Figure 3

Design and overall performance of the 44 k gene-oriented intron-exon expression oligoarray. (a) Schematic view of the 44 k combined intron-exon expression oligoarray 60-mer probe design. Probe 1 is for the antisense PIN transcripts (blue arrow). Probes 3 and 4 are a pair of reverse complementary sequences designed to detect antisense or sense TIN transcripts (black and hashed black arrows, respectively) in a given locus. Sense exonic probes 2 and 5 are for the protein-coding transcripts (red block and red arrow). Note that the latter were not systematically designed for an exon near the TIN message; in most instances a distant, 3' exon of the gene has been probed instead. (b) Average signal intensity distribution for antisense TIN (solid black line), sense TIN (dashed line), antisense PIN (blue line), or sense protein-coding exonic (red line) probes. Average intensities from six different hybridization experiments with three different human tissues, namely liver, prostate and kidney, are shown. Only probes with intensities above the average negative controls plus 2 SD were considered. The average intensity distribution for probes below this low-limit detection cutoff is shown in the curve marked as 'Not expressed RNAs' (gray line).