Nimblegen microarray 090818 vitis exp hx12

Total RNA was extracted from samples using the Spectrum plant total RNA kit (Sigma, www.sigmaaldrich.com) as recommended by manufacturer. DNase I digestion was carried out with the RNase-Free DNase Set (QIAGEN). RNA integrity and quantity were assessed with a Nanodrop 2000 spectrophotometer (Thermo Scientific) and an Agilent's Bioanalyzer 2100. Microarray hybridizations were performed at the Genomics Unit of the National Centre for Biotechnology (CNB-CSIC, Madrid).
Synthesis of cDNA, labeling, hybridization, and washing steps were performed according to the NimbleGen arrays user's guide. Each sample was hybridized to a NimbleGen microarray 090818 Vitis exp HX12 (Roche, NimbleGen), which contains probes targeted to 29,549 predicted grapevine genes and 19,091 random probes as negative controls. Images were analyzed using NimbleScan v2.6 software (Roche), which produces.xys files containing the raw signal intensity data for each.

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.

We performed cDNA synthesis, labeling, hybridization, and washing steps according to the NimbleGen Arrays User’s Guide (version 3.2). Ten μg of total RNA was used for each sample. Labeled cDNA was hybridized to 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), and 19,091 random probes as negative controls. Each microarray was scanned using an Axon GenePix 4400A (Molecular Devices, Sunnyvale, CA, USA) at 532 nm (Cy3 absorption peak) and GenePix Pro7 software (Molecular Devices) according to the manufacturer’s instructions. All microarray expression data will be made available in the Gene Expression Omnibus (GEO) website under the accession name GSE55302 on November 1, 2014.