The pdgfra-H2BGFP reporter mouse visualizes expression of Pdgfra by expression of GFP bound to histones. These leads to a strong stabilization of the GFP molecule, leading to a) a strong nuclear signal and b) retention of fluorescence even after the cells no longer express Pdgfra. In the brain of this reporter mouse, the majority of cells expressing GFP are of the oligodendrocyte lineage. However, there is a small subset of cells that are not belonging to this lineage, and present an interesting anatomical location. They are localized in close proximity to the larger vessels in the brain. In order to properly study these cells with single cell sequencing technologies, prior enrichment for the perivascular subtype of Pdgfra expressing cells is recommended. Here, we describe a protocol that allows to focus on this subtype in more detail by first isolating brain vasculature prior to single cell suspension generation. The entire protocol aims to minimize time between brain dissection and FACS sorting, and thus only takes between 60 and 75 minutes.