title: HY-2
design: RNA samples were Zhongbai hypocotyl (7 days on MS), callus 1 (21 days on CIM K5), callus 2 (21 days on CIM M13), callus 3 (21 days on CI), shoot (28 days on SIM). Total RNA was extracted from those samples using RNAprep Pure plant Kit. RNase-Free DNase I was used to remove genomic DNA contamination (Takara Company, China) following the manufacturer&apos;s instructions. The quality and integrity of the total RNA was detected using an Agilent 2100 Bioanalyzer (Nanodrop 2000) and RNA integrity number values ranged from 8.6 to 10.0. Those high-quality total RNAs was used to construct RNA-Seq library. RNA-seq libraries were prepared using Ultra RNA Library Prep Kit (NEB, #E7770L). Library preparations were sequenced on the Illumina HiseqTM 2500 system to obtain 100-nt pair-end reads. Trimmomatic script with default parameter values was used to filter low quality reads and adapter sequence (Bolger et al., 2014).