The fC-CET-enriched genomic DNAs were used directly for library preparation using the TELP protocol23 (link). A minor modification was the use of MightyAmp DNA Polymerase (TAKARA) for one round of on-bead primer extension before PCR amplification. The adaptor-ligated samples were then PCR amplified using NEBNext 2× PCR Master Mix (NEB) and indexed primers (NEB). Libraries were checked using the Agilent 2100 Bioanalyzer before loading onto the Illumina Hiseq 2500 platform. A single-end (100 bp or longer) sequencing mode was suggested for maximal data collection.
Two biological replicates of each mESCs were prepared and sequenced, which means that in parallel, two non-enriched input DNAs (Input: preAI), two AI labeled samples (Input: AI) and two pull-down output samples were sequenced simultaneously following the same procedure.
Two biological replicates of each mESCs were prepared and sequenced, which means that in parallel, two non-enriched input DNAs (Input: preAI), two AI labeled samples (Input: AI) and two pull-down output samples were sequenced simultaneously following the same procedure.
