Oligonucleotide array on glass. Microarray pattern generation. We downloaded genome and transcript sequences from the National Center for Biotechnology Information on January 8, 2003. We aligned RefSeq, mRNA, EST57 and patent transcripts to the genome using sim458 and identified all exons and exon-exon junctions. We also aligned mouse transcripts to the human genome to identify possible splice forms not yet present in human transcript databases59. An optimized 60 nt probe was designed to monitor each exon and a 36 nt probe was centered across each exon-exon junction60. Exons less than 60 nt were monitored using shorter probes attached to T-stilts. Probes predicted to perform poorly, such as those associated with repeat sequences or containing unacceptable GC-content, were discarded. In total, 383,014 oligonucleotide probes to monitor 203,672 exons and 178,351 exon-exon junctions in 17,939 genes were synthesized to a 17 array set, with each array containing 23,107 non-control probes. Arrays were ordered from Agilent (California). Probes have been mapped to the hg18 genome and can be viewed with the UCSC genome browser using a supplemental probe alignment file (see Probes.GenomeAlignments.psl linked at the foot of the record) in BED format.
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