Stochastic profiling of matrix-attached MCF10A-5E cells in 3D culture

The objective of this study was to profile the gene-regulatory heterogeneities of breast epithelial cells grown in an ECM-rich environment. The approach was to use stochastic profiling (Janes et al., Nat Methods 7(4):311-7 [2010]) to collect 10-cell pools of ECM-attached cells obtained by laser-capture microdissection and measure fluctuations in the 10-cell-averaged measurements to infer heterogeneous regulatory states. 16 random 10-cell samples of ECM-attached MCF10A-5E cells were obtained by laser-capture microdissection and their expression fluctuations compared to 16 pool-and-split controls comprised of larger microdissected cell populations extracted and split into 10-cell equivalents before poly(A) PCR preamplifcation.