ArticleCell reports methods2024
Generation of densely labeled oligonucleotides for the detection of small genomic elements.
Article in Cell reports methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- A flexible framework for automated STED super-resolution microscopy.Scientific reports · 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
- Label-free technique for universal and sequence independent detection of oligonucleotides and nuclease activity.Nucleic acids research · 2025Article
- FAIR sharing of Chromatin Tracing datasets using the newly developed 4DN FISH Omics Format.ArXiv · 2025Article
- Altered enhancer-promoter interaction leads to MNX1 expression in pediatric acute myeloid leukemia with t(7;12)(q36;p13).Blood advances · 2024Article
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Authors and funding
8 authors.
Funding
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Abstract
The genome contains numerous regulatory elements that may undergo complex interactions and contribute to the establishment, maintenance, and change of cellular identity. Three-dimensional genome organization can be explored with fluorescence in situ hybridization (FISH) at the single-cell level, but the detection of small genomic loci remains challenging. Here, we provide a rapid and simple protocol for the generation of bright FISH probes suited for the detection of small genomic elements. We systematically optimized probe design and synthesis, screened polymerases for their ability to incorporate dye-labeled nucleotides, and streamlined purification conditions to yield nanoscopy-compatible oligonucleotides with dyes in variable arrays (NOVA probes). With these probes, we detect genomic loci ranging from genome-wide repetitive regions down to non-repetitive loci below the kilobase scale. In conclusion, we introduce a simple workflow to generate densely labeled oligonucleotide pools that facilitate detection and nanoscopic measurements of small genomic elements in single cells.
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