DTF1 MeD-seq of desmoid-type fibromatosis patient 33
MeD-seq analyses were essentially carried out as previously described (PMID: 29222086). DNA samples were digested by LpnPI (New England Biolabs), resulting in snippets of 32bp around a fully-methylated recognition site that contains a CpG. These short DNA fragments were further processed using a Pippin system gel and the ThruPlex DNAseq 96D kit (Rubicon Genomics cat#R400407). Stem-loop adapters were blunt-end ligated to repaired input DNA and amplified to include dual indexed barcodes using a high fidelity polymerase to generate an indexed Illumina NGS library. The amplified end product was purified on a Pippin HT system with 3% agarose gel cassettes (Sage Science). Multiplexed samples were sequenced on Illumina HiSeq2500 systems for single read of 50bp according to manufacturers instructions. Dual indexed samples were demultiplexed using bcl2fastq software (Illumina).