Extended Data Fig. 2: sgRNA impacts on viability and EGF-independent growth in the base editing EGFR activation screen in MCF10A cells.
From: Multimodal scanning of genetic variants with base and prime editing
(a) Receiver operating characteristic (ROC) curves for each target category or predicted mutation type when comparing plasmid and day 19 (nontreated). The AUC for essential splice site sgRNAs are shown in red. (b) Scatter plot comparing the individual sgRNA LFCs between plasmid and day 19 and between nontreated and EGF-deprived samples. Negative-log FDR values for EGFR activating sgRNAs are shown. Dashed squares represent the hit inclusion criteria: LFC (plasmid versus day 19) > -0.6 and LFC (nontreated versus EGF-deprived) > 0.3. (c–e) Deep sequencing data for individual sgRNA validation in MCF10A cells. Cells were infected with the indicated sgRNA and base editor pairs in three biological replicates (n = 3) and later split into control and treatment arms deprived of EGF. The percentages of reads corresponding to the four most represented alleles at each target site are shown for both nontreated and EGF-deprived samples. Nucleotide sequences represent the coding DNA strand and black squares denote wild-type EGFR sequences. Holm-adjusted P values are shown for two-sided t-tests.
