Extended Data Fig. 9: Additional analyses of the enhancer screen.

a, Number of detected gRNAs/perturbations per cell were plotted. b, Levenshtein edit distance between the consensus sequence of a gRNA in a given cell, and the template sequence, showing that in 93 % (chr. 8) or 95 % (chr. 11) of cases, there were no mismatches between consensus and template. c, Fold change in gene expression of enhancer targets is plotted in relation to the number of gRNAs supporting an enhancer-target gene pair (ETP). Number of ETPs per confidence level: 0 = 61, 1 = 621, 2 = 612, 3 = 611, 4 = 611. d, Zoom-in on a region surrounding the IFITM locus shows identification previously known enhancers⁵⁵. e, Distance to transcription start site (TSS) was plotted against confidence level, as calculated from the number of individual gRNAs with a detected effect on the target gene. Number of ETPs per confidence level: 0 = 61, 1 = 621, 2 = 612, 3 = 611, 4 = 611. See Methods section on ‘data visualization’ for a definition of boxplot elements. f, Number of genes jumped between an enhancer and the identified target gene was plotted (main panel). Inset shows association strength, calculated from the proportion of gRNAs that support the ETP, plotted against the number of jumped genes. g, Histogram of log-fold expression differences between jumped genes and the respective true enhancer target. h, Like Fig. 3h, but including all 34,493 potential ETPs across the whole dataset, instead of just gene-proximal ETPs. i, Precision-Recall curves for classifiers trained on the dataset generated in this study, and applied to the dataset from ref. ⁹ (orange line), or classifiers trained on the dataset from ref. ⁹ and applied to this dataset.