GSM9196965: GFP_ATAC-seq_rep1; Mus musculus; ATAC-seq
ATAC-seq on the sorted methylation reporter populations was carried out following a previously described protocol (Buenrostro et al., 2013). Cells were sorted based on their fluorescence signal into independent tubes and 50.000 cells were used for ATAC. The Tn5 transposase was purified in-house by the NKI protein facility as described in Braccioli et al., 2025. Cells were collected, washed 1x in cold PBS and nuclei were lysed in 2× lysis buffer (1 M Tris–HCl pH 7.5, 5 M NaCl, 1 M MgCl2, 10% IGEPAL). The nuclei isolation buffer was removed by centrifugation and nuclei were resuspended in tagmentation buffer (20 mM Tris (hydroxymethyl)aminomethane; 10 mM MgCl2, 20% dimethylformamide, adjusted to pH 7.6 with acetic acid) containing the Tn5 and incubated for 1 hour at 37°C. Two rounds of PCR were performed using the KAPA kit to incorporate sequencing adapters and to amplify the library DNA. Libraries were size-selected with AMPure XP (Bechman) beads to retain fragments smaller than 700 bp.