Preprint: Please note that this article has not completed peer review.
Method Article

iFISH:a publically available resource enabling versatile DNA FISH to study genome architecture

Nicola Crosetto, Magda Bienko, Eleni Gelali, Gabriele Girelli, Masahiro Matsumoto, Erik Wernersson, Joaquin Custodio, Ana Mota, Maud Schweitzer, Katalin Ferenc, Xinge Li, Reza Mirzazadeh, Federico Agostini, John P. Schell, Fredrik Lanner
DOI: 10.1038/protex.2019.028

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 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

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Introduction

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Equipment

Procedure

References

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Preprint: Please note that this article has not completed peer review.
Method Article

iFISH:a publically available resource enabling versatile DNA FISH to study genome architecture

Nicola Crosetto, Magda Bienko, Eleni Gelali, Gabriele Girelli, Masahiro Matsumoto, Erik Wernersson, Joaquin Custodio, Ana Mota, Maud Schweitzer, Katalin Ferenc, Xinge Li, Reza Mirzazadeh, Federico Agostini, John P. Schell, Fredrik Lanner

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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 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.

Figures

Introduction

Reagents

Equipment

Procedure

References

Acknowledgements

Learn more about our company.