Fig. 2: Seq-Scope mouse liver data analysis.

a Representative data snapshot tile 2107 (experiment on 10 tiles). Left panel displays the full tile with four gene sets (PC marker genes, blue; PP marker genes, green; Table S10; mitochondria genes, black; nuclear genes, red; Table S13) and cell segmentations. Middle panel zooms into a subregion and displays unspliced expression densities (green), nuclear centers (crosses), gene expressions, and cell segmentations. Right panel displays the H&E staining image. b Estimated spatial expression patterns for genes in five ELLA clusters, the upper panel shows gene counts and proportions, the middle panel shows expression intensities, and the lower panel shows pattern scores. c For each cluster, one representative gene is displayed with its name, P value (3.13e-12, 0.030, 3.27e-14, 0.002, 0.032), and expression intensities overlaid on density maps. Corresponding gene expressions in five selected cells are illustrated with cell boundaries and aligned nuclear centers (crosses). d Bar plot shows the average sn/sc RNA ratio across genes in pattern clusters 1 (red), 2–5 (green; P value = 5e-36), and non-cluster 1 genes (i.e., clusters 2–5 plus the nonsignificant genes; gray; P value = 1e-20). Nuclear-enriched genes (cluster 1) exhibit higher relative snRNA levels. e Bar plot shows the average unspliced/spliced expression ratio across genes in pattern clusters 1, 2–5 (P value = 2e-26), and non-cluster 1 genes (P value = 2e-3). Nuclear-enriched genes (cluster 1) exhibit higher unspliced/spliced ratios. f Bar plot displays the average gene length, measured by four metrics (x-axis), across genes in pattern clusters 1, 2–5, and non-cluster 1 genes. Nuclear-enriched genes (cluster 1) exhibit longer gene lengths. g Bar plot displays the proportions of SRP-coded genes for genes in pattern clusters 1, 2–5 (P value = 3e-7), and non-cluster 1 genes (P value = 3e-33). Cytoplasmic enriched genes (clusters 2–5) frequently encode SRP. Statistical significance for pair-wise comparisons (*<0.05; **<0.01; ***<0.001; without adjustments for multiple comparisons) is based on two-sided Mann–Whitney U test (d–f) or Fisher’s exact test (g) sample size n = 4145 genes (d, e), data are presented as mean values ± the interquartile range (25th–75th percentile, d–f). Source data are provided as a Source data file.