Fig. 1: Experimental setup and data quality with three full transcriptome methods GeoMx, Visium and Chromium on Breast and Lung cancer, and DLBCL biobank samples. | Nature Communications

Fig. 1: Experimental setup and data quality with three full transcriptome methods GeoMx, Visium and Chromium on Breast and Lung cancer, and DLBCL biobank samples.

From: Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity

Fig. 1

a Schematics of experimental design to generate GeoMx and Visium spatial transcriptomics and Chromium single-nuclei data for three cancer types corresponding to 14 donors from FFPE blocks with 2 samples replicated for each technology. AOI - area of illumination, DLBCL - Diffuse large B-cell lymphoma, DSP - digital spatial profiler. Created in BioRender. Gottardo, R. (2025) https://BioRender.com/o13c311. b Display of block age and RNA quality measure DV200 values for all the samples with histology type, labelled by patient ID. c Gene detection rate for GeoMx AOI-s and number of genes detected in Visium spots and single nuclei. Colors in GeoMx correspond to AOI labels. d Breast cancer tSNE plots with GeoMx and UMAP plots with Visium and Chromium show good reproducibility. Technical replicates with adjacent sections from the same block are highlighted with a dashed line. GeoMx: 5 samples/117 AOIs; Visium: 5 samples/10249 spots; Chromium: 6 samples/10689 cells. B breast, L lung, D DLBCL. Source data are provided as a Source Data file.

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