library_construction_protocol: Genomic DNA extraction, followed by phenol/chloroform extraction and ethanol precipitation. RNaseA treatment was performed for 30 min at 37C Prior library preparation unmethylated Lambda phage DNA and SssI-methylated T7 DNA were spiked-in to genomic DNA samples to control bisulphite conversion rates. For WGBS, 10ug of DNA was sonicated to ca 500bp using a Bioruptor Pico. DNA was end-repaired and A-tailed using the NEB-Ultra Illumina library preparation kit (E7370). DNA fragments were ligated to methylated adapters (NEB E7535) following the NEB Ultra protocol. After adapter removal using Ampure xp beads (Beckman Coulter), DNA was converted using the Qiagen Epitect bisulphite conversion kit following the FFT sample protocol. After conversion library PCR amplification was performed with 10 cycles following NEB Ultra kit protocol, and cleaned up using Ampure xp beads.