title: RNA-Seq analysis of wild-type (JC66) Arabidopsis thaliana 12-day-old seedlings rep3
design: Twelve-day-old seedlings of wild-type GSTF8 promoter::luciferase reporter line JC66 (in Col-0 background) were grown vertically on MS agar plates. Sample consists of tissue pooled from 15-20 whole seedlings grown at the same time in the same environment, then frozen in liquid nitrogen, and stored at 80°C. Three biological replicates were conducted for each genotype. Total RNAs were extracted using the Qiagen RNeasy Plant Mini kit. DNase treatment was performed after RNA isolation using TURBO DNase followed by treatment with the DNase Inactivation reagent (Ambion). The quality and quantity of the extracted RNAs were determined by a Bioanalyzer. Illumina TruSeq libraries were generated from 1 µg of total RNA according to the manufacturer's instructions and sequenced on a HiSeq1000 platform (Illumina) as 100 bp paired-end reads. RNA-seq paired-end reads were trimmed for low-quality base-calls and Illumina adapter sequences via Cutadapt (v1.1). Reads trimmed to less than 25 bp were discarded and remaining reads sorted into pairs and singleton reads. RNA-seq reads were mapped to the TAIR10 Arabidopsis genome reference via Tophat (v2.0.9).