Transcriptomic analysis reveals new role of circadian-regulated StBBX20 protein in potato reproduction

Analysis of gene expression in the apical shoot parts and stolons of StBBX20-silenced and -overexpressed potato lines was carried out via RNA-seq (two biological replicates). 5- and 7-week-old apical shoot parts (Figure S3) and 3-week-old stolons (Figure S4) samples were collected at ZT6 from four plants per pot (pooled technical replicates). Total cellular RNA was prepared using TRI Reagent® RT (Molecular Research Center, Inc.) and treated with DNase I during RNA purification. The quality and quantity of RNA were verified using a DS-11 FX spectrophotometer (DeNovix Inc.). RNA integrity number (RIN) of samples sufficient for sequencing (= 7) and rRNA ratio (= 1.7) was checked using Bioanalyzer RNA Nano 6000 chip (Agilent Technologies, Inc.). cDNA library construction using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) and sequencing using an Illumina platform with a 2 × 150 bp PE configuration were conducted by Macrogen Inc. (Seoul, Republic of Korea).