Extended Data Fig. 2: CRISPR-Cas9 screen controls.
From: Disruption of the MSL complex inhibits tumour maintenance by exacerbating chromosomal instability
a, Relative abundance of sgRNAs in the two biological replicates of TDF cells transduced with the sgRNA library 14 d after Cas9 induction (T14). NTC: non-targeting sgRNA controls. The statistical significance of the correlation between the two replicates (two-sided Spearman correlation test) and the corresponding correlation coefficient (rs) are indicated. b, Fold change (FC) in sgRNA abundance comparing the T14 and T0 cell populations of replicate 2 (Rep 2). Individual, alphabetically ordered sgRNAs are shown. Non-targeting sgRNA controls (NTC) are spread among targeting sgRNAs rather than clustered to ease their visualization. c, Proportion of ribosomal genes depleted (average log2 FC ≤ -0.5) at T14, indicating near saturation of the screen. Four out of 83 ribosomal genes targeted in the library are not expressed in TDF cells and are excluded from the analysis. The average value from both replicates is shown. d, Fold change in sgRNA abundance comparing the T24 and T0 cell populations in the counter-screen (see Methods). The average (left) or cumulative (right) value of all sgRNAs targeting each gene is plotted. The average of both replicates is shown in the graph on the left. The graph on the right displays only depleted genes and omits ribosomal genes due to the large number of sgRNAs targeting each gene (1-42 sgRNAs, median: 14 sgRNAs/gene), which makes them not comparable with other targeted genes. The essential gene POLR2A is shown as a positive control of sgRNA depletion. NTC: non-targeting sgRNA controls. e, Filtering strategy used to select hits from both screen arms. Source data are provided.
