Oligonucleotides were incubated with the nuclear extract for 30 min at 25 °C. In competitor assays, unlabeled competitor oligonucleotides in 50-fold molar excess to the labeled oligonucleotides were added to the reaction before addition of the probe. For supershift assays, 2 µg of the antibody was added to each reaction. FOXA1 (sc-9186x), FOXA2 (sc-9187x) and IgG (sc-2028) antibodies were obtained from Santa Cruz Biotechnology (Santa Cruz, CA). DNA-protein complexes were electrophoresed on 6% polyacrylamide Novex DNA Retardation Gels (Invitrogen) in 0.5 × TBE running buffer (45 mM Tris-borate and 1 mM EDTA, pH 8.3) and then scanned with fluorescent image analyzer FLA-5100 (Fujifilm, Valhalla, NY) at 473 nm with the LPB filter.
