Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH

Sci Data. 2022 Feb 10;9(1):47. doi: 10.1038/s41597-022-01139-2.


Single-molecule DNA fluorescence in situ hybridization (FISH) techniques enable studying the three-dimensional (3D) organization of the genome at the single cell level. However, there is a major unmet need for open access, high quality, curated and reproducible DNA FISH datasets. Here, we describe a dataset obtained by applying our recently developed iFISH method to simultaneously visualize 16 small (size range: 62-73 kilobases, kb) DNA loci evenly spaced on chromosome 2 in human cells, in a single round of hybridization. We show how combinatorial color coding can be used to precisely localize multiple loci in 3D within single cells, and how inter-locus distances scale inversely with chromosome contact frequencies determined by high-throughput chromosome conformation capture (Hi-C). We provide raw images and 3D coordinates for nearly 10,000 FISH dots. Our dataset provides a free resource that can facilitate studies of 3D genome organization in single cells and can be used to develop automatic FISH analysis algorithms.

Publication types

  • Dataset
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Cell Nucleus*
  • Chromosomes
  • DNA*
  • Humans
  • In Situ Hybridization, Fluorescence
  • Single-Cell Analysis


  • DNA