Fig. 3: Induction of an early stop codon in PTPRC identifies changes in gene and cell-surface protein expression.
From: Precisely defining disease variant effects in CRISPR-edited single cells
a, Schematic of genomic editing in the PTPRC gene in primary human naive CD4+ T cells. BE4-NG base editors were used to induce a premature stop codon. PBMCs, peripheral blood mononuclear cells. b, Alleles from the PTPRC amplicon around the sgRNA. c, Allele combination with number of cells per condition and individual (column). Normalized expression of PTPRC is plotted by allelic combination. MFI, median fluorescence intensity. P-values are calculated by two-sided LRT. Boxes represent IQR; whiskers indicate 1.5 × IQR. d,e, Volcano plot of differential gene expression (d) and ADT expression (e) identified by linear modelling. P-values and betas from likelihood-ratio tests are plotted for the genotype analysis only. Dotted line represents the FDR cut-off of 0.05. f,g, Confirmation of results in bulk-edited CD4+ T cells with flow cytometry (f). Representative plots of CD4 versus CD45 are shown for the control and CRISPR conditions (g). The combination of CD4 and CD45 cell-surface expression is used to identify heterozygote (+/−) and homozygote (−/−) edited cells; n = 4 individuals. P-values are derived from LRT statistics from linear modelling. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. Boxes represent IQR; whiskers indicate 1.5 × IQR.
