title: RNA-Seq of Arabidopsis thaliana: 7d seedlings
design: Total RNA from wild type Col-0 and two SUPA-overexpression lines were purified using the Plant RNA Kit (OMEGA; R6827-01) according to the manufacturers instructions. 10 g total RNA was used for RNA-Seq analysis using the BGISEQ-500 platform (BGI, China) with paired-end sequencing, and 3 independent biological repeats were performed. In total, 9 strand-specific RNA-Seq libraries were sequenced in this study using the dUTP method. The paired-end reads were aligned to the Arabidopsis thaliana genome using tophat-2.0.11 with an anchor length of more than 8nt for spliced alignments. Only reads that could be uniquely aligned were retained for subsequent analysis. The expression levels of each gene were normalized as fragments per kilobase of transcript per million mapped reads (FPKM).