Identification of ChIP-seq and RIME grade antibodies for estrogen receptor alpha

Estrogen Receptor alpha (ERa) is a key driver of most breast cancers, and it is the target of endocrine therapies used in the clinic to treat women with ERa positive (ER+) breast cancer. ChIP-seq (chromatin immunoprecipitation coupled with deep sequencing) has improved our understanding of ERa function during breast cancer progression and in response to anti-estrogens. A critical component of the ChIP-seq protocol is the antibody that is used to pull down the bait protein. To date, most of the ChIP-seq experiments for the study of ERa have been performed using the sc-543 antibody from Santa Cruz Biotechnology. However, this antibody has been discontinued, thereby severely impacting the study of ERa in normal physiology as well as diseases such as breast cancer and ovarian cancer. Here, we compare the sc-543 antibody with other commercially available antibodies, and we show that 6-935 (EMD Millipore) and ab3575 (Abcam) antibodies can successfully replace the sc-543 antibody for ChIP-seq experiments. Overall design: ChIP-seq in breast cancer cell lines to identify high-quality, ChIP-grade antibodies for ERa.