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

We preformed RNA seq to charachterize the transcriptome of cancer associates fibroblasts (pCAF) compared to normal mammary fat pad fibroblasts (NMF) Overall design: 4t1 cells were injected orthotopcally into the mammary fat pad of balb\c mice, tumors were harvested and digested after reaching a size of 1 cm and pCAF were collected by fluorescence-activated cell sorting (FACS) based on negative selection excluding EpCAM-, CD45-, and Ter119- and positive selection using PDPN. NMF were collected by harvsting the mammary fat pad of age matched Balb\c mice, and facs sorting was performed with the above mentioned negative selection markers