Systematic identification of cell-cell communication networks in the developing brain

In the current study, we describe Brain-FACS, a method to simultaneously isolate neural, microglial, mural and endothelial cells from the developing brain to more than 94% purity in around 4 hours. Utilising Brain-FACS, we isolate, transcriptionally analyse and build a cell-cell communication map of the mouse brain at embryonic day E14.5. Transcriptomic analyses on FACS-isolated cell populations provide a ~20-fold increase in sensitivity over single single-cell RNA sequencing methods and allow us to bioinformatically identify 1,710 unique ligand-receptor interactions between neural, endothelial, mural and microglial cells including previously unidentified relationships. Together, this study provides a comprehensive map that reveals the richness of communication within the developing brain. Mouse E14.5 WT and Mof KO brains were dissociated and either mCEL-Seq2 protocol for scRNA-seq or population-based FACS-sorting and bulk RNA-seq was performed.