Fig. 4

Quantification of chromosome intermingling using iFISH chromosome-spotting probes. a Representative image of the territories of five different chromosomes visualized in IMR90 cells. Gray, DNA. Scale bar: 10 μm. b Scheme of how the mixing index is calculated for a given pair of chromosomes, A and B. For simplicity, dots are represented in 2D. The mixing index is the ratio between the number of squares containing dots in both colors and the total number of squares with dots in one or two colors. c Average mixing index for 31 chromosome pairs visualized in IMR90 cells. d Distributions of mixing index values per cell, in each of the 31 chromosome pairs visualized in c. e Example of six chromosomes exhibiting complete lack of territoriality and intermingling at a large extent, in the nucleus of one hESC. Gray, DNA. Scale bar: 10 μm. f Average mixing index, in hESCs, for six of the chromosome pairs shown in c. g Comparison between the distributions of mixing index values per cell, for the six chromosome pairs visualized in both hESCs and IMR90 cells. All the microscopy images in this figure are the maximum intensity z-projection of each channel. In all the violin plots, the bottom or leftmost line represents the 25th percentile, the top or rightmost line represents the 75th percentile, and the midline represents the median. n, number of cells in which the corresponding chromosome pair was visualized