Fig. 2

Single-cell analyses identify chromosomal amplifications in “jackpot” drug-resistant lineages. a Plot depicts barcode distributions in scRNA-seq data for 1268 individual cells from Experiments #1 and #2 at day 28. Blue circles indicate the number of barcodes (left axis) that were detected in the indicated number of cells (x-axis). The “jackpot” lineage identified by gDNA analysis of Experiment #2 (e86var) was detected in the largest number of cells (n = 30). The red line indicates the cumulative fraction of cells (right axis) for which a lineage barcode was detected. b t-SNE plot displays single cells (points) clustered based on their transcriptomes and colored by experiment. c t-SNE plot as in panel b with cells colored by their expression score for cell cycle signature genes. d t-SNE plot as in panel b with cells that correspond to the jackpot lineage e86vac (red) or other lineages (orange) indicated. Gray points indicate cells for which lineage could not be determined. e Barplot depicts fraction of cells positive for the cell cycle signature (y-axis). Data are shown for cells assigned to the jackpot e86vac or other lineages. f Rank-ordered plot shows chromosomal bands that harbor genes that are higher expressed in the e86vac lineage relative to all others. Chromosome 13 bands are highlighted in red and the three most significant bands are labeled