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

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

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

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.

ISSN: 1471-2164