FOXA1 ChIP-seq analysis of genome-edited T47D ESR1 mutant cell models

This study is designed to comprehensively characterize the FOXA1 cistromes of Y537S and D538G mutated ER versus WT ER in breast cancer cells. Overall design: Genome-edited T47D cells were hromone derpvied (with one group of WT cells treated with 1nM E2 for 45 min). Chromatin DNA was then extracted from each sample. The immunoprecipitation was performed using FOXA1 (abcam, ab23738) antibodies. Pooled DNA samples from individual clones were sent to sequencing with Illumina NextSeq Platform. ChIP-seq reads were aligned to either hg19 genome assembly using Bowtie 2.0, and peaks were called using MACS2.0 with q value below 0.05. DiffBind was used to perform principle component analysis, identify differentially expressed binding sites and analyze intersection ratios with other data sets. Genomic feature distribution were called using ChIPseeker.