Fig. 4

The HD CRISPR library efficiently identifies core, non- and context-dependent essential genes. a Workflow of a pilot screen conducted with the HD CRISPR library in HAP1 cells. The screen was performed in parallel in the Cas9-expressing bulk population and two highly editing single cell clones for both libraries independently. Successfully transduced cells were selected with puromycin for 48 h and then split into two independent replicates. The screen was performed for a duration of 14 days. b Core essential genes were strongly depleted over the course of screening with either of the two libraries, HD CRISPR libraries A and B, in contrast to nonessential genes. Stronger depletion was observed in the two single cell clones with high Cas9 editing efficiency. c Empirical cumulative distribution function for viability screens conducted with different HAP1 Cas9 cell lines and both HD CRISPR sub-libraries. Shown are results for sgRNAs targeting genes from core essential or nonessential gene sets or representing non-targeting controls. d Area under the curve (AUC) values for individual replicates of the empirical cumulative distribution functions shown in c. e Comparison of HAP1 essential genes as identified with the HD CRISPR library, a gene trap screen by Blomen et al. [41] and two CRISPR screens using either the TKOv1 or TKOv3 library by Hart et al. [17]. f Number of essential genes detected with increasing number of sgRNAs per gene using BAGEL (left; BF > 6) or MAGeCK RRA (right; FDR < 5%). sgRNAs were subsampled from the combined HD CRISPR library (sub-libraries A and B). Each data point represents the average of 5 samples. Error bars are ±1 s.e.m