GeneAtlas® Transcriptomic analysis platform

GeneAtlas® System : Transcriptomic analysis platform dedicated to gene expression study in model plants.

 B&PMP laboratory has set in 2014 the GeneAtlas System from Affymetrix Company. This system allows performing, quickly and on site, all steps necessary for transcriptome data acquisition. Gene expression data are acquired by hybridization of microarrays (organized by indivisible strips of 4 microarrays). To date, the system provides access to gene expression of model plants such as Arabidopsis thaliana, Medicago, Soybean and Rice. For example, Arabidopsis microarrays provide expression data for more than 28.000 genes, including precursors of miRNAs.

The simplicity of the system allows everyone to experience its transcriptome whenever he wants. The protocol leading to the acquisition of labeled cDNA is a classical molecular biology experiment. Hybridization of microarrays takes place in a dedicated ‘Hybridization Station’. A first robotic device called ‘Fluidics station’ allows washing and staining of microarrays. An ‘Imaging Station’ then is used to image the 4 microarrays in parallel. Finally, a computer dedicated to data analysis is available. On this computer, the software Expression Console enables to assess the quality of the microarrays and the software controls Transcriptome Analysis Console (TAC) allows the data normalization followed by an analysis leading to the identification of differentially expressed genes when comparing treatments 2 by 2 (Statistical analysis using t.test).

This tool allows to bypass some limitations: the budget required for hybridization of a microarray is reduced, the system is less complex and avoid relocating his experiences on platforms (control of protocols, timing, data, etc … ). With the widespread use of Systems Biology approach, involving an iterative and systematic approach in which each transcriptomic analysis feeds the regulatory network model, this tool allows us to unravel signaling and gene regulation network that controls homeostasis of nutrients in Arabidopsis thaliana and other model plants in B&PMP.

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Sandrine Ruffel
Scientist Manager
Phone: +33 4 99 61 27 12
Office: 162

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Shahzad Z, Canut M, Tournaire-Roux C, Martinière A, Boursiac Y, Loudet O, Maurel C✉ (2016) A potassium-dependent oxygen sensing pathway regulates plant root hydraulics.Cell, 167(1):87-98.e14

Medici A, Marshall-Colón A, Ronzier E, Szponarski W, Wang R, Gojon A, Crawford NM, Ruffel S, Coruzzi GM, Krouk G✉ (2015) AtNIGT1/HRS1 integrates nitrate and phosphate signals at the Arabidopsis root tip. Nat. Commun., 6:6274

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