Transcript mapping with GeneChip® Tiling Arrays enables you to interrogate genomes at regular intervals, including both annotated and unannotated regions. With their unbiased approach to genome interrogation, GeneChip Tiling Arrays are an important tool in discovering novel transcripts and building newer, more up-to-date annotations. Recently, Affymetrix tiling arrays have played an important role in the ENCODE project, where they have been used to challenge the traditional protein-coding, gene-centric view of the human genome.

Unbiased Design, Industry-leading Content

Tiling arrays used for transcript mapping utilize perfect-match and mismatch probes and, in combination with Affymetrix' industry-leading 6.4 million features per array, provide the greatest coverage available. Whole-genome sets are available for human and mouse and single-array designs for Arabidopsis, Drosophila, Caenorhabditis elegans, Saccharomyces cerevisiae and Schizosaccharomyces pombe—detect more, with fewer arrays. Single-array designs are also available for chromosome 21/22, ENCODE regions.

GeneChip® Tiling Arrays for Transcript Mapping

GeneChip® Tiling Arrays for transcript mapping employ an unbiased array design strategy that enables you to interrogate entire genomes without relying on annotations. With 6.4 million features per array and 25-mer probes spaced every 10 base pairs (bp), GeneChip Tiling Arrays offer more content per array than any other platform.

• Human Tiling 1.0R Array Set
• Mouse Tiling 1.1R Array Set
• Drosophila 2.0R Array
• Arabidopsis Tiling 1.0R Array
• C. elegans 1.0R Array
• S. pombe Tiling 1.0FR Array
• S. cerevisiae Tiling 1.0R Array
• Chromosome 21/22 2.0R Array
• Encode 2.0R Array

Tiling Array Tools

Tiling Array Software (TAS) and the Integrated Genome Browser (IGB) are available for preliminary data analysis and visualization of peaks. Advanced data analysis can be performed with a variety of GeneChip-compatible™ and academic software packages.

Transcript Mapping Publications

Denoeud F., et al. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Research 17:746-759 (2007).

Kapranov P., et al. Genome-wide transcription and the implications for genomic organization. Nature Reviews Genetics 8:413-423 (2007).

Kapranov P., et al. Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Research 15:987-997 (2005).

Rozowsky J.S., et al. The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci. Genome Research 17:732-745 (2007).

The ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816 (2007).