GSM5509391: pADamID_CTCF_GSK_24h_Dam_r1; Mus musculus; OTHER
1 million permeabilized cells were processed with pA-DamID (van Schaik, 2020) with a LaminB1 antibody and for a Dam control condition, to specifically deposit m6A marks at peripherally positioned chromatin. Genomic DNA was isolated using the Bioline Isolate II Genomic DNA Kit. The full protocol is described in Leemans, 2019, except that the DpnII digestion is omitted. 500 ng of genomic DNA was digested at Dam-methylated GATC sequences with DpnI and ligated to adapters. DNA fragments were amplified with 15-19 PCR cycles. Amplified fragments were further processed with end-repair, 3A-overhang tailing and Y-shaped adapter ligation, before a final round of 10-12 PCR cycles with illumina index adapters.