The ENCODE Project (Encyclopedia of DNA Elements) has been undertaken to identify all of the functional elements of the human genome sequence.
The GeneChip® ENCODE01 1.0 Array is a tool for genomic research and discovery. It can be used for de novo transcription mapping, chromatin immunoprecipitation (ChIP) assays, and other studies.
The ENCODE01 1.0 Array is designed to study the pilot ENCODE regions of DNA, comprised of 30 Mb of DNA, or approximately one percent of the human genome. These 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.
Half of the content on the ENCODE01 1.0 Array was manually selected by the NHGRI committee, while the remaining 50 percent was 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 includes 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. Content for the array was run against RepeatMasker and only non-repetitive sequences were included.
