Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis (time series)

A novel experimental design strategy (A Mead et al, in preparation), based on the principle of the “loop design”, was developed to enable efficient extraction of information about key sample comparisons using a two-colour hybridisation experimental system. With 192 distinct samples (four biological replicates at each of 24 time points in mock and treated conditions) to be compared, the experimental design included 288 two-colour microarray slides, allowing four technical replicates of each sample to be observed. One third of the slides were devoted to assessment of changes in gene expression between time points, using a simple loop design to link samples from time points across the 24 sampled times, directly comparing samples collected on adjacent sampling times (i.e. 2 hrs post-infection with 4 hrs post-infection, 4 hrs post-infection with 6 hrs post-infection, etc.). With the remaining slides, four separate loops were constructed comparing treatments, biological replicates and samplling times. infected vs. mock, 24 time points, randomized loop, 576 Imagene files