Figure 1.

Dye-swap hybridization experiment. (a,b) Dye-swap hybridization protocol on microarrays fabricated with cDNAs from EST projects 606 (immature ear, IME), 614 (4-day seedling roots, 4DR), and 707+945 (mixture of adult tissues). Each image was obtained from co-hybridization of two dye-labeled targets on a single microarray. Two false-color images were superimposed to represent the relative amount of transcripts in the samples. (a) IME labeled with Cy3 (green) and 4DR with Cy5 (red); (b) samples labeled reciprocally. Arrows and arrowheads in (a) and (b) indicate a few obvious examples of organ-specific expression (see (d)). (c) Consistency of hybridization was examined by calculating signal-ratio differences from the dye-swapping experiment for each microarray element. Log₂ signal ratios of 4DR over IME were calculated from each hybridization, followed by subtraction of the log₂ ratios from slide (a) by those on slide (b). (d) Relative transcript abundances in the two samples were plotted against the sum of signal intensities from both channels. Log₂ signal ratios of 4DR over IME were averaged from the dye-swap experiment. Difference of log₂ ratio and average of log₂ ratio are given by [log₂(4DR/IME)a]/ [log₂(4DR/IME)b] and [log₂(4DR/IME)a + log₂(4DR/IME)b]/2, respectively.