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Quantitative PCR, transcriptome, and methylation analysis RNA was isolated using TRIzol, DNase I-digested and cleaned using R1014 RNA Clean & Concentrator-5 kit (Zymo Research), cDNA synthesized using the qScript Flex cDNA kit (95049 Quanta) using oligo dT, and real-time quantitative PCR (qPCR) was carried out using the PerfeCTa SYBR Green FastMix (Quanta), both as previously reported [107], using primers listed in Table S2
