ArticleNature communications2019
iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
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- Chromatin-associated intronic RNAs from long genes form introsomes that shape nuclear architecture in neuronal cells.bioRxiv : the preprint server for biology · 2026Article
- Applications and development of in situ nucleic acid visualization techniques.Frontiers in bioengineering and biotechnology · 2026Review
- Nanoscale dynamics of enhancer-promoter interactions during exit from pluripotency.Nucleic acids research · 2025Article
- OligoY pipeline for full Y chromosome painting.Briefings in bioinformatics · 2025Article
- Generation of Dual-Color FISH probes targeting 9p21, Xp21, and 17p13.1 loci as diagnostic markers for some genetic disorders and cancer in Egypt.Journal, genetic engineering & biotechnology · 2025Article
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- Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images.Nature methods · 2024Article
- High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue.Nature communications · 2024Article
- scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells.Nature communications · 2024Article
- Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes.Nature communications · 2024Article
- Designing Oligonucleotide-Based FISH Probe Sets with PaintSHOP.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project.Molecular cell · 2023Review
- Oligonucleotide Fluorescence In Situ Hybridization: An Efficient Chromosome Painting Method in Plants.Plants (Basel, Switzerland) · 2023Review
- Cytogenetic screening of a Canadian swine breeding nucleus using a newly developed karyotyping method named oligo-banding.Genetics, selection, evolution : GSE · 2023Article
- Probabilistic establishment of speckle-associated inter-chromosomal interactions.Nucleic acids research · 2023Article
- Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights.BMC genomics · 2023Article
- Single-cell detection of primary transcripts, their genomic loci and nuclear factors by 3D immuno-RNA/DNA FISH in T cells.Frontiers in immunology · 2023Article
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15 authors.
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No grant is acknowledged in the PubMed record.
Abstract
DNA fluorescence in situ hybridization (DNA FISH) is a powerful method to study chromosomal organization in single cells. At present, there is a lack of free resources of DNA FISH probes and probe design tools which can be readily applied. Here, we describe iFISH, an open-source repository currently comprising 380 DNA FISH probes targeting multiple loci on the human autosomes and chromosome X, as well as a genome-wide database of optimally designed oligonucleotides and a freely accessible web interface ( http://ifish4u.org ) that can be used to design DNA FISH probes. We individually validate 153 probes and take advantage of our probe repository to quantify the extent of intermingling between multiple heterologous chromosome pairs, showing a much higher extent of intermingling in human embryonic stem cells compared to fibroblasts. In conclusion, iFISH is a versatile and expandable resource, which can greatly facilitate the use of DNA FISH in research and diagnostics.
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