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The GeneChip Rat Exon 1.0 ST Array is a single array with almost 4 million unique 25-mer oligonucleotide features constituting approximately 1 million probe sets. Based on annotations against the June 2003 build of the rat genome sequence, these 1 million probe sets can be grouped into over 850,000 exon clusters (1 or more overlapping exons) and over 73,000 transcript clusters (groups of putative alternatively spliced transcripts from the same gene) containing more than 1 probe set for the most comprehensive genome-wide expression profiling at the exon level. The design includes (not mutually exclusive):
• 195,943 probe sets with Ensembl transcript support
• 92,038 probe sets with putative full-length mRNA support
• 211,451 probe sets with EST support
• 272,061 probe sets with human or mouse mRNA support
• 875,666 probe sets with gene prediction support
The design of the Rat Exon 1.0 ST Array adopts an inclusive design strategy by projecting both the publicly available, empirically obtained, cDNA-based content and results from gene prediction algorithms on the rat genome assembly from June 2003. Combining all of the input sequence information, boundaries of exons and probe selection regions (PSRs) are defined. Probe sets are then selected for the PSRs of 25 bases or more in length. Empirical sequences are obtained from sources such as rat RefSeq, GenBank® mRNAs, and dbEST. Mouse and human cDNAs are mapped onto the rat genome using genome synteny information from the genome browser group at the University of California, Santa Cruz. Gene predictions include those from published algorithms such as GENSCAN, GENSCAN Suboptimal, Ensembl, geneid, sgp, and TWINSCAN. Other miscellaneous content on the array includes the microRNA Registry.