DNA methylation landscape and transcriptome of tumor-associated macrophages reveals pathways, transcription factors, and prognostic value relevant for breast cancer patients [RNA-seq]

We performed RNA-seq to characterize the transcriptome of tumor-associated macrophages (TAMs), bone marrow-derived monocytes from healthy and tumor-bearing mice (BMDM-Ts/BMDM-Hs) and, macrophages from healthy mammary fat pad (MGMs). 4t1 cells were injected orthotopically into the mammary fat pad of balb\c mice. Tumors were harvested and digested after reaching a size of 1 cm. TAMs were collected by enrichment for CD45 positive cells following fluorescence-activated cell sorting (FACS) based on CD11b+ Gr1-and F4/80+. from tumor-bearing mice, Tibia and Femur leg bones were dissected flushed, and BMDM-Ts were facs sorted by CD11b+, Gr1+ and F4/80 low. MGMs were collected by harvesting the mammary fat pad of age-matched Balb\c mice, facs sorting was performed with CD11b and F/80 markers same procedure were also done for the Tibia and Femur leg bones of healthy mice and BMDM-Hs were collected as the BMDM-Ts.