Figure 2
High consistency of log-ratio measurements across a 20-fold range of hybridized material. Heat map of mean-centered log2(Cy5/Cy3) ratios for six genes representing a 32-fold intensity range (see Figure 1A) across a 20-fold range of hybridized material. For each gene the maximum percent fold-difference (Δmax) between any two of the triplicate averages is also shown. As a final assessment of array performance relative transcript abundances at eight IDC time points were measured at 6-hour intervals. At each time-point P. falciparum strain 3D7 total RNA was isolated, reverse transcribed, and Cy5-coupled. These eight samples were each hybridized to one of the eight arrays on a single 8x15K slide, along with an equal amount of Cy3-labelled reference pool. To illustrate correspondence of these results with previously published work, 47 periodically expressed reference genes were chosen that peak in expression within successive three-hour windows [9]. This reference set (available as a table in Additional file 7) can be used for easy visualization of a variety of time-course attributes such as synchrony, progression through the IDC, correct ordering of time-points, etc. As expected, the abundance profiles of these reference transcripts reproduced the characteristic “barber-pole” pattern of the IDC transcriptional cascade (Figure 3) and mirrored existing results at corresponding time points (median Pearson’s = 0.95). [11, 49]. The results remained consistent when extending this comparison genome-wide (median Pearson’s r = 0.83).