Single nucleus transcriptome of the brains response to ischemic stroke

The mammalian brain consists of heterogeneous cell populations with distinct responses to injury. Here we used single nucleus RNA sequencing (snRNAseq) to analyze cell type specific transcriptional responses of the rodent brain to ischemic stroke, 48h after the induction of middle cerebral artery occlusion. Cerebral ischemia was induced by permanent intraluminal occlusion of the right middle cerebral artery (MCAO). 48h after filament based occlusion of the middle cerebral artery infarction, or the absence of infarction in Sham operated animals was confirmed via T2-weighted MRI. Brain samples were harvested, snap frozen in liquid nitrogen, nuclei were extracted from frozen brain tissue using nuclei extraction buffer (Miltenyi) and standard discontinuous iodixanol gradient separation, followed by library preparation using standard 10x Genomics workflows and snRNAseq (NovaSeq 6000, Illumina). In total brains from n=4 Sham operated rats (=Sham), n=3 rats with moderate MCAO induced infarctions (mMCAO) and n=4 rats with severe MCAO induced infarctions (sMCAO) were sequenced. Left and right hemispheres were sequenced separately. Hence, we obtained datasets from the left and right hemispheres of Sham operated rats (Sham L and Sham R, respectively), as well as left (=contralateral to ischemic lesion) and right (= ipsilateral to ischemic lesions) hemispheres of mMCAO and sMCAO infarcted rats. The following datasets were generated: Sham L = left brain hemispheres of Sham operated controls ; Sham R = right hemispheres of Sham operated controls; mMCAO contra: left brain hemispheres of MCAO group animals, with moderate infarction severity, hemispheres contralateral to infarction; mMCAO ipsi: right brain hemispheres of MCAO group animals, with moderate infarction severity, hemispheres ipsilateral to infarction, sMCAO contra: left brain hemispheres of MCAO group animals, with severe infarction severity, hemispheres contralateral to infarction; sMCAO ipsi: right brain hemispheres of MCAO group animals, with severe infarction severity, hemispheres ipsilateral to infarction.