Extended Data Fig. 4: Comparison of Slide-tags to Bulk RNA-seq, Slide-seqV2 and DBiT-seq.

a, Slide-tags snRNA-seq vs. bulk RNA-seq. b, Slide-seqV2 vs. bulkRNA-seq. c, Slide-seqV1 vs. bulkRNA-seq. Log₁₀ transformations are shown in each bulk comparison case. d, Violin plots of log₁₀-transformed genes and UMIs per nucleus (Slide-tags) or 20 μm spatial spot (Slide-seqV2 and DBiT-seq / spatial-ATAC-RNA-seq) in the mouse brain. n = 839 nuclei for Slide-tags, n = 18,950 20 μm pixels for Slide-seq, and n = 9,215 pixels for DBiT-seq. e, Elbow plot of standard deviations of principal components from Slide-tags snRNA-seq, Slide-seqV2, and DBiT-seq in the mouse brain. f, UMAP embeddings of snRNA-seq profiles from Slide-tags snRNA-seq (cell type labels), Slide-seqV2 (de novo clusters), and DBiT-seq (RNA clusters from Zhang et al.¹³) in the mouse brain. g, Dotplot expression of select markers across transcriptome clusters from Slide-tags snRNA-seq, Slide-seqV2, and DBiT-seq in the mouse brain. Boxplots show: centre line, median; box limits, upper and lower quartiles; whiskers, 1.5x interquartile range; points, outliers.