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. Overall design: 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.

为识别人类乳腺中转录细胞状态的个体间差异，我们对28名接受乳房缩小成形术的健康绝经前供者采集的86136个细胞开展了单细胞RNA测序（scRNAseq）分析。为获取上皮与基质细胞的无偏快照，我们通过荧光激活细胞分选（FACS）从所有样本中分离出活的（DAPI阴性）单个细胞。针对部分样本，我们还额外收集了纯化上皮细胞，或纯化的腔上皮细胞与基底/肌上皮细胞。本研究采用MULTI-seq条形码编码与计算机基因分型技术进行样本解复用，以最小化样本间的技术变异。整体实验设计如下：涵盖28份健康乳房缩小成形术组织样本的单细胞表达谱。其中Set 1至Set 17均为单一样本，经细胞分选富集（详见样本特征的“分选门控”字段）；Set 18至Set 22为条形码编码的多重测序样本，每份均在10X测序的单个泳道上运行（详见样本特征的“多重样本数量”字段）。部分样本曾在多个泳道上机（例如单一样本与多重测序样本通过多组分选门控进行测序，部分样本同时纳入多重测序与单泳道测序流程），以此作为实验对照。