Extended Data Fig. 1: Data quality and initial clustering without cross-sample alignment.
From: Molecular characterization of selectively vulnerable neurons in Alzheimer’s disease
a-b, Mean number of genes (a) or UMIs (b) detected per cell across individual samples for major cell types identified in each dataset. Grubman et al.15 did not resolve excitatory neurons from inhibitory neurons. Pericytes were identified only in Mathys et al.14 Cell type abbreviations: Exc – excitatory neurons, Oligo – oligodendrocytes, Astro – astrocytes, Inh – inhibitory neurons, OPC – oligodendrocyte precursor cells, Micro – microglia, Endo – endothelial cells, Per – pericytes. c-d, tSNE projection of cells from the EC (c) and SFG (d) clustered without first performing cross-sample alignment, colored by individual of origin (center) or cluster assignment (outer). e-f, Heatmap and hierarchical clustering of clusters and cluster marker expression (top subpanels); “High” and “Low” relative expression reflect above- and below-average expression, respectively (see Methods). Expression of cell type markers (bottom subpanels).
