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). 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