CTCF_ER_ChIP
CTCF_ER_ChIP
MCF-7 cells were grown in DMEM containing 10% heat-inactivated FBS, 2 mM L glutamine, 50 U/ml penicillin and 50 _g/ml streptomycin and ZR75-1 cells were grown in RPMI containing 10% heat-inactivated FBS, 2 mM L glutamine, 50 U/ml penicillin and 50 _g/ml streptomycin.  MCF10A cells were maintained in Mammary Epithelium Cell Growth Medium bullet kit (Clonetics, Lonza, MD, USA), containing mammary epithelium basal medium supplemented with bovine pituitary extract, human epidermal growth factor, hydrocortisone and GA-1000 (Gentamicin Sulfate and Amphotericin-B). To hormone deprive the cells, cells were grown in steroid-depleted medium for three days and then treated with vehicle (ethanol), 100 nM estrogen or 1 uM tamoxifen for 45 minutes or three hours. The antibodies used were anti-ER (sc-543) from Santa Cruz Biotechnologies and anti-CTCF (07-729) from Millipore.  At least four 15 cm dishes of cells were used per chromatin immunoprecipitation (ChIP) and samples were processed according to standard ChIP procedures.  The CTCF ChIP samples were performed as described in Carroll, 2005, Cell and the ER ChIP samples were performed as described in Schmidt, 2009, Methods.  The immunoprecipitated DNA was subsequently amplified as previously described for Illumina sequencing Schmidt, 2009, Methods.
Experimental Factor: CELL_LINE
MCF-7
Experimental Factor: IMMUNOPRECIPITATE
input
Experimental Factor: COMPOUND
none
Experimental Factor: DOSE
0 nM