Analysis of 3D gene expression patterns in plants using whole-mount RNA in situ hybridization

2014 ◽  
Vol 9 (10) ◽  
pp. 2464-2475 ◽  
Author(s):  
Frédérique Rozier ◽  
Vincent Mirabet ◽  
Teva Vernoux ◽  
Pradeep Das
Keyword(s):  
Gene Expression ◽  
In Situ Hybridization ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Whole Mount ◽  
Rna In Situ Hybridization ◽  
3D Gene

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.

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 Spatially multiplexed RNA in situ hybridization to reveal tumor heterogeneity

2019 ◽  
Vol 48 (3) ◽  
pp. e17-e17 ◽  
Author(s):  
Lena Voith von Voithenberg ◽  
Anna Fomitcheva Khartchenko ◽  
Deborah Huber ◽  
Peter Schraml ◽  
Govind V Kaigala
Keyword(s):  
Gene Expression ◽  
In Situ Hybridization ◽  
Spatial Heterogeneity ◽  
Tumor Heterogeneity ◽  
Expression Patterns ◽  
Spatial Multiplexing ◽  
Local Analysis ◽  
Tissue Sections ◽  
Rna In Situ Hybridization

Abstract Multiplexed RNA in situ hybridization for the analysis of gene expression patterns plays an important role in investigating development and disease. Here, we present a method for multiplexed RNA-ISH to detect spatial tumor heterogeneity in tissue sections. We made use of a microfluidic chip to deliver ISH-probes locally to regions of a few hundred micrometers over time periods of tens of minutes. This spatial multiplexing method can be combined with ISH-approaches based on signal amplification, with bright field detection and with the commonly used format of formalin-fixed paraffin-embedded tissue sections. By using this method, we analyzed the expression of HER2 with internal positive and negative controls (ActB, dapB) as well as predictive biomarker panels (ER, PgR, HER2) in a spatially multiplexed manner on single mammary carcinoma sections. We further demonstrated the applicability of the technique for subtype differentiation in breast cancer. Local analysis of HER2 revealed medium to high spatial heterogeneity of gene expression (Cohen effect size r = 0.4) in equivocally tested tumor tissues. Thereby, we exemplify the importance of using such a complementary approach for the analysis of spatial heterogeneity, in particular for equivocally tested tumor samples. As the method is compatible with a range of ISH approaches and tissue samples, it has the potential to find broad applicability in the context of molecular analysis of human diseases.

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