Enriched methylome sequencing of cells
Enriched methylome sequencing was performed on cfDNA or acoustically sheared genomic DNA (400-500bp). Briefly, both sides of input DNA molecules ligate on a unidirectional adapter (Adapter A) that will serve as a blocker for untargeted background molecules and a primer landing site for targeted molecules. This is followed by a double-stranded cut, which we performed with the MspI nuclease to selectively create new, unblocked DNA ends. These newly exposed ends at the cut site are targeted through a second ligation with a second adapter (Adapter B) that is also needed for sequencing library formation. Only molecules with both Adapters A and B are amplified and sequenced, excluding untargeted DNA that only have one type of adapter on both ends. We then performed enzymatic methylation conversion, followed by amplification and library pooling. Libraries were sequenced on an Illumina Novaseq 6000 using 100 cycle S2 kits configured as paired-end 2x50 bp with up to 15% PhiX or WGS libraries for nucleotide diversity.