Extended Data Fig. 7: Reproducibility of Deep-STARmap and Deep-RIBOmap, spatial translatome-transcriptome comparison.

a, 3D molecular cell-type maps of two independent biological replicates for Deep-STARmap (left) and Deep-RIBOmap (right) in 150-µm-thick coronal mouse brain sections. Each dot represents an individual cell, colored by its assigned cell type. b, Dot plot visualization of gene expression profiles across major cell types in batch 2. The color scale represents the log₂ fold change in gene expression compared to the mean gene expression values across all cells. The dot size indicates the percentage of cells expressing the genes within each major cell type. c, Heat map showing the gene clustering using the RIBOmap and STARmap results by cell type (Z-score expression). d, Visualization of enriched GO terms within each gene module, categorized and color-coded by module. In the enrichment map, nodes represent enriched GO terms, with the size of each node reflecting the number of genes associated with that term. Edges between nodes indicate shared genes among the GO terms. e, Heat map displaying gene clustering based on Deep-STARmap and Deep-RIBOmap results across the three oligodendrocyte lineage cell types (left). The right panel shows the relative translational efficiency (RTE) of these genes within each oligodendrocyte lineage cell type (Z-score expression). Statistical significance was assessed using pairwise Mann-Whitney U tests with Benjamini-Hochberg FDR correction. Sample sizes: gene module 1 (n = 18), Gene module 2 (n = 30), Gene module 3 (n = 26).