Supplementary Figure 4: Clonal analysis in primary tumors and lung metastases at ≥0.001% frequency.
From: In vivo profiling of metastatic double knockouts through CRISPR–Cpf1 screens
a, Tukey box plots (IQR boxes with 1.5 × IQR whiskers) detailing the distribution of clone frequencies in pre-injection cell pools (n = 6), indicated by the abundances of each BC array in each sample (n = 164,597, 184,002, 170,638, 172,803, 171,011 and 171,509 BC arrays, from top to bottom). b, Bar plot of the number of clones present at ≥0.001% frequency in cell pools, primary, tumors and lung metastases. c, Violin density plots with overlaid data points of the log2 number of clones present at ≥0.001% frequency in cell pools (gray, n = 6 cell replicates), primary tumors (orange, n = 10 mice) and lung metastases (blue, n = 37 from ten mice). Cells versus primary tumors (two-sided Wilcoxon rank sum test, P = 0.0002), cells versus lung metastases (P = 0.0001) and primary tumors versus lung metastases (P = 0.0162). d, Dot plot of the relative frequencies of clones at ≥0.001% frequency. Relative frequencies are expressed as percentages of total reads in each sample. Points are colored and labeled below by cell sample/mouse ID as in b. e, Empirical CDF of all clones at ≥0.001% frequency, expressed as percentages of total reads in each sample, aggregated by sample type: cell pools (gray, n = 6 cell replicates), primary tumors (orange, n = 10 mice) and lung metastases (blue, n = 37 from ten mice). The clone size distributions in primary tumors and lung metastases were significantly different (two-sided Kolmogorov–Smirnov test, P < 2.2 × 10–16). f, Violin density plots of Shannon diversity indices in cell pools (gray, n = 6 cell replicates), primary tumors (orange, n = 10 mice) and lung metastases (blue, n = 37 from ten mice) for clones at ≥0.001% frequency. Cells versus primary tumors (two-sided Wilcoxon rank sum test, P = 0.0002), cells versus lung metastases (P = 3.28 × 10–7) and primary tumors versus lung metastases (P = 0.0212).
