Single-cell RNA-sequencing of breast cancer cells growing in invasion permissive and non-permissive 3D matrices

Murine breast cancer organoids (MMTV-PyMT) were embeded in basement membrane extract (BME, invasion non-permissive) or collagen I (invasion-permissive). Organoids were harvested after 5days for single-cell RNA-sequencing (SORT-seq). Overall design: Organoids were isolated from the 3D BME or 3D Collagen I, dissociated into single cells. Single cells from either BME or Collagen I were single cell sorted by FACS into 3 x 384 well plate each (3 replica per ECM condition) and analyzed by single cell RNA sequencing

本数据集采用的小鼠乳腺癌类器官（MMTV-PyMT），分别被包埋于侵袭抑制型的基底膜提取物（basement membrane extract，BME）与侵袭允许型的I型胶原蛋白体系中。培养5天后收获类器官，用于单细胞RNA测序（SORT-seq，single-cell RNA-sequencing）。
实验整体设计：从3D BME与3D I型胶原蛋白体系中分别分离类器官，将其解离为单细胞悬液；随后通过荧光激活细胞分选（Fluorescence Activated Cell Sorting，FACS），将两类来源的单细胞各接种至3块384孔板，每种细胞外基质（Extracellular Matrix，ECM）条件设置3个生物学重复，最终完成单细胞RNA测序分析。