2.2 RNA extraction and sequencing
The frozen berries were ground to a fine powder under liquid nitrogen using mortar and pestle. Total RNA was isolated from approximately 120 mg tissue powder by using Spectrum Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO, USA) following the manufacturer’s instructions. Contaminating DNA was removed with on-column digestion using DNase I (Sigma-Aldrich).
For constructing RNA libraries, the RNA was qualified with both NanoDrop 2000c UV–vis spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and Experion Bioanalyzer (Bio-Rad laboratories, Hercules, CA, USA). To segregate the mRNA from total RNA, poly-A was captured using oligo (dT) Dynabeads (Invitrogen, Carlsbad, CA, USA). Before library preparation, all the samples were qualified by an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The libraries were prepared with NEBNext Ultra II RNA Library Prep Kit (New England Biolabs Inc., Ipswich, MA, USA). Sequencing of RNA libraries was performed using an Illumina Hiseq2000 platform (Illumina, San Diego, CA, USA) with paired-end sequencing strategy (PE-150bp) at the Novogene sequencing services facility (Cambridge Science Park, UK). Libraries were prepared with three biological replicates for each blue, red, and white (control) light treatments.