Fig. 3

A Heatmap of the differential expression significance values (-log₁₀ adjusted p-value) for each of the four gRNAs targeting each of the positive control perturbations, when comparing the expression of the expected gene in perturbed cells versus non-targeting controls. Different classes of targets are indicated by colored bars (TSS — yellow, LCR — blue and Gasperini enhancers — red). The barplots to the right indicate how many of the four gRNAs reach statistical significance. B Distributions of the log₂ fold-change values for all expected genes from positive control perturbations, split by target class. C Representative examples of targets from each class. Normalized expression values in cells with targeting gRNAs (red) versus NT controls (gray) are shown. The title of the plot indicates the gene plotted. D Plot depicting the effect of gene expression levels on our ability to detect downregulation effects upon perturbation of TSS and non-coding targets. At the bottom, all genes in the human genome are ranked by decreasing average expression in the scRNA-seq dataset. Only genes detected in at least 5% of the cells (dark gray) were considered in the differential expression analyses. Non tested genes (light gray) include both genes not expressed in T cells and genes not detected by scRNA-seq. Then, expected genes in positive control perturbations that were significantly differentially expressed (***) are indicated, separately for TSS (yellow triangles) and non-coding control perturbations (red squares for Gasperini_ENH target genes, blue square for CD2). Above, expected genes that were detected but not recovered as significantly downregulated upon perturbation (NS)