Total RNA was extracted from leaf mibrids and petioles using the Qiagen Extraction Kit protocol (Qiagen Inc, Vanecia, CA). RNA quality and quantity were determined using a Nanodrop 2000 instrument (Thermo Scientific, Wilmington, DE) and a Bioanalyzer Chip RNA 6000 Nano LabChip kity (Agilent, Santa Clara, CA).
Label
Cy3
Label protocol
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Hybridization protocol
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
Scan protocol
The microarray was scanned using a ScanArray 4000XL (Perkin-Elmer) at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers’ instructions. Images were analyzed using NimbleScan v2.5 software (Roche).
Data processing
Data were processed using NimbleScan v2.5 software (Roche). RMA normalized data were obtained using the affy package of the R statistical programming language.
A microarray analysis highlights the role of tetrapyrrole pathways in grapevine responses to stolbur phytoplasma, phloem virus infections and recovered status
