Single nucleus RNA sequencing of the cortex of antibiotic and vehicle treated APPPS1-21 mice

Previously, we and others have shown that broad spectrum antibiotic treatment from postnatal day 14-21 reduces neuroinflammation in the APPPS1-21 model of AD-related amyloidosis. In the current study, we used single-nucleus RNA sequencing (snRNAseq) to assess cell-type specific transcriptional changes in antibiotic treated mice and controls. We also assessed changes in astrocyte subclusters in these groups. Overall design: We treated antibiotic and vehicle treated APPPS1-21 male mice (N=4/group) with broad spectrum antibiotics (4 mg/ml kanamycin, 0.35 mg/ml gentamicin, 8,500 U/ml colistin, 2.15mg/ml metronidazole, 0.45 mg/ml vancomycin in autoclaved water) or vehicle control from postnatal day 14-21. Mice were transcardially perfused at 3 months of age and following perfusion, the the right cortex was sub-dissected and flash frozen in liquid nitrogen. The cortex was used to generate single nucleus suspensions for downstream sequencing and analysis