Extended Data Fig. 10: Imaging of both nascent transcripts and chromatin structure at the Sox2 locus.

a, Example images of RNA FISH(left) and chromatin tracing(right) in the same cells. Circles indicate individual nuclei. RNA probes targeting Sox2, efgp, and mcherry are color-coded. Transcripts from the CAST allele are indicated by dots in purple pseudo color. Transcripts from the 129 allele are indicated by dots in cyan pseudo color. Arrows highlight examples of bursting alleles. b, Bursting frequencies of the CAST and 129 allele in the 4CBS clone and the control clone with 4CBS inserted downstream of the Sox2 SE. The numbers of bursting chromosomes and total chromosomes are indicated on the top of each bar. c, Median spatial distance matrices of the CAST and 129 allele in the 4CBS and the control clone (4CBS inserted downstream of the Sox2 super-enhancer). Multiplexed DNA FISH experiments were performed in the same cells following the RNA FISH experiments. d, Enhancer-promoter distances of the bursting and resting chromosomes in the 4CBS and the 4CBS downstream clone. A two-sided KS test between the distributions and a two-sided Wilcoxon test were performed.