4.3. Preparation and Sequencing of the RNA-Seq Library

A total of eight shoot tissue samples (two inbred lines × two treatments × two biological replicates) were collected at the same point in the light/dark cycle as 10 a.m. time point, immediately frozen in liquid nitrogen, and stored at –80 °C until further processing. Shoot tissues from three different plants were pooled to obtain sufficient RNA for each extraction. For RNA-seq library construction, total RNA was isolated from shoot tissue and cDNA was synthesized as described by Jung et al. [32]. The RNA-seq libraries were created using the Illumina TruSeq RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol. The RNA-seq library was PCR-amplified and sequenced on an Illumina HiSeq 2000 platform. A 101-bp paired-end sequencing protocol was used, and two biological repeats were performed for each sample. All raw, read data generated in this study were deposited in the Gene Expression Omnibus (GEO) functional genomics data repository of National Center for Biotechnology Information under accession number {"type":"entrez-geo","attrs":{"text":"GSE125875","term_id":"125875"}}GSE125875: lists the GEO DataSeries.