Extended Data Fig. 8
From: Frequent aneuploidy in primary human T cells after CRISPR–Cas9 cleavage
Enrichment in the number of genes with no detected expression among cells identified as having a chromosome 14 loss (A), a chromosome 14 gain (B) or a chromosome 7 truncation (C) (Fig.4d). The x-axis represents the fold-change in the number of genes with no detected expression between cells with or without a chromosome 14 loss or gain or a chromosome 7 truncation, based on the InferCNV analysis (Fig. 4d). The dark gray lines represent the empirical values obtained for each chromosome, except for chromosome 14 or 7 in the respective plots. The orange line is the empirical value for chromosome 14 or chromosome 7. The black bars are the results of 10,000 permutations. D. Differential gene expression analysis for chromosome 2. Each dot represents the mean inferred copy number of genes coded on chromosome 2 in each cell treated with a non-specific gRNA (left) or a combination of the TCRα, TCRβ and PDCD1- targeting gRNAs (right). Cells are marked with dots spread along the x-axis. The dots are colored blue when corresponding to cells with a chromosome 2 loss, if their mean inferred gene copy number is >2 standard deviations from the population’s mean. n = 8619 and 6326 for cells treated with a non-specific gRNA (left) or a combination of the TCRα, TCRβ and PDCD1- targeting gRNAs (right), respectively. ****, p < 0.0001 for Fisher’s exact test comparing chromosome 2 loss between cells treated with the PDCD1 gRNA and cells treated with a non-specific gRNA.
