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Figure 1 | Genome Biology

Figure 1

From: Gene-expression profile comparisons distinguish seven organs of maize

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.

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