EPIC Methylation array profiling of MCF-7 cells

To study the effect of FOXA1 knock-down on DNA methylation patterns, we performed DNA methylation profiling of MCF-7 cells in three conditions, (1) control cell line, (2) cell line subjected to siRNA-mediated knockdown of endogenous FOXA1 expression and (3) cell line whose endogenous FOXA1 knockdown is rescued with transient expression of FOXA1-V5. EPIC methylation array profiling of MCF-7 cells was made in three different treatment conditions and three biological replicates. (1) MCF-7 cells treated with siCtrl (cat.no 1027281, Qiagen), (2) MCF-7 subjected to siRNA- mediated KD of endogenous FOXA1 using siFOXA1 (sense 5′-GAGAGAAAAAAUCAACAGC-3′ and antisense 5′-GCUGUUGAUUUUUUCUCUC-3′), (3) Rescue of siRNA-mediated endogenous FOXA1 KD with transient expression of C-terminally V5 tagged FOXA1 (RefSeq accession ID NM_004496).