Fig. 2

CRISPRi radiation modifier screen in glioma cells. a Experimental design. Eight Gy radiation was delivered in 4 fractions throughout the screen. b Volcano plot of radiation growth phenotypes (average of two replicate screens) for the top 3 sgRNAs targeting each lncRNA TSS (x-axis) and negative log₁₀(Mann-Whitney U p value) of all sgRNAs for a given gene at T12 as compared to T0 (y-axis). Screen threshold was determined by the product of the x- and y-axes that resulted in an empirical FDR of 0.0025. Neighbor hits are defined as any lncRNA hit with an expressed protein coding gene within 1 kb of the lncRNA TSS. Phenotype refers to the relative log2 enrichment of barcodes in the final timepoint divided by the enrichment of barcodes at the initial timepoint [8, 11]. c Comparison of screen scores, defined as the average phenotype of the top three sgRNAs against a given gene multiplied by the negative log10(Mann-Whitney U p value) for that gene, from screens conducted without radiation (x-axis) with scores from screens conducted with radiation (y-axis), with thresholds set at 5 (FDR = 0.0025). Thirty-three lncRNA hits had radiation screen scores greater than no radiation screen scores. CTC-338 M12.4 (lncGRS-1) is indicated. d LncRNA expression across 2 DIPG and 3 GBM cultures (subpanel 1), no radiation screen scores (subpanel 2), radiation screen scores (subpanel 3), and sensitizer scores (subpanel 4) for each of the 9 lncGRS candidates. Sensitizer score is defined as the ratio of the radiation modifier screen score in irradiated cells to the growth screen score in non-irradiated cells