Transcriptome analysis of the course of ischemic stroke from acute to chronic phase in mice

We examined comprehensive gene expression in the mouse brain under physiological conditions at single cell-transcriptomic levels. In addition, Sytox-negative cells were sorted and analyzed for gene expression. We performed single cell RNA-seq for mouse brain and found that the neurons could no recovered for further analyses. We successfully obtained oligodendrocyte progenitor cells (OPCs), oligodendrocytes, microglia, endothelial cells, and pericytes, but were unable to obtain neurons. Additionally, we were only able to obtain astrocytes to a limited extent.We were able to examine comprehensive gene expression in the physiological brain. Overall design: B6.129S4-Pdgfratm11(EGFP)Sor/J mouse brain were dissociated enzymatically, and then the cell suspensions were isolated by cell sorting (FACS) according to absence of Sytox signal. The sorted cells were analyzed using single cell RNA sequencing.