Individual berries of Vitis vinifera Pinot Noir clone 48 berries were sampled from one vineyard at three development stages (prevéraison, midvéraison, and harvest)
Extracted molecule
total RNA
Extraction protocol
Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA). DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).
Label
Cy3
Label protocol
Labeling was performed in Deluc's Lab following NimbleGen cDNA synthesis and labeling reactions operating protocol. See www.nimblegen.com.
Hybridization protocol
Hybridization was performed by the Center For Genome Research and Biocomputing, OSU following their standard operating protocol. See www.nimblegen.com.
Scan protocol
Scanning was performed by the Center For Genome Research and Biocomputing, OSU following their standard operating protocol. See www.nimblegen.com. Each microarray was scanned using an Axon GenePix 4400A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.
Description
LDL4121-22
Data processing
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the ANAIS package software (Simon and Biot, 2011)
