Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution

To identify inter-individual differences in transcriptional cell state in the human breast, we performed scRNAseq analysis on 86,136 cells collected from 28 healthy premenopausal donors who underwent reduction mammoplasty surgery. To obtain an unbiased snapshot of the epithelium and stroma, we collected live (DAPI negative) / singlet cells from all samples by fluorescence activated cell sorting (FACS). For a subset of samples, we also collected purified epithelial cells or purified luminal and basal/myoepithelial cells. We used MULTI-seq barcoding and in silico genotyping for sample demultiplexing to minimize technical variability between samples. Single-cell expression profiles in 28 healthy reduction mammoplasty tissue samples. The samples named Set 1 - Set 17 are each from an individual sample, enriched by cell sorting (see the Sample Characteristics "sort gate" field). The samples named Set 18 - Set 22 are barcoded/multiplexed samples, each run on one lane of a 10X run (see the Sample Characteristics "number of multiplexed samples" field). Some samples were run across multiple lanes (e.g. individual samples and multiplexed samples were run across multiple sort gates, some samples were included in both multiplexed and individual lanes) as an experimental control.