be1-3 2 days on SIM
be1-3 hypocotyl explants for RNA-seq were culture on CIM for 7 days, and were subsequently transferred onto SIM and cultured for 2 days. Total RNA was prepared using an RNApure Plant Kit with DNase I (Beijing Cowin Biotech Co., LTD, Cat. No. CW0559) according to the manufacturer’s instructions. Purified RNA was assessed for integrity using an Agilent 2100 Bioanalyzer. RNA-seq was performed at Beijing Genomics Institute (BGI) (China). mRNA was isolated with Oligo(dT) magnetic beads, and then broken into short fragments (about 200 bp). Taking these short fragments as templates, first-strand cDNA and second-strand cDNA were synthesized. The double strand cDNA was purified with a QiaQuick PCR extraction kit (QIAGEN, Cat. No.28106) and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Next, the short fragments were ligated to Illumina sequencing adaptors. The fragments of a selected size were purified by agarose gel electrophoresis and enriched by PCR amplification. Finally, all amplified libraries were simultaneously sequenced using an Illumina HiSeq™ 2000 sequencing machine.