Fig. 1

a Schema of generation of single-edited Ba/F3 cell lines. b CRISPR-seq NGS validating the presence of gene edits in the 6 independent single-edited cell lines. c Single-cell DNA-seq analysis overview. First, sequenced reads are filtered and trimmed, after which they are assigned to individual cells by cell barcodes, and aligned to each amplicon using CRISPResso2. Finally, the modification rates at each editing on- and off-target in each cell are compiled. d Heatmap showing modification rates across 4328 cells (rows) at the 6 on-target loci. A scale bar showing the percent of mutated reads ranging from 0% modification (blue color) to 100% modification (red color) is shown. e Example of zygosity analysis at one of the on-target loci. Analytical thresholds (described in the “Methods” section) identify WT/WT (purple), WT/Mut (green), Mut/Mut2 (red), and Mut/Mut (blue) cells that are highlighted in the figure. f Pie chart showing heterozygous/homozygous subpopulations of gene edits within the Atm on-target locus. Numbers and percentage read counts for each sub-group are shown. g Cumulative zygosity analyses across the 6 on-targets for cells that have at least one mutated allele (WT/WT are omitted). h Absolute counts of live single-edited cell lines (and Cas9 control line) cultured for 9 days under IL-3 withdrawal. P value, RM-ANOVA with Dunnett’s correction for multiple comparisons