ZebraFISH: Fluorescent In Situ Hybridization Protocol and Three-Dimensional Imaging of Gene Expression Patterns

Zebrafish ◽  
2006 ◽  
Vol 3 (4) ◽  
pp. 465-476 ◽  
Author(s):  
Monique C.M. Welten ◽  
Simon B. de Haan ◽  
Niels van den Boogert ◽  
Jasprien N. Noordermeer ◽  
Gerda E.M. Lamers ◽  
...  
Keyword(s):  
Gene Expression ◽  
In Situ Hybridization ◽  
Fluorescent In Situ Hybridization ◽  
Expression Patterns ◽  
Three Dimensional ◽  
Gene Expression Patterns ◽  
Three Dimensional Imaging ◽  
Hybridization Protocol

scholarly journals RNA In Situ Hybridization for Detecting Gene Expression Patterns in the Abdomens and Wings of Drosophila Species

2021 ◽  
Vol 4 (1) ◽  
pp. 20
Author(s):  
Mujeeb Shittu ◽  
Tessa Steenwinkel ◽  
William Dion ◽  
Nathan Ostlund ◽  
Komal Raja ◽  
...  
Keyword(s):  
Gene Expression ◽  
In Situ Hybridization ◽  
Expression Patterns ◽  
Drosophila Species ◽  
Gene Expression Patterns ◽  
Probe Design ◽  
Tissue Preparation ◽  
Design And Synthesis ◽  
Rna In Situ Hybridization

RNA in situ hybridization (ISH) is used to visualize spatio-temporal gene expression patterns with broad applications in biology and biomedicine. Here we provide a protocol for mRNA ISH in developing pupal wings and abdomens for model and non-model Drosophila species. We describe best practices in pupal staging, tissue preparation, probe design and synthesis, imaging of gene expression patterns, and image-editing techniques. This protocol has been successfully used to investigate the roles of genes underlying the evolution of novel color patterns in non-model Drosophila species.

Determination of gene expression patterns using in situ hybridization to Drosophila testes

2009 ◽  
Vol 4 (12) ◽  
pp. 1807-1819 ◽  
Author(s):  
Ceri A Morris ◽  
Elizabeth Benson ◽  
Helen White-Cooper
Keyword(s):  
Gene Expression ◽  
In Situ Hybridization ◽  
Expression Patterns ◽  
Gene Expression Patterns

scholarly journals Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images

2009 ◽  
Vol 26 (6) ◽  
pp. 761-769 ◽  
Author(s):  
Daniel L. Mace ◽  
Nicole Varnado ◽  
Weiping Zhang ◽  
Erwin Frise ◽  
Uwe Ohler
Keyword(s):  
Gene Expression ◽  
In Situ Hybridization ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Rna In Situ Hybridization

scholarly journals Orientation and repositioning of chromosomes correlate with cell geometry–dependent gene expression

2017 ◽  
Vol 28 (14) ◽  
pp. 1997-2009 ◽  
Author(s):  
Yejun Wang ◽  
Mallika Nagarajan ◽  
Caroline Uhler ◽  
G. V. Shivashankar
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Three Dimensional ◽  
Gene Expression Patterns ◽  
Cell Behavior ◽  
Global Changes ◽  
Cell Geometry ◽  
Transcription Inhibition ◽  
Regulate Gene Expression

Extracellular matrix signals from the microenvironment regulate gene expression patterns and cell behavior. Using a combination of experiments and geometric models, we demonstrate correlations between cell geometry, three-dimensional (3D) organization of chromosome territories, and gene expression. Fluorescence in situ hybridization experiments showed that micropatterned fibroblasts cultured on anisotropic versus isotropic substrates resulted in repositioning of specific chromosomes, which contained genes that were differentially regulated by cell geometries. Experiments combined with ellipsoid packing models revealed that the mechanosensitivity of chromosomes was correlated with their orientation in the nucleus. Transcription inhibition experiments suggested that the intermingling degree was more sensitive to global changes in transcription than to chromosome radial positioning and its orientations. These results suggested that cell geometry modulated 3D chromosome arrangement, and their neighborhoods correlated with gene expression patterns in a predictable manner. This is central to understanding geometric control of genetic programs involved in cellular homeostasis and the associated diseases.

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