Vitis Microarray Expression Analysis

Ten μg of total RNA from each sample was used for hybridization onto a NimbleGen microarray 090818 Vitis exp HX12 (Roche, NimbleGen Inc., Madison, WI, USA), which contains probes targeted to 29,549 grapevine genes predicted from the V1 annotation of the 12x grapevine genome (https://urgi.versailles.inra.fr/Species/Vitis/Annotations). cDNA synthesis, labeling, hybridization, and washing steps were performed by MOgene (St. Louis, MO, USA) according to the NimbleGen Arrays User’s Guide (version 3.2). Data were processed, normalized and analyzed as in [41 (link)]. As in Cramer et al. [41 (link)], a note of caution should be held when examining the microarray data sets due to the likelihood of cross-hybridization of certain Vitis gene families with high similarity and are denoted in pink in Additional file 5.