Fig. 1: Evaluation of gene detection sensitivity across ST platforms. | Nature Communications

Fig. 1: Evaluation of gene detection sensitivity across ST platforms.

From: Systematic benchmarking of high-throughput subcellular spatial transcriptomics platforms across human tumors

Fig. 1

a Experimental workflow. For each tumor type (COAD, HCC, OV), samples were divided into three parts: (1) FFPE blocks were used for Visium HD FFPE, CosMx 6K, and Xenium 5K; (2) fresh-frozen OCT-embedded tissue was used for Stereo-seq v1.3; (3) dissociated tissue was subjected to scRNA-seq. Sections adjacent to each ST slide were profiled by 16-plex CODEX for spatial proteomics. b H&E staining and EPCAM expression from ST data, along with PanCK staining from adjacent CODEX sections of COAD samples across the four ST platforms. Color intensity reflects the transcript count per 8 μm bin. Scale bars, 1 mm. c Mean transcript count per 8 μm bin for selected marker genes, computed across all bins with non-zero expression values over the entire tissue sections. d Pearson correlation of gene expression levels between ST data and scRNA-seq data. For each gene, the total transcript counts across three cancer types were averaged and log10 transformed. Each data point represents one gene. The diagonal red line indicates a slope of 1, and color intensity corresponds to relative gene counts. R denotes the correlation coefficient, and n indicates the number of genes included in the analysis. e Log2-transformed total transcript count per gene across the ten selected regions (400 × 400 μm each) in HCC and OV. Each data point represents one gene (n = 17,134 for Stereo-seq v1.3 and Visium HD FFPE, n = 6175 for CosMx 6K, n = 5001 for Xenium 5K). Center lines indicate the median value, and lower and upper hinges represent the 25th and 75th percentiles, respectively. The whiskers denote 1.5× the interquartile range. f Log2-transformed gene and transcript counts per 8 μm bin within the ten selected regions in HCC and OV. Each data point represents one bin. Center lines indicate the median value, and lower and upper hinges represent the 25th and 75th percentiles, respectively. The whiskers denote 1.5× the interquartile range. g Mean sequencing saturation across the 10 selected regions for human transcripts detected by Stereo-seq v1.3 and Visium HD FFPE, calculated at stepwise increasing sequencing depths. Panel a created with BioRender.com. Source data are provided as a Source Data file.

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