Extended Data Fig. 4: High quality and reproducibility of optimized in vivo CRISPR screens and analysis of the CPD co-essential module.

a, A CRISPR sgRNA library targeting 911 hits with differential growth effects in 3D versus 2D (Supplementary Table 4) was introduced into H23 cells, and introduced by subcutaneous injection into NSG mice. After 30 days, tumours were collected and sgRNAs were amplified. In vivo growth phenotypes of 911 genes were highly reproducible between experimental replicates (left). Sequencing counts of T0 samples and day 30 samples from the in vivo batch-retest screens (right). In the left plot, the data are fit by a linear regression line (blue dotted line). b, Cumulative distribution of sequencing reads for sgRNAs in the batch-retest library in H23 cells. Read counts were normalized by total reads for each sample and the cumulative sums of sgRNAs were plotted as relative percentages of the number of expected sgRNAs. c, The 4,034 co-essential gene modules based on the DepMap CRISPR dataset are plotted as volcano plots for KRASi 2D phenotype scores. The y axis shows significance of enrichments of co-essential modules as measured in log P values from the two-sided Mann–Whitney U-test (see Methods); the x axis shows average gene effects of members in CERES modules. d, Genes in the CPD module are indicated among 17,634 genes sorted by their correlations to CPD. Pearson correlation coefficients between CPD and other genes are measured in batch-corrected CERES effects in the DepMap CRISPR dataset. e, CERES effects of CPD, FURIN and IGF1R are shown as correlation plots. CERES effects are batch-corrected before plotting²¹. Blue lines, regression lines. Blue shaded translucent bands, 95% confidence intervals. f, Lack of correlation between CPD and OR2A25, an olfactory receptor, in their CERES effects across 517 cancer lines.