MeDIP-seq of human embryonic lung fibroblast cell line: WI-38
DNA was sheared into ~200 bp fragments using a Covaris S220 focused ultrasonicator. Libraries were constructed with 1.2 g of DNA using a NEBNext Ultra II DNA library prep kit for Illumina following the manufacturers guidelines. Immunoprecipitation with a 5mC antibody was conducted using a Diagenode MagMeDIP kit as described in the manufacturers protocol with starting volume of 15 L. The immunoprecipitated adaptor-ligated DNA and Input fraction were purified with a Diagenode IPure kit v2 according to the manufacturers instructions. The libraries from the Input fraction and IP DNA were linked to unique dual index primers (New England Biolabs) and amplified by PCR using a NEBNext Ultra II DNA library prep kit for Illumina with 8 for the IP samples. The PCR products were further purified and size selected using NEBNext sample purification beads. Libraries were quantified using a KAPA library quantification kit.