title: Illumina HiSeq 2500 paired end sequencing; XAB2 binds genome-wide on putative DNA elements (e.g. enhancers, promoters) that are known to regulate gene expression
design: XAB2 binds genome-wide on putative DNA elements (e.g. enhancers, promoters) that are known to regulate gene expression
library_construction_protocol: For ChIP assay,cells were cross-linked at room temperature for 2.5 min with 1% formaldehyde. Chromatin was prepared and sonicated on ice for 8 min using a Covaris S220 Focused-ultrasonicator. Samples were immunoprecipitated with antibodies (5-6μg) overnight at 4οC followed by incubation for 3 h with protein G Sepharose beads (Millipore) and washed sequentially. Naive mESCs were cultured on gelatinized tissue culture dishes in medium containing Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 50μg mL-1 streptomycin, 50 U mL-1 penicillin (Gibco), 2mM L-glutamine (Gibco), 1% non-essential amino acids (Gibco), 0.1mM β-Mercaptoethanol (Applichem), 1μM MEK inhibitor PD0325901 (Selleck), 3μM GSK inhibitor CHIR99021 (Selleck). The complexes were eluted and the crosslinking was heat reversed. Purified DNA fragments were analyzed by sequencing. Standard TruSeq ChIP library construction protocol