Measurement of Spatial Contact Map Using Sequential FISH

The spatial organization of genomes within the cell nucleus is fundamental to gene expression and chromosome folding processes. DNA sequential fluorescence in situ hybridization (DNA-seqFISH) facilitates the examination of higher-order genome structures across the genome by spatially mapping specific genomic coordinates. Leveraging this spatial data allows for the precise calculation of distances between genomic regions within cells, allowing analyses of region-associated gene transcription and protein localization at single-cell and single-allele resolutions. This chapter presents a methodology for generating DNA spatial distance maps using bright spot coordinate data derived from DNA-seqFISH. The corresponding code is available on GitHub ( https://github.com/hirohishi/MicEASH.git ).