Breast cancer is one of the most common cancers worldwide, with over 2 million new cases in 2018. While some breast cancers in the early stages can be cured through surgery and chemotherapy, tumour progression and relapse are more challenging to treat and are responsible for poor prognosis. Therefore, understanding the basic mechanisms driving breast cancer progression and resistance to chemotherapy is imperative for developing new treatment strategies. Previous research has found that some tumour cells are more resistant to chemotherapy than others and some “chemoresistant” cells can regenerate the tumour even if only a few of them remain. These cells are known as cancer stem cells. The host laboratory previously identified a population of cancer stem cells that can initiate luminaltype mammary gland tumours in a mouse model of breast cancer. The cancer stem cells they identified are marked by a protein on their surface called Lgr6, which also exists in humans.The aim of this project was to use genetically engineered mouse models to separate out the tumour cells marked by Lgr6 from the rest of the tumour cells, and determine the molecular differences between the two populations using a technique called RNA sequencing. In conclusion, this project identified genes associated with cancer stem cell behaviour, which in the future might be targeted to inhibit breast cancer relapse.