Fig. 3: Polymer fiber karyotyping on interphase mESCs.

a, Schematic of polymer fiber karyotyping by iterative path subtraction. For every plausible polymer found, all nodes visited on the polymer path are subtracted before a new graph is constructed for additional rounds of spatial genome alignment. Paths are extended until no physical plausible paths can be discovered. b, The score of each path is recorded, interpreted as the CDF of the polymer and compared to a physically unlikely threshold. Paths are extended for a given chromosome in a cell until either no more paths can be extended or a path extended has a score above threshold. c, Boxplot (center line, median; box, 25th to 50th percentile; bars, minima and maxima): of predicted copy number and total detected loci per chromosome (including spots omitted by spatial genome alignment) of mESC (n = 1,160 cells examined over four experiments). For every extra chromosome detected by polymer fiber karyotyping, we find a stepwise multiplicative increase in the total detected loci (for example, 1 chr, 100 points, 2 chr, 200 points, …). Pearson correlation coefficient evaluates this trend of detected loci per increase in assigned ploidy. d, Hierarchical clustering of mESCs by copy number similarity. Copy number of chromosomes is congruent across the mouse genome in a given cell with the exception of chrX in this male cell line. A dominant faction of cells is 2N in addition to a smaller faction of 3N cell with unsynchronized replication and a smaller faction of 4N cells postreplication. e, Heatmap of pairwise comparisons of copy number assigned by different chromosomes, with agreement scored by Cohen’s kappa.