Figure 4
Targeted barcode libraries in K562 cells. (a) Schema for targeting barcodes to the CCR5 locus. Targeting vector (repair template; top) includes a UBC-driven GFP gene upstream of a 20 bp barcode, and the P5 Illumina adapter sequence in reverse between CCR5 arms of homology. HSV-TK (herpes simplex virus thymidine kinase) is included outside of the arms of homology to allow drug selection against clones with off-target integration of the vector. Middle: the site of the ZFN-induced double strand DNA break. Bottom: the correctly targeted locus after homologous recombination with the targeting vector. (b) Clones were counted and binned in Log 2 bins based on percentage (frequency) within the population, from least to greatest. The percentage of the clones in each bin is shown. Inset shows magnification of larger bins. K562 biological replicate A of the CCR5-targeted barcode experiment is shown (others are shown in Additional file 7). (c) The percentage of clones, ranked from most to least frequent, plotted by what percentage of the population they made up. (d) The percentage of the population made up by the top indicated percentages of the clones in each sample. (e) The number of clones found in each sample. (f) Rank order clones by percentage of the population for each sample; greatest to least. Any clones ≥1% are delimited by white sections, the remaining population of clones smaller than 1% are represented by black in each column. The same clone occurring as a major clone in more than one sample is indicated with color.