Extended Data Fig. 7: Allele classification by multiplexed DNA FISH. | Nature Genetics

Extended Data Fig. 7: Allele classification by multiplexed DNA FISH.

From: CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains

Extended Data Fig. 7

a-c, Bar plots showing detect efficiency of the 42 segments of chromatin tracing experiments in the ‘4CBS’ clone (a), the ‘4CBS mutant’ clone (b), and the ‘4CBS downstream’ clone (c). Detect efficiency of each segment was calculated as the fraction of chromosomes that showed a positive fluorescence signal at the specific imaging round. d, Exemplary images of allele classification. Left, nuclei segmentation and the positions of CAST and 129 allele in the nucleus. Right, images of the forty-two 5-kb segments (chr3:34,601,078-34,811,078) of the CAST and 129 allele. The hybridization probes of the 26th segment (highlighted in the red box) specifically targeted the 4CBS sequence. The chromosome positive for the 26th segment (inserted 4CBS) was classified as CAST allele, the negative chromosome in the same cell was classified as 129 allele. Cells with both chromosomes positive or both chromosomes negative for the 26th segment were discarded.

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