CytoTRACE analysis

The CytoTRACE R package was used for this purpose²⁸. Three thousand cells from each cluster was randomly chosen in the mouse integrated data. The original five data were subset for the selected cells, merged with Scanorama-based integration, and evaluated regarding the GCS and CytoTRACE score (iCytoTRACE). For the human normal breast data, 15,000 cells were randomly selected from the integrated data and evaluated with the iCytoTRACE function. Besides, the entire data from Giraddi et al.¹⁰ and Bach et al.¹² were individually scored using the CytoTRACE function, to confirm the results in the non-integrated data. The barcode samplings were performed due to the limitation of the computer memory. The results were visualized on UMAP and by box plots grouped by the different life stages (Supplementary Fig. 7a, b). In this case, the sample that only included the specific cell types [Adult_Basal(G)] or the samples that received the HRT treatment [OVX_E2(S), OVX_E2_PBDE(S), OVX_E2_P4(S), and OVX_E2_P4_PBDE(S)] were excluded.