GSM9872912: Standard WGBS, 50 ng Arabidopsis leaf DNA, replicate 3; Arabidopsis thaliana; Bisulfite-Seq
Flash-frozen Arabidopsis thaliana leaf tissue was cryo-milled using a TissueLyser II and lysed with Proteinase K. A serial dilution series of the extracted genomic DNA (5 pg-50 ng) was processed using the EZ DNA Methylation-Direct kit (Zymo Research), which performs bisulfite conversion directly from the digested lysate without a separate DNA purification step. Bisulfite-converted DNA was processed using a post-bisulfite adapter tagging (PBAT) workflow adapted from the single-cell methyl-seq (snmC-seq) protocol: random priming with a P5L-indexed primer (Klenow Fragment exo-), enzymatic removal of excess primer (Exonuclease I / rSAP), single-stranded adapter ligation to the 3' end using the xGen Adaptase module, and indexing PCR (KAPA HiFi HotStart, 19-21 cycles) to introduce P5/P7 indexes. Standard bulk WGBS libraries (50 ng input, samples S45_1-3) were prepared conventionally for comparison.