array scanning and feature extraction protocol
Agilent G2565BA Microarray Scanner and Feature ExtractionVersion: 11.0, http://www.chem.agilent.com/Library/usermanuals/Public/G2566-90017.pdf, Scanner manual for software release 7.0. Data extraction using protocol GE1_1105_Oct12
nucleic acid hybridization to array protocol
17 h at 65°C following Agilent One-Color_GE_5.7 protocol
nucleic acid labeling protocol
500ng RNA was used for labelling as described in the Agilent one color microarray-based gene expression analysis protocol version 5.7
sample collection protocol
Leaf discs were taken from three to five plants per biological replicate at each time point. Tuber parenchyma samples were taken from individual tubers. Tuber samples were taken at harvest. Tubers grown at normal temperatures and exhibiting a normal growth phenotype were used as control. Tubers subjected to the heat treatment and exhibiting a second-growth phenotype (chain tubers) were grouped into primary (attached to stolon from plant) and secondary tubers (attached to stolon from primary tuber).
nucleic acid extraction protocol
RNA extraction was performed according to Logeman et al. (1987) and purified using Rneasy Kit (Qiagen).
control conditions were 21°C at day and 19°C at night at an 16h light / 8h dark cycle. Heat conditions were 29°C at day and 27°C at night.
Plants were grown in greenhouse under ambient conditions (21°C/ 19°C, 16h light, 8h dark) until tubers were visible (47 days). Ten plants were transferred to elevated temperatures (29°C at day and 27°C at night) in a phytochamber for 1 week and then transferred back to control temperatures for 2 more weeks until harvest. Tubers were harvested 2 weeks after retransfer. Leaves were sampled before heat stress, at the end of heat stress and at time of harvest. Control plants were kept greenhouse under ambient conditions (21°C/ 19°C, 16h light, 8h dark) for the duration of the experiment.