Global DNA methylation analysis of cancer-associated fibroblasts reveals extensive epigenetic rewiring linked with RUNX1 upregulation in breast cancer stroma [ly6c]

We performed RNA seq to charachterize the transcriptome of specific cancer associates fibroblasts (pCAFs) sub-populations (Ly6c+ vs Ly6c- pCAFs) 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. Ly6c+ and Ly6c- pCAF were collected by fluorescence-activated cell sorting (FACS) based on negative selection excluding EpCAM-, CD45-, and Ter119- and positive selection using PDPN. To subset the pCAFs we used anti-Ly6C antibody to separate between the negative and positive subsets.