Supplementary Figure 5: Similarities and differences in the transcriptome response at the gRNA and gene level | Nature Methods

Supplementary Figure 5: Similarities and differences in the transcriptome response at the gRNA and gene level

From: Pooled CRISPR screening with single-cell transcriptome readout

Supplementary Figure 5

a) Mean and standard deviation of pairwise distances (L2-norm) between CROP-seq transcriptomes for pairs of gRNAs that target the same gene (orange) or different genes (blue). Statistical significance was assessed with the Mann-Whitney U test. b) Pairwise distances as in panel a, shown separately for gRNAs targeting specific genes and for naïve as well as anti-CD3/CD28 stimulated cells. The dotted line indicates the 99th percentile of the distribution of distances between non-targeting gRNAs. c) Statistical significance of the transcriptome-wide effect induced by gRNAs targeting specific genes relative to cells with non-targeting gRNAs (based on the Mann-Whitney U test). The dotted line indicates a p-value of 0.01. d) As in panel c, but aggregated at the gene level by combining pvalues using Fisher's method. Insets show scatterplots for the expression of two example genes with low (left) and high (right) systematic effects on the transcriptome compared to cells expressing non-targeting control gRNAs in the same stimulation condition (y-axis)

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