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

Mota A, Schweitzer M, Wernersson E, Crosetto N, Bienko M

Sci Data 9 (1) 47 [2022-02-10; online 2022-02-10]

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.

Spatial Proteomics [Technology development]

PubMed 35145120

DOI 10.1038/s41597-022-01139-2

Crossref 10.1038/s41597-022-01139-2

pmc: PMC8831585
pii: 10.1038/s41597-022-01139-2

Publications 9.5.0