Sugarcane Drought Stress Transcriptome Analysis

Oligoarray sample preparation and analysis was performed as described in Lembke et al. [20 (link)], using two biological replicates for control and treated samples from: (i) 4 or 6 days of water privation, and 2 days of re-watering (greenhouse-grown plants); and (ii) 7 months after planting (field-grown plants). Only RNA samples with RIN ≥ 6.5 were selected, and hybridizations were performed using the customized sugarcane Agilent oligoarray platform [20 (link)]. The arrays contained probes to detect the sense and antisense expression of 14,522 different Sugarcane Assembled Sequences (SAS), which are reference sequences for sugarcane transcripts [42 (link)]. Hybridized oligoarray slides were scanned in GenePix 4000B scanner (Molecular Devices, San Jose, CA, USA), and image data were extracted with the aid of the Feature Extraction 9.5.3 (Agilent Technologies, Santa Clara, CA, USA) using the two-color oligoarray referential in the Agilent platform intensity [105 (link)] from Cy3 and Cy5 was corrected and normalized using the Lowess function [106 (link)] implemented in the R software. Microarray data files are deposited at the Gene Expression Omnibus (GEO) public database, series record GSE125069.