Using the signature genes for each cluster and the known markers for the epithelial cell populations, we assigned these cell populations as: 1 –BC, highly expressing KRT5; 2~3 –club cells, highly expressing SCGB1A1; 4~6 –intermediate alveolar cells, expressing both type II (SFTPC, ABCA3) and I (AGER, HOPX) alveolar cell markers; 7 –type I alveolar cells, highly expressing AGER and HOPX (Fig 2B and 2C, S3A Fig and S3 Table in S1 File). Here, HOPX is linked to breast cancer.