GSM7050869: WGBS20 [pool 04]; Populus nigra; Bisulfite-Seq
Total genomic DNA was extracted from fresh leaves with the Qiagen Plant DNA kit (Hilden, Germany). The integrity of the DNA was assessed on 1.5% agarose gels, and DNA quantification was performed with Quant-iT™ PicoGreen® dsDNA Assay Kit (Thermo Fisher Scientific, Massachusetts, USA) using a Synergy HT plate reader (BioTek, Vermont, USA). Up to 250 ng of DNA was fragmented to 300 bp with a Covaris S2 sonicator prior to whole-genome library preparation (NEBNExt Ultra II kit), ligation of methylated adaptors and size selection on 2% E-gels (400-550 bp). Bisulfite conversion was performed using the EZ DNA methylation gold kit (Zymo Research), followed by an enrichment PCR of 12 cycli. Paired-end 100-bp sequencing of the library fragments was performed on an Illumina Novaseq S2 sequencer, generating on average 83,886,466 ± 14,181,156 reads (mean ± SD) and an average read depth of approximately 17x.