Extended Data Fig. 3: Evaluation of screening reproducibility and detection sensitivity.
From: Prime editor-based high-throughput screening reveals functional synonymous mutations in human cells
a, Correlation of zLFC values between two eBARs replicates for epegRNA with the third eBAR’s |LFC| ≥ 0. b, Correlation of zLFC values between two eBARs for epegRNAs with |AGCA LFC| ≥ 1 and |CACT LFC| ≥ 1. c, Pearson correlation analysis of LFC values between two eBARs across varying thresholds of absolute LFC values from the third eBAR. The x-axis indicates the absolute LFC threshold applied to each eBAR, while the y-axis represents the Pearson correlation coefficient between the remaining two eBARs. d, Correlation of LFC values between two eBARs for epegRNAs with the third eBAR’s |LFC| ≥ 1. e, Correlation of LFC values between two eBARs for epegRNAs with the third eBAR’s |LFC| ≥ 0. For panels a, b, d, and e, Pearson correlation coefficient (r) is labeled. N indicates the number of epegRNAs shown in these figures (for panels a and e, excluding those with zero sequencing read counts and black lines indicate density-based contours). f–g, Correlation analysis of enriched mutations in the HCT116 screen across three eBARs, based on LFC values (f) or zLFC values (g). Diagonal panels show histograms of value distributions, lower left panels show scatter plots of pairwise correlations, and upper right panels present Pearson correlation coefficient (r). The dataset includes 1,717 epegRNAs with nonsynonymous mutations and 417 epegRNAs with synonymous mutations. h, Boxplot of the relationship between the degree of reduction in counts of simulated deleterious variants in the experimental group (x-axis) and the calculated |screen score| (y-axis). n = 492 per group (number of epegRNAs). The gray dashed lines correspond to thresholds of 3 and 2.2. Boxplots are depicted as follows: the center line represents the median, the box limits denote the upper and lower quartiles, and whiskers extend to 1.5 times the interquartile range. i, Corresponding to h, the x-axis represents the average counts of these simulated deleterious variants in day 0, and the y-axis indicates the percentage reduction in day 35. Green labels highlight points where the |screen score| after reduction exceeds the selection threshold (3).
