Figure 7From: Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicingDependence of negative discrimination on junction probe length. Intensity of probes of different length tiled across the junction between exon 9 and exon 12, which are not connected in the RB1 transcript. Light blue, length 30 nucleotides; red, 40; dark blue 50; green, 60. Vertical colored dotted lines mark where probes make a transition from completely within an exon to chimeric junction probes spanning both exons. At 35% formamide, the intensities of the 20-nucleotide probes are largely at background levels and are not shown, while 60-mers (green) show little decrease in signal while spanning a 'false' junction. Background level is shown by the black dashed line at the bottom of the figure.Back to article page