Supplementary Figures S16-S18 from Ultra High-plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

Abstract

<p>Supplementary Figure S16: Representative grey scale images of used in the assessment of spatial proteogenomic data quality across mouse tissue types. FFPE sections were stained with the GeoMx NGS Mouse Protein modules (137-plex), GeoMx Mm WTA, and antibodies against CD45 (Immune), PanCK (Tumor) and Syto13 (nuclear, DNA). Supplementary Figure S17: ROI-to-ROI comparison of the proteogenomic data to the single analyte controls. Mouse FFPE sections were stained with 137-plex GeoMx NGS Mouse Protein modules and GeoMx Mm WTA. The Pearson’s R was calculated between each ROI from the proteogenomic assay against all ROIs in the single analyte (A) RNA and (B) protein controls. Protein targets with SNR ≥ 3 and RNA targets with SNR ≥ 4 were used in the analysis. Supplementary Figure S18: Expression levels of select matching RNA and protein targets in several mouse tissue types. For protein targets with SNR ≥ 3 and the respective RNA target with SNR ≥ 4, a pairwise scatter plot was generated to visualize the concordance between respective analytes.</p>