Cells were collected in single cell suspension using trypsin and sorted to obtain ~100k cells based on MERVL-GFP to obtain MERVL- mESC and MERVL+ 2CLC.  ULI-NChIP was conducted according to the protocol published by Brind'Amour et al. (PMID 25607992). 1ug H3K9me2 antibody ab1220 was used. ULI-NChIP libraries were prepared using the Thru-PLEX DNA-seq kit with adapters from Takara (cat. R400666). The quality of the libraries was checked using a DNA tape-station and sequencing conducted by the Weill Cornell Genomics core.