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Browse MedicagoPLEX Experiment Data

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affy_root-dvt-nitrogen_medicago: Genetic determinism of root development in Medicago truncatula
Sandrine Balzergue, INRA, Department of URGV, Evry, France (balzerg@evry.inra.fr)
Experiment design (12 hybridizations)
genotype
•J5(wild type) •Tr185(mutant)
nutrient
•1mM KNO3 •10mM KNO3

This experiment has been imported by PLEXdb from NCBI GEO (GSE18318)

Series_summary:
affy_root-dvt-nitrogen_medicago. The biological...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: affy_root-dvt-nitrogen_medicago: Genetic determinism of root development in Medicago truncatula
Accession No: ME12
Microarray: Medicago61k
Visibility: public
Experiment Type:
Experiment Factor(s):
genotype
•J5(wild type)   •Tr185(mutant)
nutrient
•1mM KNO3   •10mM KNO3
Quality Control: biological replicates
Treatment summary:
 genotype  nutrient  # replicates
 J5(wild type)  1mM KNO3  3
 J5(wild type)  10mM KNO3  3
 Tr185(mutant)  1mM KNO3  3
 Tr185(mutant)  10mM KNO3  3
Total hybridizations: 12
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE18318)

Series_summary:
affy_root-dvt-nitrogen_medicago. The biological question is the study of root development adaptation to external nitrogen availability. One of the typical responses to low N provision consists of an increased root branching which promotes soil exploration. In order to differentiate between genes specifically involved in nitrate response and genes of root development, we had performed experiments on both a wild type and a mutant affected in root architecture, both supplied with two different levels of nitrate. Global gene expression profiling of root cells using microarray analysis will be conducted to identify genes expressed during root branching. First, analysing the differential gene expression between the wild type and the mutant both at low and high level of nitrate, we will identify genes of root development but also genes specifically involved in nitrate response. Then, additional comparisons will concern the modifications of wild type and mutant gene expression between the two levels of nitrate. These genes will be compared to those found to be expressed in the wild type roots under submitted to various nitrogen sources (Ruffel et al., 2008). All together these results will allow us to determine which genes, among the firstly underlined, are specifically involved in root development. The kinetics of expression in different tissues of the most relevant of these genes will be further analysed by qRT-PCR. Three successive experiments in growth chamber were performed on two different genotypes of Medicago truncatula. Each experiment constituted a biological replicate. For each of them, after 4 days of seed cold-treatment followed by 4 days of germination, individual plantlets were transferred onto hydroponic culture tanks containing vigorously aerated nutrient solution. Each tank contained 6 plantlets of J5 and 6 plantlets of the mutant. On one shelf of the growth chamber, nutrient solution in the tanks was supplemented by 1mM of KNO3; on the other shelf, the level of KNO3 in the solution was of 10mM. Nutrient solution was renewed every week. Roots of the two genotypes were harvested separately but at the same time, 10 days after the plantlets transfer onto hydroponic culture tanks.
Keywords: dose response, wt vs mutant comparison

Series_overall_design:
12 arrays - Medicago.
WT and mutant (tr185) under 1mM or 10mM KNO3. Three biological replicates each genotype/condition.
Publication: none
Created: 2011-06-23 10:38:43
Last Update: 2011-06-27 15:49:29
Released: 2011-06-27
GEO Accession GSE18318
Submitter: PLEXdb Curator
Name: Sandrine Balzergue
Institution: INRA, Department of URGV, Evry, France
Head of Laboratory: Sandrine Balzergue
email(s):
Homepage:

 
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