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Complementarity of medium-throughput in situ RNA hybridization and tissue-specific transcriptomics: case study of Arabidopsis seed development kinetics.

Francoz E, Ranocha P, Pernot C, Le Ru A, Pacquit V, Dunand C, Burlat V - Sci Rep (2016)

Bottom Line: Integration of results illustrates the complementarity of both datasets.Moreover, depending on the tissues and the developmental stages considered, one or the other technique appears more sensitive than the other.For each tissue/developmental stage, we finally determined tissue-specific transcriptomic threshold values compatible with the spatiotemporally-specific detection limits of ISH for lists of hundreds to tens-of-thousands of genes.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet Tolosan, France.

ABSTRACT
The rationale of this study is to compare and integrate two heterologous datasets intended to unravel the spatiotemporal specificities of gene expression in a rapidly growing and complex organ. We implemented medium-throughput RNA in situ hybridization (ISH) for 39 genes mainly corresponding to cell wall proteins for which we have particular interest, selected (i) on their sequence identity (24 class III peroxidase multigenic family members and 15 additional genes used as positive controls) and (ii) on their expression levels in a publicly available Arabidopsis thaliana seed tissue-specific transcriptomics study. The specificity of the hybridization signals was carefully studied, and ISH results obtained for the 39 selected genes were systematically compared with tissue-specific transcriptomics for 5 seed developmental stages. Integration of results illustrates the complementarity of both datasets. The tissue-specific transcriptomics provides high-throughput possibilities whereas ISH provides high spatial resolution. Moreover, depending on the tissues and the developmental stages considered, one or the other technique appears more sensitive than the other. For each tissue/developmental stage, we finally determined tissue-specific transcriptomic threshold values compatible with the spatiotemporally-specific detection limits of ISH for lists of hundreds to tens-of-thousands of genes.

No MeSH data available.


Related in: MedlinePlus

Flowchart of the method used for medium throughput in situ hybridization based on/compared to published tissue-specific transcriptomic data.This flowchart is labelled according to the paragraph numbers appearing in the Material and Methods and Supplementary Methods sections.
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f1: Flowchart of the method used for medium throughput in situ hybridization based on/compared to published tissue-specific transcriptomic data.This flowchart is labelled according to the paragraph numbers appearing in the Material and Methods and Supplementary Methods sections.

Mentions: The overall flowchart of the method is presented in Fig. 1. The following sections explain the principle of the 6 main steps of the method displayed in Fig. 1. Extended details of the methods and step-by-step protocol are provided in the Supplementary Method in the same order.


Complementarity of medium-throughput in situ RNA hybridization and tissue-specific transcriptomics: case study of Arabidopsis seed development kinetics.

Francoz E, Ranocha P, Pernot C, Le Ru A, Pacquit V, Dunand C, Burlat V - Sci Rep (2016)

Flowchart of the method used for medium throughput in situ hybridization based on/compared to published tissue-specific transcriptomic data.This flowchart is labelled according to the paragraph numbers appearing in the Material and Methods and Supplementary Methods sections.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4837347&req=5

f1: Flowchart of the method used for medium throughput in situ hybridization based on/compared to published tissue-specific transcriptomic data.This flowchart is labelled according to the paragraph numbers appearing in the Material and Methods and Supplementary Methods sections.
Mentions: The overall flowchart of the method is presented in Fig. 1. The following sections explain the principle of the 6 main steps of the method displayed in Fig. 1. Extended details of the methods and step-by-step protocol are provided in the Supplementary Method in the same order.

Bottom Line: Integration of results illustrates the complementarity of both datasets.Moreover, depending on the tissues and the developmental stages considered, one or the other technique appears more sensitive than the other.For each tissue/developmental stage, we finally determined tissue-specific transcriptomic threshold values compatible with the spatiotemporally-specific detection limits of ISH for lists of hundreds to tens-of-thousands of genes.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet Tolosan, France.

ABSTRACT
The rationale of this study is to compare and integrate two heterologous datasets intended to unravel the spatiotemporal specificities of gene expression in a rapidly growing and complex organ. We implemented medium-throughput RNA in situ hybridization (ISH) for 39 genes mainly corresponding to cell wall proteins for which we have particular interest, selected (i) on their sequence identity (24 class III peroxidase multigenic family members and 15 additional genes used as positive controls) and (ii) on their expression levels in a publicly available Arabidopsis thaliana seed tissue-specific transcriptomics study. The specificity of the hybridization signals was carefully studied, and ISH results obtained for the 39 selected genes were systematically compared with tissue-specific transcriptomics for 5 seed developmental stages. Integration of results illustrates the complementarity of both datasets. The tissue-specific transcriptomics provides high-throughput possibilities whereas ISH provides high spatial resolution. Moreover, depending on the tissues and the developmental stages considered, one or the other technique appears more sensitive than the other. For each tissue/developmental stage, we finally determined tissue-specific transcriptomic threshold values compatible with the spatiotemporally-specific detection limits of ISH for lists of hundreds to tens-of-thousands of genes.

No MeSH data available.


Related in: MedlinePlus