GSM6185737: H3K27me3 ChIPseq TRB1 ZF replicate 2; Arabidopsis thaliana; ChIP-Seq
ChIP seq: Libraries were prepared with Ovation Ultra Low System V2 kits following the manufacturer's instructions. BS seq: 300 ng of DNA was sheared to 200bp with a Covaris S2 (Covaris). Libraries were prepared with the Epitect Bisulfite Conversion kit (QIAGEN) and the Ovation Ultralow Methyl-seq kit (NuGEN) following the manufacturer's instructions. RNA seq: 1 ug of total RNA was used for library preparation with TruSeq Stranded mRNA kit (Illumina). Libraries were sequenced on HiSeq 2500 or NovaSeq 6000 (Illumina). Plants total RNAs were extracted with TRIzol and Direct-zol RNA Miniprep kit (Zymo, R2050). Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina) following the manufacturer instructions. RNA-seq library preparation: Plants total RNAs were extracted with TRIzol and Direct-zol RNA Miniprep kit (Zymo, R2050). Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina) following the manufacturer instructions. ChIP-seq library preparation: 10 grams of inflorescence and meristem tissues were used for Flag, H3, H3K4me3, and H3K27me3 ChIP-seq. ChIP were performed as described previously60 with anti-FLAG M2 (Sigma), anti-H3 (Ab1791, Abcam), anti-H3K4me3 (Milipore Sigma 04-745),  andanti-H3K4me3 (Milipore Sigma 07-449) antibodies. BS-PCR and McrBC assay for FWA tandem repeat: For BS-PCR of FWA tandem repeat, genomic DNA was extracted from leaf tissue of TRB-ZF T2 lines as well as fwa with CTAB-based method and converted using the Epitect Bisulfite kit kit (Qiagene research). Methylation level of FWA promoter region and several control regions have been amplified with primers described previously46. HiSeq 2500 (Illumina) sequencing libraries were made from purified PCR products using a Kapa Hyper DNA Library Prep kit. For McrBC of FWA tandem repeat, genomic DNA was extracted from leaf tissue with CTAB-based method, and treated with PureLink RNase (Invitrogen) and then with McrBC (NEB) for 4 hours at 37°C. FWA tandem repeat region was quantified by qPCR.