ChIP-seq analysis of genome-edited MCF7 and T47D ESR1 mutant cell models

This study is designed to comprehensively characterize the cistromes of Y537S and D538G mutated ER versus WT ER in breast cancer cells. Genome-edited MCF7 and T47D cells were hormone deprived and treated with or without E2 for 45 minuts. Chromatin DNA was then extracted from each sample. The immunoprecipitation was performed using ERα (Santa Cruz Biotechnologies, sc543) antibody. Pooled DNA samples from individual clones were sent to sequencing with Illumina Hiseq 2500 Platform. ChIP-seq reads were aligned to either hg38 genome assembly using Bowtie 2.0, and peaks were called using MACS2.0 with p value below 10E-5. 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. Individual clones of genome-eidted MCF7 and T47D cell lines with knock-in of WT/Y537S/D538G ER were hromone deprived and treated with veh or 1 nM E2 for 45 minutes. Chromatin DNA was then extracted from each sample. The immunoprecipitation was performed using ERα (sc543) antibody (Santa Cruz Biotechnologies). Pooled DNA samples from individual clones were sent to sequencing with Illumina Hiseq 2500 Platform.