Overview of probe design: genomic coordination of TSSs and CAGE-TSSchip probes. The upper four tracks are an arrangement example of full-length transcripts (cDNA) and 5'-ends of transcripts derived from various methods (cap analysis gene expression [CAGE], 5'-expressed sequence tag [EST], and 5'-end of gene identification signature/gene signature cloning ). Tag clusters (TC; green arrow) are the overlapping regions of the 5'-ends. The most frequent transciption start site (TSS) for each TC is the representative position (vertical line from TC arrows). Fragments for the probe design, of 120-nucleotide long genomic sequences, starts from the representative position of each TC fragment, shown by cyan arrows. If the fragment overlaps the 5'-end of any exon-intron junction (diamond of cDNA and 5'-EST transcripts), the fragment skips the intron to the next exon. According to the Agilent probe design service, the 60-nucleotide appropriate region within each fragment would then be suggested for array probes (probe; blue arrows). Details of probe preparation are available in Additional data file 8.
Katayama et al. Genome Biology 2007 8:R42 doi:10.1186/gb-2007-8-3-r42