GeneChip® ENCODE 2.0R Array is an updated research tool for studying ENCODE human pilot DNA regions
	•	Versatile array is compatible with multiple applications
	•	Exceptionally high-resolution 7 base pair tiling design offers most detailed genomic view
	•	25-mer probes yield the most specific hybridization results available

Array Profile

The ENCODE Project (Encyclopedia of DNA Elements) has been undertaken to identify all of the functional elements of the human genome sequence. The ENCODE Project is further described at: www.nhgri.nih.gov/10005107. The GeneChip ENCODE0 2.0 Array is a tool for genomic research and discovery. It can be used for de novo transcription mapping, chromatin immunoprecipitation (ChIP)-chip assays, and methylation studies.

The ENCODE 2.0 Array is the second generation GeneChip® Array designed to study the ENCODE pilot DNA regions, comprised of 30 Mb of DNA, or approximately 1 percent of the human genome. The ENCODE 2.0R Array offers updated genomic content and a greater genomic resolution than the previous generation ENCODE01 1.0 Array. Genomic content for the ENCODE 2.0R Array is drawn from NCBI human genome assembly (Build 35). Oligonucleotide probes to interrogate the ENCODE pilot DNA sequence are tiled at an average resolution of 7 base pair, as measured from the central position of adjacent 25-mer oligos, creating an overlap of approximately 18 base pairs. Repetitive elements were removed by RepeatMasker.

ENCODE pilot regions were selected by a committee of the National Human Genome Research Institute (NHGRI) and will serve as a pilot for further microarray-based ENCODE research. The UCSC genome browser includes ENCODE content at the following site: http://genome.ucsc.edu/ENCODE/regions.html. Half of the content on the ENCODE 2.0 Array was manually selected by the NHGRI committee, while the remaining 50 percent were randomly selected. The manually selected regions were chosen based on the presence of well-studied genes or other known sequence elements, and the existence of a substantial amount of comparative sequence data. A total of 14.82 Mb of sequence was manually selected and include 14 targets ranging in size from 500 kb to 2 Mb. To ensure good sampling of genomic regions varying widely in their content of genes and other functional elements, the randomly selected content includes thirty 500 kb regions, selected based on gene density and level of non-exonic conservation.

Instrument and Software Requirements