Nuclei were extracted from mouse brain tissue with or without formaline fixation. Neuronal nuclei were collected by FACS. Cromatin was fragmented by Mnase digestion (histone ChIP) or sonication (CTCF ChIP), and immunoprecipitated by different antibodies. ChIP DNA was end repaired (End-it DNA Repair kit; Epicentre) and A tailed (Klenow Exo-minus; Epicentre). Adaptors (Illumina) were ligated to the ChIP-DNA (Fast-Link kit; Epicentre) and then PCR amplified using Illumina TruSeq ChIP Library Prep Kit. Library DNA with expected size (NChIP, ~275bp; XChIP, 350bp to 500bp) was selected by Pippin.