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Method Article
Nicola Crosetto
Bienko and Crosetto Laboratories
Corresponding Author
Magda Bienko
Bienko and Crosetto Laboratories
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
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 validated 153 probes in our repository, and harnessed 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.
Keywords
DNA FISH,open-source repository,chromosomal organization,genome architecture
Figure 1
The authors declare no competing financial interests.
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Subject Areas
Cell biology
Biotechnology
Biological techniques
Molecular Biology
Computational biology and bioinformatics
Genetics
Associated Publications
iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture
by Eleni Gelali, Gabriele Girelli, Masahiro Matsumoto, +12
Nature Communications (09 April, 2019)
An open repository of community-contributed protocols sponsored by Nature Research.
Learn more about Protocol Exchange
Method Article
Nicola Crosetto
Bienko and Crosetto Laboratories
Corresponding Author
Magda Bienko
Bienko and Crosetto Laboratories
Corresponding Author
Version History
CURRENT STATUS: Posted
Version 1
Posted 22 May, 2019
No community comments so far
Metrics
Comments: 0
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
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 validated 153 probes in our repository, and harnessed 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.
Figure 1
The authors declare no competing financial interests.
Loading...
Associated Publications
iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture
by Eleni Gelali, Gabriele Girelli, Masahiro Matsumoto, +12
Nature Communications (09 April, 2019)