GSM9045727: TWGBS batch_C_cdca7ab_1_G8,rep2; Arabidopsis thaliana; Bisulfite-Seq
Genomic DNA was extracted from rosette leaves with the DNeasy Plant Pro kit (Qiagen, reference 69206), following the manufacturer's instructions. Illumina libraries of sodium bisulfite-converted DNA were prepared with a tagmentation-based approach (Wang et al. 2013) with modifications (Montgomery and Berger, 2023, bioRxiv). Briefly, we tagmented 50 ng of DNA with Tn5 (Molecular Biology Services, IMP, Vienna, Austria). Tagmented DNA was purified with the Zymo DNA Clean and Concentrator kit (Zymo Research) instead of SPRI beads. After oligonucleotide replacement, gap repair, and purification, we used the entirety of the eluted DNA for bisulfite conversion, which was performed with the EZ DNA Methylation-Gold Kit from Zymo (reference D5006). The rest of the protocol was performed as indicated by Wang et al (2013). Directional libraries were amplified with Nextera-compatible unique dual indices and sequenced on a NovaSeq 6000 instrument using an S4 flow cell to generate paired-end 150 bp reads with around 25 million reads per sample.