Comparison of FACS-isolated mammary epithelial populations (CD49f/CD61)

To validate the CD49f/CD61 flow cytometry panel for resolving the three major mammary epithelial lineages, mammary epithelial cells from MMTV-Cre mice were collected by FACS and analyzed by RNA-seq for comparison to previously published single-cell RNA-seq studies, which non-biasedly identified the three major lineages: basal, alveolar progenitor (AP), and hormone-sensing luminal (HSL) cells. Six nulliparous MMTV-Cre animals were raised to 12 weeks of age. Mammary tissues were collected from these animals, then minced and treated with collagenase/hyaluronidase/DNaseI for 1hr at 37C. Then, resulting parenchymal cells were isolated by centrifugation and further digested by dispase and trypsin successively. Cells were pipetted through a 40um filter, then blocked and stained with antibodies for FACS. FACS markers: CD49f, CD61, EpCAM, Lin (CD31/CD45/Ter119). By FACS, individual populations were isolated - basal cells, alevolar progenitors (AP, also called 'luminal progenitors'), and hormone-sensing luminal cells (HSL, HR+ population, also called 'mature luminal cells'). See Sample Characteristics 'cell population' field for FACS markers per cell type.