Chapter title |
Automated 3D Gene Position Analysis Using a Customized Imaris Plugin: XTFISHInsideNucleus
|
---|---|
Chapter number | 32 |
Book title |
Plant Chromatin Dynamics
|
Published in |
Methods in molecular biology, January 2018
|
DOI | 10.1007/978-1-4939-7318-7_32 |
Pubmed ID | |
Book ISBNs |
978-1-4939-7317-0, 978-1-4939-7318-7
|
Authors |
Mariamawit S. Ashenafi, Célia Baroux |
Abstract |
Fluorescence in situ hybridization (FISH) is commonly used to visualize chromosomal regions or genomic loci within the nucleus, and can largely contribute to unraveling the link between structure and function in the nucleus. Three-dimensional (3D) analyses are required to best capture the nucleus' organizing principles, but the experimental setup and computational analyses are far from trivial. Here, we present a robust workflow for 3D FISH against repeats and single copy loci in embedded intact nuclei from Arabidopsis leaves. We then describe in detail the image acquisition, subsequent image deconvolution before 3D image processing, and the image reconstruction. We developed an automated batch image processing pipeline using a customized, open source plugin implemented in the Imaris environment. |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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Unknown | 7 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
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Student > Ph. D. Student | 1 | 14% |
Student > Bachelor | 1 | 14% |
Researcher | 1 | 14% |
Student > Doctoral Student | 1 | 14% |
Unknown | 3 | 43% |
Readers by discipline | Count | As % |
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Agricultural and Biological Sciences | 2 | 29% |
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Biochemistry, Genetics and Molecular Biology | 1 | 14% |
Unknown | 3 | 43% |