Transcriptome Analysis of Arabidopsis Transgenic Lines

RNA was extracted using Direct-zol RNA Miniprep kit (Zymo). For RNAseq involving ZF108–TET1cd and ZF108–YPet plants, 75 ng of total RNA was used to prepare libraries using the Neoprep stranded mRNA-seq kit (Illumina). For RNA-seq involving ZF1CACTA1–TET1cd, ZF2CACTA1–TET1cd, SunTagFWAg4-14aa, and SunTagFWAg4-22aa plants, 1 μg of total RNA was used to prepare libraries using the TruSeq Stranded mRNA-seq kit (Illumina). Reads were first aligned to the TAIR10 gene annotation using Tophat (46 (link)) by allowing up to two mismatches and only keeping reads that mapped to one location. When reads did not map to the annotated genes, the reads were mapped to the TAIR10 genome. Number of reads mapping to genes were calculated by HTseq (47 (link)) with default parameters. Expression levels were determined by RPKM (reads per kilobase of exons per million aligned reads) using customized R scripts.