Top: Violin/box plots of DNA FISH (black, gray) and RNA FISH (orange) quantifications showing 3D focal distances between tsh-tio and their respective equidistant controls (gray, ctr) at stage 11. Dashed line indicates 250 nm. Bottom: Barplot of percentage of alleles with distances <250 nm. (Error bars indicate standard deviation.) Distances of tsh-tio loci were measured in the anterior (inactive) and posterior (active, orange) parts of the embryo. RNA FISH probes were generated from the indicated genes introns when possible (nascent) or both introns and exons. Number (n) of nuclei measured indicated underneath, N = number of embryos. For all violin plots with boxplots, boxplots display the standard features median, 25th, and 75th percentile (hinges) and the whiskers (at most 1.5*interquartile range of the hinges) and outliers (data points beyond whiskers). Standard for geom.boxplot in ggplot2.
