ChIP-Seq in human MCF7 and HEPG2 cells
ChIP-Seq in human MCF7 and HEPG2 cells
Cells were grown in phenol red-free DMEM supplemented with 5% charcoal dextran treated serum for at least three days (cell cycle analysis) or in full media (RNAi-ChIP-seq). Cells were transfected with siRNA for 48 hours using Lipofectamine2000 (Invitrogen, CA, USA). AllStars Negative Control siRNA (Qiagen) was used as negative (mock) controls. CTCF RNAi (Invitrogen Stealth, sense: GCGCUCUAA-GAAAGAAGAUUCCUCU, antisense: AGAGGAAUCUUCUUUCUUAGAGCGC). RAD21#1 (Invitrogen Stealth; sense: CAGCUUGAAUCAGAGUAGAGUGGAA, antisense: UUCCACUCUACUCUGAUUCAAGCUG) RAD21#2 (ON-TARGETplus SMARTpool L-006832) ChIP experiments were performed with well-characterized antibodies against CTCF (Millipore, 07-729), STAG1 (abcam, ab4457), RAD21 (abcam, ab992), ERa (santa cruz, sc-543), CEBPa (santa cruz, sc-9314) and MED12 (abcam, ab70842). ChIP-seq experiments were performed as recently described (Schmidt et al. 2009)
Experimental Factor: IMMUNOPRECIPITATE
input_DNA
Experimental Factor: CELL_LINE
MCF7
Experimental Factor: COMPOUND
oestrogen
Experimental Factor: KNOCK_DOWN
CTCF