Extended Data Fig. 3: Isolation, longitudinal profiling and functional mapping of drug resistant clones.

a. Schematic for longitudinal tracking and profiling of drug resistant colonies. Colonies were isolated, expanded and maintained over 4 to 6 weeks. Paired initial and late samples were sequenced at a bulk-level. b. Paired initial and late samples display minimal phenotypic drift in principal component (PC) space for top 500 most variable genes. Insets show brightfield images of representative samples. c. Euclidean distance (in PC1 and PC2) measured between paired initial and late samples and equivalent number of random initial-late pairs of samples. Lower Euclidean distance in true pairs as compared to random pairs implies that paired initial and late samples are transcriptionally more similar (closer in PC space) than any pair of initial and late samples. d. Scree plot depicting cumulative variance explained by PCs. Dotted line represents that most of the variance can be explained by the first 25 PCs alone. e. Euclidean distance (in first 25 PCs) measured between paired initial and late samples and equivalent number of random initial-late pairs of samples. Lower Euclidean distance in true pairs as compared to random pairs implies that paired initial and late samples are transcriptionally more similar (closer in PC space) than any pair of initial and late samples. f. Euclidean distance measured between paired early and late samples and equivalent number of random initial-late pairs of samples. Euclidean distance was measured in PC1 and PC2 space for top 200, 500 and 1000 variable genes. g. Euclidean distance measured between paired initial and late samples and equivalent number of random initial-late pairs of samples. Euclidean distance was measured in the PC space created by the first 25 PCs for top 200, 500 and 1000 variable genes. h. Mapping of invasiveness onto the single-cell RNA sequencing dataset from FateMap by comparing genes differentially expressed between the two slowest and the two fastest invading resistant colonies (UMAP colored for similarity score). The slowest invading colonies have a high similarity score for cluster 15 (and to some extent 4 and 6), while the fastest invading colonies have a high similarity score for cluster 8 (and to some extent 1).