Global DNA methylation analysis of cancer-associated fibroblasts reveals extensive epigenetic rewiring linked with RUNX1 upregulation in breast cancer stroma [co-culture]

We performed RNA seq to characterize the transcriptome of normal mammary fibroblasts (NMFs) co-cultured with 4T1 cancer cells for 3 and 5 days as well as mono-cultured NMFs. Overall design: Fresh mammary fat pad tissue was extracted from 12-week-old female BALB/c mice and NMFs were isolated. The NMFs were cultured on a collagen layer for 1 week of recovery and then co-cultured with 4T1-GFP cancer cells for 3 and 5 days. NMF were isolated by FACS sorting using negative selection for GFP and positive selection for PDPN and RNA sequencing was preformed.