Expression profile analyze to explore the genome-wide transcriptional landscape dictated by BnaA9.NST3

we conducted RNA-Seq analysis using WT, BnaA9.NST3-OE and BnaA9.NST3-KO leaves before flowering to explore the genome-wide transcriptional landscape dictated by BnaA9.NST3 in B. napus. The juvenile leaves at the vegetative state (30 days after seeding when six leaves fully expanded) were collected from wild-type (WT), BnaA9.NST3-overexpressing (three lines: OE-8, OE-10, and OE-11), and BnaA9.NST3-KO (two lines: KO-1 and KO-3), respectively, and immediately placed in liquid nitrogen and stored at -80 degrees centigrade. Total RNA was extracted using EZ-10 DNAaway RNA Mini-Prep Kit (Sangon Biotech, China) according to the manufacturer's instructions. RNA was pooled to yield six RNA samples, WT, OE-8, OE-10, OE-11, KO-1, and KO-3. Each sample has two biological replications. High-quality RNA was sent to Biomarker Technologies Co., Ltd. (Beijing, China) for sequencing and analysis. TopHat2 software was used for mapping to the reference genome (Darmor-bzh v4.1). The transcript abundance was calculated based on the fragments per kilobase of exon model per million mapped reads (FPKM).