How is this array design principle different from the GeneChip® Human Genome U133 type of arrays?
The GeneChip® Exon Arrays represent a new array design philosophy for the most comprehensive and informative coverage with the exon as the basic unit of expression analysis. Such an inclusive design enables discovery of new and novel splicing events not previously observed experimentally. Some of the key differences are summarized below using the human arrays as an example; refer to the "GeneChip® Exon Array Design" Technical Note and the "Design and Performance of the GeneChip® Human Genome U133 Plus 2.0 and Human Genome U133A 2.0 Array" Technical Note for more details.
Array Statistics Summary |
GeneChip® Human Exon 1.0 ST Array |
GeneChip® Human Genome U133 Plus 2.0 Array |
|---|---|---|
| Probe sets | 1.4 million | 54,000 |
| Exon clusters | > 1 million | N/A |
| Supported by putative full-length mRNA | 289,961 probe sets | N/A |
| # of perfect match probes for each probe selection region | 4 | 11 |
| Background subtraction strategy | Median intensity of up to 1,000 background probes with the same GC content | One mismatch probe for every PM probe |
| Probe selection region location | Along the entire length of the transcripts | Most 3' end |
| Probe selection region length | Median 123 bp | 600 bp |
| Number of probes for each RefSeq Sequence | Median 30 - 40 | 11 |
| Interrogated strand | Sense | Antisense |