Extended Data Fig. 2: Validation of pooled CRISPRi screens.
a, Heatmaps of gene-level sgRNA log2 FC for 16 genes selected for validation; white: not significant (two-sided Mann–Whitney test P > 0.1). b, Schematic of individual sgRNA expression construct. Puro: puromycin resistance gene. c, Correlation of single sgRNA phenotype from growth competition assays [log2 (-/+Dox)] and log2 FC of the same sgRNA in the pooled CRISPRi screen (Spearman’s R, P < 0.05) for the two most active sgRNAs (sgRNA1 and sgRNA2) for each gene in the screens. Solid lines denote linear regression model; grey shading denotes 95% confidence interval. d, Knockdown efficiency of genes from (a) compared to a non-targeting control (sgControl) measured by quantitative RT-PCR for the most active sgRNA from the screens (sgRNA1; n = 2 biological replicates, each with n = 3 technical replicates). e, Correlation plot of cell type specificity (hiPSCi log2 FC minus HEK293i log2 FC) calculated for individual sgRNAs from growth competition assays [∆log2 FC (validation), n = 2 biological replicates] and the same sgRNAs in the pooled CRISPRi screen [∆log2 FC (screen); n = 3 biological replicates]. Solid line denotes linear regression model; grey shading denotes 95% confidence interval. f, Heatmaps of significant (pairwise two-tailed t-test, FDR < 0.01) protein-level log2 FC for screening targets in (a) measured by mass spectrometry in the indicated cell types in comparison to hiPSCi (n = 3 biological replicates; numbers in brackets indicate isoforms). g, Immunoblot analysis of ZNF598, ASCC3, HBS1L, and PELO in sgRNA-transduced cells after KRAB-dCas9 induction ( + Dox) and in matched uninduced controls (-Dox).
