RESEARCH ARTICLE The edlan ode cell li nt出 n's correlat (od) NA d in g METH ned essentiaRESEARCH Article Extended Data Fig. 1 | Project Score CRISPR–Cas9 screening pipeline, data quality control and analysis set. a, CRISPR–Cas9 screening pipeline workflow, including quality control steps and go/no-go decisions. b, Genomic characterization of the CRISPR–Cas9-screened cell lines. c, Average Pearson’s correlation of replicate sgRNA counts (n = 86,875) for individual cell lines. d, Data quality control threshold based on the distributions of Pearson’s correlation values of sgRNA fold change values between replicates of the same cell line (in green) and all possible pairwise comparisons (in grey), considering the 838 highly informative sgRNAs (described in the Methods). e, Percentage of experiments passing the quality control filter defined in d. f, Pearson’s correlation values as described in d for the cell lines in the final analysis set. g, ROC and precision/recall curves were obtained after classifying predefined essential (n = 354) and non-essential (n = 747) genes based on gene-level rank positions calculated using depletion fold changes. The median areas under the curve across all cell lines are reported. h, Glass’s Δ scores quantifying the depletion effect size for genes that encode ribosomal proteins (n = 61) and a priori known essential (n = 354) genes for all cell lines. i, Cell lines in the final analysis set grouped by tissue (inner ring) and cancer-type (outer ring). j, Median gene-level depletion fold change (FC) values and interquartiles for reference gene sets defined in g and h for the 324 cell lines included in the analysis set. GEX, gene expression; METH, methylation; CNA, copy number alteration; WES, whole-exome DNA sequencing; AUROC, area under receiver operating characteristic; AUPR; area under precision/recall curve