Illumina HiSeq 2500 paired end sequencing; Genome-wide profiling of CTCF binding (ChIP-seq) in A549 and U2OS cells
Genome-wide profiling of CTCF binding (ChIP-seq) in A549 and U2OS cells
Cells were cultured to confluency and treated for 90 min with 1μM dexamethasone. Chromatin was fixed at room temperature for 3 min with 1% formaldehyde. After quenching with 200mM glycine, the cells were sonicated using a Bioruptur (Diagenode). ChIP-assays targeting CTCF were essentially done as previously described (Meijsing, S.H., et al., Science, 2009. 324(5925): p. 407-10.) using a polyclonal CTCF-antibody (Active Motif, Cat. No. 61311) except that a modified RIPA wash buffer (50 mM HEPES-KOH, 1 mM EDTA, 1% NP40, 0.7% Na-deoxycholat, 500 mM LiCl, pH 7.5) was used.
Experimental Factor: U2OS
cell line
Experimental Factor: input
immunoprecipitate