ignated cell types that will be used by all investigators. These common cell typ es include both cell lines and primary cell types, and plans are being made to e xplore the use of primary tissues and embryonic stem (ES) cells. Cell types were selected largely for practical reasons, including their wide ava ilability, the ability to grow them easily, and their capacity to produce suffic ient numbers of cells for use in all technologies being used by ENCODE investiga tors. 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 al so made to select at least some cell types that have a relatively normal karyoty pe. The cell types and rationales for their selection are described below: Tier 1: GM12878 is a lymphoblastoid cell line produced from the blood of a female donor with northern and western European ancestry by EBV transformation. It was one of the original HapMap cell lines and has been selected by the International HapMa p Project for deep sequencing using the Solexa/Illumina platform. This cell line has a relatively normal karyotype and grows well. Choice of this cell line offe rs potential synergy with the International HapMap Project and genetic variation studies. It represents the mesoderm cell lineage. Cells will be obtained from t he Coriell Institute for Medical Research [coriell.org] (Catalog ID GM12878). K562 is an immortalized cell line produced from a female patient with chronic my elogenous leukemia (CML). It is a widely used model for cell biology, biochemist ry, and erythropoiesis. It grows well, is transfectable, and represents the meso derm linage. Cells will be obtained from the America Type Culture Collection (AT CC) [atcc.org] (ATCC Number CCL-243). H1 human embryonic stem cells will be obtained from Cellular Dynamics Internatio nal [cellulardynamics.com]. Tier 2: HeLa-S3 is an immortalized cell line that was derived from a cervical cancer pat ient. It grows extremely well in suspension and is transfectable. It represents the ectoderm lineage. Many data sets were produced using this cell line during t he pilot phase of the ENCODE Project. In addition, these cells have been widely used in biochemical and molecular genetic studies of gene function and regulatio n. Cells will be obtained from the America Type Culture Collection (ATCC) [atcc. org] (ATCC Number CCL-2.2). HepG2 is a cell line derived from a male patient with liver carcinoma. It is a m odel system for metabolism disorders and much data on transcriptional regulation have been generated using this cell line. It grows well, is transfectable, and represents the endoderm lineage. Cells will be obtained from the America Type Cu lture Collection (ATCC) [atcc.org] (ATCC Number HB-8065). HUVEC (human umbilical vein endothelial cells) have a normal karyotype and are r eadily expandable to 108-109 cells. They represent the mesoderm lineage. Cells w ill be obtained from Lonza Biosciences [lonza.com]. Tier 2.5: SK-N-SH IMR90 (ATCC CCL-186)

A549 (ATCC CCL-185) MCF7 (ATCC HTB-22) HMEC or LHCM CD14+ CD20+ Primary heart or liver cells Differentiated H1 cells Additional information about the ENCODE common cell types, including cell growth protocols being used by ENCODE investigators, is available at http://genome.ucs c.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 an tibodies to DNA-binding proteins can be found at www.genome.gov/12513455. Top of page