5hmC-Seal-seq of mus musculus: Chx10-TET (Tet1/Te2/Tet3-floxed and Chx10-cre) retina
DNA was fragmented via sonication to produce 200 bp DNA fragments using Covaris M220. Prior to the 5hmC enrichment, fragmented DNA was spike-in with an equimolar mixture of methylated (5mC) and hydroxymethylated (5hmC) different double strand DNA (dsDNA) fragments from the rabbit IgH locus (#55023, Active Motif). To capture DNA fragments containing 5hmC, we used the 5hmC Profiling Kit (#55023, Active Motif) based on the 5hmC-Seal technology. To prepare NGS libraries, we used NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S, New England Biolabs) and NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs, E6440S, New England Biolabs) according to manufacturer's instructions. 5hmC-Seal NGS libraries were sequenced from both ends using a 2150 PE configuration using the NovaSeq X Plus system (Illumina)