Extended Data Fig. 8: Analysis of large-scale pgFARM screens. | Nature Genetics

Extended Data Fig. 8: Analysis of large-scale pgFARM screens.

From: RNA isoform screens uncover the essentiality and tumor-suppressor activity of ultraconserved poison exons

Extended Data Fig. 8

a, HeLa/iCas9 cells (n = 4 biological replicates) treated with the poison exon pgRNA library and grown in the presence ( + dox) or absence (- dox) of active Cas9. b, Scatter plots comparing normalized fold-changes (day 14 vs. day 0; n = 963 targeted exons) estimated with each replicate of the cell viability screen in HeLa/iCas9 cells. Pearson correlations for individual replicate comparisons are indicated. c, Normalized fold-changes for pgRNAs targeting exons in unexpressed (TPM ≤ 1; n = 96 for HeLa/iCas9 and 128 for PC9-Cas9) or highly expressed (TPM ≥ 10; n = 681 for HeLa/iCas9 and 661 for PC9-Cas9) genes. Each dot represents the median fold-change computed over all pgRNAs targeting exons in the indicated groups for a representative replicate from the screens in HeLa/iCas9 (left; n = 5) and PC9-Cas9 (right; n = 4) cells. TPM, transcripts per million. d, Normalized fold-changes for pgRNAs targeting lowly expressed genes (TPM < 5) located in genomic regions with the indicated copy numbers (n = 6, 165, and 14 per group, left to right, for HeLa/iCas9; n = 60, 107, and 45 per group, left to right, for PC9-Cas9). e, Rank plot of mean normalized fold-changes for conserved poison (orange) or upstream constitutive exons (purple) based on all replicates of the HeLa/iCas9 viability screen. f, As (e), but for all replicates of the PC9-Cas9 viability screen. For box plots, the center line, hinges, and whiskers represent median, 25th and 75th percentiles, and most extreme datapoints within 1.5X interquartile range from hinges, respectively.

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