Comprehensive FISH probe design tool applied to imaging human immunoglobulin class switch recombination.
We present a web engine boosted fluorescence in-situ hybridization (webFISH) algorithm using a genome-wide sequence similarity search to design target-specific single-copy and repetitive DNA FISH probes. The webFISH algorithm featuring a user-friendly interface (http://www.webfish2.org/) maximizes t...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0051675&type=printable |
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| author | Jakub Nedbal Philip S Hobson David J Fear Rainer Heintzmann Hannah J Gould |
| author_facet | Jakub Nedbal Philip S Hobson David J Fear Rainer Heintzmann Hannah J Gould |
| author_sort | Jakub Nedbal |
| collection | DOAJ |
| description | We present a web engine boosted fluorescence in-situ hybridization (webFISH) algorithm using a genome-wide sequence similarity search to design target-specific single-copy and repetitive DNA FISH probes. The webFISH algorithm featuring a user-friendly interface (http://www.webfish2.org/) maximizes the coverage of the examined sequences with FISH probes by considering locally repetitive sequences absent from the remainder of the genome. The highly repetitive human immunoglobulin heavy chain sequence was analyzed using webFISH to design three sets of FISH probes. These allowed direct simultaneous detection of class switch recombination in both immunoglobulin-heavy chain alleles in single cells from a population of cultured primary B cells. It directly demonstrated asynchrony of the class switch recombination in the two alleles in structurally preserved nuclei while permitting parallel readout of protein expression by immunofluorescence staining. This novel technique offers the possibility of gaining unprecedented insight into the molecular mechanisms involved in class switch recombination. |
| format | Article |
| id | doaj-art-82c1c6d2fcdc4ce6856bc9b219d53122 |
| institution | Kabale University |
| issn | 1932-6203 |
| language | English |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-82c1c6d2fcdc4ce6856bc9b219d531222025-08-20T03:26:38ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-01712e5167510.1371/journal.pone.0051675Comprehensive FISH probe design tool applied to imaging human immunoglobulin class switch recombination.Jakub NedbalPhilip S HobsonDavid J FearRainer HeintzmannHannah J GouldWe present a web engine boosted fluorescence in-situ hybridization (webFISH) algorithm using a genome-wide sequence similarity search to design target-specific single-copy and repetitive DNA FISH probes. The webFISH algorithm featuring a user-friendly interface (http://www.webfish2.org/) maximizes the coverage of the examined sequences with FISH probes by considering locally repetitive sequences absent from the remainder of the genome. The highly repetitive human immunoglobulin heavy chain sequence was analyzed using webFISH to design three sets of FISH probes. These allowed direct simultaneous detection of class switch recombination in both immunoglobulin-heavy chain alleles in single cells from a population of cultured primary B cells. It directly demonstrated asynchrony of the class switch recombination in the two alleles in structurally preserved nuclei while permitting parallel readout of protein expression by immunofluorescence staining. This novel technique offers the possibility of gaining unprecedented insight into the molecular mechanisms involved in class switch recombination.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0051675&type=printable |
| spellingShingle | Jakub Nedbal Philip S Hobson David J Fear Rainer Heintzmann Hannah J Gould Comprehensive FISH probe design tool applied to imaging human immunoglobulin class switch recombination. PLoS ONE |
| title | Comprehensive FISH probe design tool applied to imaging human immunoglobulin class switch recombination. |
| title_full | Comprehensive FISH probe design tool applied to imaging human immunoglobulin class switch recombination. |
| title_fullStr | Comprehensive FISH probe design tool applied to imaging human immunoglobulin class switch recombination. |
| title_full_unstemmed | Comprehensive FISH probe design tool applied to imaging human immunoglobulin class switch recombination. |
| title_short | Comprehensive FISH probe design tool applied to imaging human immunoglobulin class switch recombination. |
| title_sort | comprehensive fish probe design tool applied to imaging human immunoglobulin class switch recombination |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0051675&type=printable |
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