5hmC and gene expression data in breast cancer cell lines treated with an antioxidant

In this study, we identify genes with enriched 5-hydroxymethyl-cytosine (5hmC) modifications correlated with gene expression in breast cancer cell lines treated with an antioxidant. Results of our differential analysis showed that treatment with an antioxidant caused significant changes to gene-localized 5hmC enrichment patterns in MDA-MB-468 breast cancer cells. The 5hmC enrichment results were validated in a set of patient specimens when compared with adjacent non cancer tissue. Overall design: PVU-Seq and RNA sequencing of the triple negative breast cancer cell line MDA-MB-468 in triplicate. PVU-Seq of 2 breast tumor patients (2 tumor samples and the 2 matched normal) by enzymatic digestion of PvuRts1l coupled with high-throughput sequencing (PVU-Seq).