RNA-seq profiling of mammary duct macrophages from virgin, pregnant, lactating and post-weaning mice

Macrophages are diverse immune cells that reside in all tissues. Although macrophages have been implicated in mammary gland function, their diversity has not been fully addressed. By exploiting high-­resolution 3D imaging and flow cytometry, we have identified a unique population of tissue-­resident ductal macrophages (DMs) that form a contiguous network between the luminal and basal layers of the entire mammary gland throughout post-­natal development. DMs are long-­lived and constantly survey the epithelium though dendrite movement based on advanced 3D intravital imaging. While they initially originate from embryonic precursors, DMs derive from monocytes as they expand during puberty. Moreover, they undergo proliferation in pregnancy to maintain complete coverage of the epithelium in lactation, where they are poised to phagocytose milk-­producing cells post-­lactation and facilitate remodelling. Interestingly, DMs strongly resemble mammary tumour macrophages and form a network that pervades the tumour epithelium. Thus, the mammary epithelium programs specialised resident macrophages in both physiological and tumorigenic contexts. To explore expression changes as DMs profilerate in pregnancy and lactation, we sorted DMs from the mouse mammary glands of virgin, pregnant, lactating and post-weaning mice and undertook RNA-seq profiling. Results from this data series are shown in Figure 5 of Dawson et al (2020). Three biological replicates were prepared of ductal macrophages from the breast tissue of female mice at four developmental time points: virgin, 16.5 days pregnant, lactating and 1 month post weaning.