The PanCancer Pathways Panel accurately detects major cell types and their spatial distribution across cancerous tissue samples​

Strong Correlations between Technical Replicates, Bulk RNA-seq Data and Tissue Preservation Types​

FIGURE 4

Figure 4: The PanCancer Pathways Panel reproducibly detects gene expression across cancer types. (A) Correlation of MERFISH data from two melanoma sections of the same tissue block. Each blue point corresponds to a given gene included in the PanCancer Pathways Panel. The X and Y axes correspond to the number of transcript counts identified per gene in the 2 technical replicates. This correlation describes the global similarity of the transcript quantities identified in each experiment. (B) Correlation of MERFISH data from a melanoma section run on the MERSCOPE® Platform with block-matched bulk RNA-seq data. Each dot represents a given gene in the PanCancer Pathways Panel. Here, the Y axis corresponds to the transcript counts per gene in a melanoma MERFISH dataset, while the X axis corresponds to the FPKM for each given gene in the PanCancer Pathways Panel, as quantified by bulk RNA-seq on the same tissue block. This correlation describes the global similarity between an individual MERSCOPE experiment and orthogonal methods of evaluating transcription. (C) Table detailing the correlations between technical replicates of the various tumor types. FF refers to fresh-frozen sample replicates and FFPE refers to formalin-fixed, paraffin-embedded technical replicates. The final column shows the correlation of expression across different preservation methods. Lung and colon cancer samples are patient-matched. Tissues types not investigated are marked by grey boxes.