Skip to main content

Table 3 Comparison of hybridization signals between oligonucleotide and PCR probes.

From: A novel design of whole-genome microarray probes for Saccharomyces cerevisiae which minimizes cross-hybridization

Exp. A Total number of spots Median Mean
   Background Probes Background Probes TA
Oligonucleotide       
Cy5 channel 1718 162 1616 166 4561 27.5
Cy3 channel 1718 299 1535 301 3760 12.5
PCR 6      
Cy5 channel 9962 155 1619 157 2181 13.9
Cy3 channel 9962 291 1666 295 2123 7.2
Exp. B Total number of spots Median Mean
   Background Probes Background Probes TA
Oligonucleotide       
Cy5 channel 1576 177 845 175 3512 20.0
Cy3 channel 1576 339 822 350 2280 6.5
PCR       
Cy5 channel 9936 172 2047 170 3093 18.2
Cy3 channel 9936 346 1600 355 2194 6.2
  1. Intensities and corresponding background values were computed separately for oligonucleotide and PCR probes. Experiments were done twice (Exp. A and B) using microarrays from batch J100B. Cy3- and Cy5-labelled cDNA targets were prepared from the total RNA isolated from the wild-type strain BY4742 and Δydr225w, respectively. For each channel, the distribution of intensities for all genes was computed for oligonucleotide or PCR probe. Results are given by median and mean of the intensities. The transcript abundance (TA) is the mean intensity of probe over mean intensity of background.