GSM3317933: Col-0_RNAseq_rep2; Arabidopsis thaliana; RNA-Seq
For H3K9me2 ChIP-seq, nuclei were extracted with Honda buffer and digested with MNase, the resulting histone-DNA complexes were isolated with antibody. For GFP ChIP-seq, the nuclei were cross-linked by 1% formaldehyde and sonicated,  histone-DNA complexes were isolated with antibody. For BS-seq, DNA was extracted from 14-day-old leaves with CTAB. After complete bisulfite conversion of 2μg DNA with EZ DNA Methylation-Gold Kit (Zymo Research ,D5005), the DNA was sonicated to 250bp (Covaris) for library construction. For RNA-seq, total RNA was extracted from 14-day-old leaves using Trizol (Ambion). ChIP-seq Libraries were constructed using ACCEL-NGS®1S PLUS DNA LIBRARY KIT ( Swift Biosciences ,Cat. No. 18096) according to the manufacturer. BS-seq library was constructed following Illumina's manufacturer Instructions(Swift Biosciences, ACCEL-NGS® METHYL-SEQ DNA LIBRARY KIT, 30024). For RNA-seq, Libraries for two biological replicates of each genotype were constructed and sequenced according to the manufacturer's protocol (NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina®). The rRNA was depleted from total RNA using Ribo-ZeroTM rRNA removal Kit (Illumina). Illumina libraries were generated and sequenced using a 2x150 paired-end (PE) configuration on the HiSeq instrument (Illumina).