Two-color 3D FISH probing of the Igh locus and Runx1 was performed in pro-B cells, pre-B cells, and thymocytes. Line graphs show cumulative distributions of distances <1 m between the Igh locus and genes of interest in three cell types. The closest signal pairs in each cell were used. n = number of nuclei analyzed. Bar graphs show distribution of distances grouped into four brackets (<0.5, 0.5–0.8, 0.8–1, and >1 m). Dashed line denotes the probability of a random interaction at a distance of <1 m of 6.9%. The p values were calculated using the Fisher’s exact test with Bonferroni correction. Representative images of single nuclei are shown. The nuclear area was stained with DAPI, the Igh probes were labeled with Alexa Fluor 488 (green), and probes for genes of interest were labeled with Alexa Fluor 555 (red). The Igh(DJ) probe (BAC RP23-109B20) was used for pro-B and thymus, and the Igh(V) probe (BAC RP23-70F21) for pre-B (compared inFigure S7; discussed inSTAR Methods).
