Extended Data Fig. 7: Cell-to-cell variability of cytokine expression in single cell in situ RNA hybridization assay combined with flow cytometry (PrimeFlow).
From: Gene expression variability across cells and species shapes innate immunity
PrimeFlow measurement of two cytokine genes (IFNB and CXCL10) that show high cell-to-cell variability in scRNA-seq. As controls, two genes matched on expression levels (ATXN2L and ADAM32) but that show low cell-to-cell variability in scRNA-seq data are shown. As the expression of cytokines is at the low end of the distribution, we also chose two genes with middle-range expression values (ADAMTSL3 and BRD2) as additional controls. The experiment was performed in n = 2 independent replicates, originating from the same individual. Both replicates are shown. a, Pseudocolour contour plot for RNA target expression in dsRNA-stimulated human fibroblasts. The x-axis shows area of side scatter (SSC-A) and the y-axis shows fluorescent signal for target RNA probes. RNA targets detected by the same fluorescent channel are displayed together. Top, IFNB and control genes BRD2 and ATXN2L, type 1 probe, Alexa FluorTM 647. Bottom, CXCL10 and control genes ADAMTSL3 and ADAM32, type 10 probe, Alexa FluorTM 568. The cytokine genes display a broader range of fluorescence signal than the controls. b, Histograms comparing fluorescence of cytokine and control pairs (IFNB–BRD2 for type 1 probe and CXCL10–ADAM32 for type 10 probe). The histograms show a bimodal distribution of expression signal for the two cytokine genes (IFNB and CXCL10, red), but not for controls (blue). This agrees with scRNA-seq data in which CXCL10 and IFNB display high levels of cell-to-cell variability.
