Fig. 2: Comparison of the sensitivity of data generated by different platforms.

a, Schematic plot illustrating the extraction of regions with known morphology from fully processed samples of the adult mouse hippocampus and E12.5 mouse eye. Total UMI counts are presented as a function of stepwise downsampled sequencing depths for each platform. b,c, The data originate from mouse hippocampus (b) and E12.5 mouse eye (c) regions. A vertical dashed black line marks the read count used for generating the subsequent downsampled data. d, Total UMI counts were computed for selected regions using all reads and downsampled data for the mouse hippocampus. e, Total UMI counts for selected regions using all reads and downsampled data for the E12.5 mouse eye. f, The summed UMI counts for marker genes across individual 50 × 50 μm regions (n = 4) in the mouse hippocampus, along with mean and standard deviation. g, The summed UMI counts for marker genes across individual 50 × 50 μm regions (n = 4) in the E12.5 mouse eye, along with mean and standard deviation. h, Total UMI counts of detected genes are compared between Visium(polyA) (x axis) and Stereo-seq (y axis). Each dot represents a gene, shown in black. Genes that display expression at the 90th percentile with Stereo-seq but are at the tenth percentile in Visium(polyA) are highlighted in red and labeled with their gene symbols. i, A heatmap displays the \({\log }_{10}\)-transformed expression of genes that are specifically not captured by Visium(polyA) but are captured by Stereo-seq for E12.5 mouse eyes.