Extended Data Fig. 1: Establishment of aneuploid cell lines from HMECs and RPTECs.
From: Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns
(a) Distributions of mRNA log2FC for Breast-specific (n = 44), Kidney-specific (n = 190), and non-specific (n = 11691) genes in RPTECs vs HMECs (left) and in KIRC vs BRCA tumors (right). RNA-seq data for RPTECs and HMECs generated in this study; RNA-seq data for human tumors is from the TCGA database. Breast- and Kidney-specific genes were annotated by the Human Protein Atlas. (b) Scatter plots of mRNA log2FC values from the differential expression analysis in (a). P value (P = 4.4 × 10−257) calculated from linear regression analysis. (c) Low-coverage DNA-seq pipeline for copy number calling. Read counts of raw sequencing data in 100 kb bins is shown after each step of the data analysis pipeline, and final inferred copy number states. (d) Single-cell profiles of hTERT-HMECs treated with reversine for 48 hours, clustered by Euclidean distance. (e) Single-cell profiles of hTERT-RPTECs treated with reversine for 48 hours, clustered by Euclidean distance. (f) Bright field images (left) and propidium iodide staining FACs analysis (right) of the hTERT-HMEC parental population (top) and a tetraploid-range clone (bottom). Gating strategy for G1 population and parameter extraction shown. (g) Density plots of PI fluorescence (x-axis) corresponding to scatterplots in (f). (h) Tetraploid HMEC clones are larger in size than diploid clones based on image analysis from a group of 43 representative clones. (i) Mean forward scatter (x-axis) and G1 peak PI fluorescence of HMEC aneuploid clones normalized to parental diploids from both control and reversine-treated populations (top). Tetraploids form a separate cluster. Same is shown for RPTEC clones (bottom; one HMEC tetraploid is included for comparison). (j) Copy number profiles of clones selected from HMEC tetraploid screens, replicate #1 (top) and replicate # 2 (bottom), clustered by Euclidean distance. Clone names from this set start with ‘F’ (that is FA, FB, FC, etc.). (k) Copy number profiles of diploid HMEC screen replicate #2. (l) Copy number profiles of diploid RPTEC screen replicate #2.
