Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH.
Ana MotaMaud SchweitzerErik WernerssonNicola CrosettoMagda BienkoPublished in: Scientific data (2022)
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.
Keyphrases
- single molecule
- induced apoptosis
- genome wide
- circulating tumor
- high throughput
- cell cycle arrest
- single cell
- deep learning
- atomic force microscopy
- living cells
- machine learning
- cell free
- copy number
- endoplasmic reticulum stress
- genome wide association study
- signaling pathway
- nucleic acid
- oxidative stress
- minimally invasive
- gene expression
- convolutional neural network
- mass spectrometry
- data analysis
- cell proliferation
- quantum dots
- high speed