Ambient RNA analysis of cortex-specific single-nuclei RNA-Seq (snRNA-seq) data in the sham and bilateral carotid artery stenosis (BCAS) groups
When compared with the sham group, ambient RNAs were more predominant in the BCAS group, which originated from damaged neuronal nuclei. After CellBender and subcluster cleaning treatments, detectable ambient RNA contamination could be largely reduced, and cortex-specific transcriptomic maps in the sham and BCAS groups were generated successfully. The underlying cellular and molecular mechanisms related to cortex damage and glial activation after severe cerebral hypoperfusion were further investigated at single nuclei resolution. Overall design: Cortex-specific gene expression profiling analysis at single-nuclei resolution was performed using data obtained from RNA-seq in sham and BCAS mice