Protocol for the undifferentiated ES cells biological replicate: Chromatin immunoprecipitation was performed as previously described (Nelson & Denisenko, Nat Protoc. 2006;1(1):179-85). After cross-linking cells for 10 min with 1% formaldehyde and sonicating chromatin with a Diagenode Bioruptor, chromatin was immunoprecipitated using 25 µl (~25 µg) of CTCF antibody (Millipore 07-729, lot 2054523) or 25 µg of IgG (Santa Cruz Biotechnology, Sc-2027) for 20E6 cells. 10 ng of CTCF immunoprecipitated DNA, IgG immunoprecipitated DNA or input were used for library preparation according to NEBNext ChIP-Seq library protocol (NEB #E6200S/L) using AMPure XP Beads (Agencourt #A63880) and with 14 cycles PCR enrichment using index primers for multiplexing. Indexes were as follows: CTCF, acagtg; IgG, cgatgt; input, tgacca. DNA fragment size was verified using a Bioanalyzer (Agilent #5067-4626) and the libraries were sequenced as 50 bp single-reads with the Illumina hiSeq sequencing system.