Fig. 2

Accurate ploidy estimation based on read density. a Read depth \(\rho\) versus observed read density (see Fig. S2 for an illustration) for cells sorted into different cell cycle stages (apoptotic (D), G1, G2, and S phase) via FACS using DAPI staining. Each panel represents a different library: T-47D is a cancer cell line, and A73044A and A90553C are libraries consisting of normal cells (GM18507 cell line/SA928). Models of expected read density for a given read depth \(\rho\) based on a reference populations of cells sequenced with DLP+ are indicated in cyan. \(\rho =75\) is indicated by the red dashed line. b Read depth \(\rho\) versus observed read density for PEO1 cells sorted into different cell cycle stages (apoptotic (D), G1, G2, and S phase) via the FUCCI cell cycle marker system. Each panel represents a systematic downsampling of cells (100%, and to 50% and 25% of original read depth). A model of expected read density for a given read depth \(\rho\) based on a reference populations of cells in G1 and S phase sequenced with mDLP+ is indicated in blue, and a model from a is included for reference. c Read depth \(\rho\) versus residual of the observed read density compared to the expected from the trained model in a for cells sorted into different cell cycle stages via FACS using DAPI staining. d Read depth \(\rho\) versus residual of the observed read density compared to the expected from the trained model in b (PEO1 FUCCI) for cells sorted into different cell cycle stages via FUCCI cell cycle marker system. Additionally, residuals for cell multiplets are included. Cell multiplets are colour coded by ploidy state as determined experimentally via mixing of cell multiplets containing 1, 2, 3, 4 or 5 individual cells representing 3N, 6N, 9N, 12N, and 15N ploidy, within a single well prior to library preparation and sequencing. Cell multiplets and FUCCI cells are downsampled to 25% and 50% of original read depth to be included where appropriate