Genome-wide maps of DNA methylation and gene expression for multiple regions within a breast tumor [RRBS]

As the differentiation state of the cells is affected by epigenetic modification regulation, the abnormal epigenetic modification is an important factor leading to the intratumoral heterogeneity. To further understand of the intratumoral epigenetic heterogeneity, we performed Reduced Representation Bisulfite Sequencing and RNA sequencing for multiple regions within a breast tumor and exhibited the epigenetic maps of different regions. We detected intratumoral heterogeneity-related molecular features and further explored the correlation between tumor heterogeneity and tumor hypoxic microenvironment. Our tumor samples were derived from a patient with HER2 breast invasive ductal carcinoma at stage II. The size of tumor was 45 mm×22 mm and the patient was without prior neoadjuvant therapy. For RNA and DNA libraries preparation, the tissues of tumor center, 12 o'clock, 3 o'clock, 6 o'clock and 9 o'clock of tumor periphery as well as adjacent of the tumor were taken for 0.6 mg, respectively. Another case of normal breast tissue was used as a control. Totally, 7 samples were examined by RRBS and RNA sequencing.