Affymetrix announces new ChIP-On-Chip array range
its designers hope will provide drug researchers with new
whole-genome tools to assist scientists discover DNA-Protein
interactions.
Laboratory researchers can use the GeneChip tiling arrays to map sites of DNA-protein interaction in chromatin immunoprecipitation (ChIP)-on-chip experiments to discover new RNA transcripts or investigate global epigenomic changes like methylation or acetylation.
Affymetrix tiling arrays interrogate all of the non-repetitive portions of the various genomes. For example, the human tiling arrays interrogate nearly 90 million data points at regular 35 base pair intervals across the human genome.
The complete tiling array systems include an assay kit, analysis software and an integrated browser that enables researchers to compare experimental results to computational results.
Affymetrix has also released a tested and qualified assay protocol for chromatin immunoprecipitation experiments.
The tiling array products to be made available include the Human Tiling 2.0R Array Set, a seven-array set designed for ChIP-on-chip experiments (A-G arrays also available separately)
The Human Promoter 1.0R Array is an array comprised of more than 4.6 million probes tiled to interrogate more than 25,500 human promoter regions, enabling researchers to easily identify thousands of regulatory sequences
Affymetrix's Mouse Tiling 2.0R Array Set is available as a seven array set for ChIP-on-chip experiments (A-G arrays also available separately) as is the Mouse Promoter 1.0R Array an array comprised of more than 4.6 million probes tiled to interrogate more than 28,000 mouse promoter regions, enabling researchers to easily identify thousands of regulatory sequences
Tiling array products made available during the second quarter, include the ENCODE01 1.0R Whole-genome Human Tiling Arrays, an array designed to study the pilot ENCODE regions of DNA, or approximately one per cent of the human genome.
The ENCODE Project (Encyclopedia of DNA Elements) has been undertaken to identify all of the functional elements of the human genome sequence.
"We are pleased with the performance of the GeneChip tiling arrays for mapping transcription factor binding sites by ChIP-on-chip," said Myles Brown, associate professor of Medicine, Harvard Medical School and participant in Affymetrix' Tiling Array Early Access Program.
"These arrays have allowed us to comprehensively explore the non-repetitive regions of the entire human genome. This unbiased approach is already leading us to important new insights into the gene regulatory networks controlled by steroid hormones and their receptors."
For the past six years, Affymetrix scientists have been pioneering tiling microarray technology. Thomas Gingeras, vice president of biological science, and his team at Affymetrix Research Laboratories have used the tiling arrays to uncover broad transcriptional activity in large regions of the genome that were once considered "junk" DNA.
"Affymetrix tiling array technology is revealing a very important and unappreciated genetic realm that is challenging fundamental concepts of biology," said Gingeras.
"Using these arrays, we have been able to discover novel non-coding RNA transcripts and map the sites of DNA-protein interactions."
