Stereo-seq cell type abundance analysis

To test for differential abundance of cell types between age groups, we used mixed effects modelling of associations of single cells (MASC). MASC tests whether cell type membership of individual cells is influenced by an experimental covariate of interest, while accounting for technical covariates and biological variation. We specified mouse genotype as a fixed covariate and mouse of origin as a random effect in the generalized, mixed-effect model. Changes in cell type abundance were considered significant at FDR- P < 0.01.