IFISH is a publically available resource enabling versatile DNA FISH to study genome architecture

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

doi:10.1038/s41467-019-09616-w

Eleni Gelali, John P Schell + Show 13 more

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https://doi.org/10.1038/s41467-019-09616-w

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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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DNA fluorescence in situ hybridization (DNA FISH) is a powerful method to study chromosomal organization in single cells
We create a large resource of validated DNA FISH oligo probes and probe design tools—which we name iFISH— that can be freely used by individual researchers, as well as diagnostic laboratories, to visualize multiple regions of the genome at high resolution, as well as to design probes in regions currently not covered by our repository
In order to enable versatile design of DNA FISH probes, we initially developed an algorithm that, given a genome-wide database of oligos and a genomic region of interest, identifies the most suitable window(s) within that region of interest and designs FISH probe(s) by selecting from the database the oligos that map within that window(s), based on various parameters that we have identified as important

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DNA fluorescence in situ hybridization (DNA FISH) is a powerful method to study chromosomal organization in single cells. 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. At present, there is no publicly available repository of individually tested and validated probes against multiple loci on different chromosomes Such repository would enormously facilitate the use of DNA FISH among genome biologists and, importantly, help establish standardized probe collections, which in turn would improve interlaboratory reproducibility. Toward this goal, we establish a database of oligos supporting DNA FISH probes design, and targeting a substantially larger fraction of the human genome than the available databases. We show that iFISH probes can be used as chromosome-spotting probes to visualize multiple pairs of chromosomes in the same cells, and propose an analytical approach to quantify the extent of intermingling between heterologous chromosomes

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