Arabidopsis thaliana
5 day old seedlings were grown under white light and then were treated by shade for 1 hr or not treated. RNA was extracted from shoot tissues using the SpectrumTM plant total RNA kit from Sigma Aldrich (STRN250). Spectrum PolyA RNA was isolated from total RNA using the polyA Purist Kit (Ambion). One hundred nanograms of polyA-selected RNA was used in strand-specific RNA library construction following the manufacturer's protocol for the Whole Transcriptome Kit (Ambion). Amplified libraries were size selected using Ampure XP beads (Beckman) and sequenced for 50 bps on the SOLiD4 platform (Life Technologies).