GSM9759105: OX_Col_VIM24_Col_4-2; Arabidopsis thaliana; Bisulfite-Seq
Genomic DNA was extracted from leaf tissue of T1 plants. 200 ng of genomic DNA was sheared with a Covaris R230 ultrasonicator into 350 bp fragments. Libraries were generated following the protocol of NEBNext Ultra II DNA Library Prep kit (E765S, NEB) in combination with NEBNext EM-seq Adaptor (E7165AVIAL, NEB) and NEBNext Multiplex Oligos for Enzymatic Methyl-seq (E7140L, NEB). Bisulfite conversion was performed with the EZ-96 Methylation-Gold MagPrep kit (D5042, Zymo Research) prior to the PCR enrichment step, where the NEB Q5 polymerase was substituted by KAPA HiFi HotStart Uracil+ReadyMix (KK2801, Roche) to enable the amplification of uracil-containing DNA. Size selection and cleanup were performed with magnetic beads (AMPure XPbeads, A63881, Beckman Colter), and the quality of the final libraries was assessed with the Qubit dsDNA HS Assay Kit (Q32851, Invitrogen). Sequencing was performed by Novogene using an Illumina NovaSeq X Plus (PE150) platform.