Extended Data Fig. 3: Tracing lineages in cancer cells under 5-FU treatment.

All the experiments were performed in MDA-MB-468 cells. a. Experimental design showing the infection of cells with a lentivirus produced from the plasmid barcode library (pRRL-CMV-GFP-BCv2AscI). Cells were then treated with indicated drugs and scRNA-seq was performed. b. Histogram of the fraction of cells with detected lineage barcodes in scRNA-seq data for each sample. Numbers above bars are the number of cells with a lineage barcode. c. Clustering of lineage barcode frequencies - detected by bulk and scRNA-seq - using Spearman’s correlation score. The size of the dots is proportional to the correlation score. d. Heatmap showing the frequency of individual lineage barcodes (rows), measured by bulk sequencing in different samples for experiment #3 (columns) and color coded as indicated. Normalized frequencies are clustered with hierarchical clustering, with Spearman’s correlation score and Ward method. e. Dotplot of Shannon diversity indexes calculated from bulk datasets at each different time points under 5-FU or DMSO treatment, diversities were compared using a two-sided Wilcoxon rank test. f. Scatter plot representation comparing normalized barcode frequency in simulated population versus initial population (D0), based on bulk data from experiment #3. Correlation scores and associated p-value are indicated. g. Scatter plot comparing normalized barcode frequency in the DMSO-treated cells at D50 and D147 (Left) or 5-FU-treated cells at D77 and D147 (Right) compared to the initial population at D0, based on bulk data from experiment #3. Spearman’s correlation scores and associated p-value are indicated. h. UMAP representation of lineage-barcoded cells. Cells in orange are untreated cells having a lineage barcode found in at least one persister cell. Cells in red are matched persister cells. Cells in grey are cells having a lineage barcode which is not common between persister and untreated cells. i. Volcano plot of differential analysis between ‘persisting’ and ‘non persisting’ untreated cells. j. Distribution of correlation scores between barcode frequencies of two replicates.