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Browse PoplarPLEX Experiment Data

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Transcriptomic response to aluminum stress in roots of aspen (Populus tremula L.)
Stefan Zoller, University and ETH Zurich, Department of Functional Genomics Center Zurich, Zurich, Switzerland (szoller@fgcz.ethz.ch,christoph.sperison@wsl.ch)
Experiment design (18 hybridizations)
compound
•aluminum •control
time
•6 hrs •54 hrs •246 hrs

This experiment has been imported by PLEXdb from NCBI GEO (GSE19297) Series_summary: Background: Solubilized aluminum (Al) is rhizotoxic and ca...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Transcriptomic response to aluminum stress in roots of aspen (Populus tremula L.)
Accession No: PT18
Microarray: Poplar61k
Visibility: public
Experiment Type:
Experiment Factor(s):
compound
•aluminum   •control
time
•6 hrs  •54 hrs  •246 hrs
Quality Control: biological replicates
Treatment summary:
 compound  time  # replicates
 aluminum  6 hrs  3
 aluminum  54 hrs  3
 aluminum  246 hrs  3
 control  6 hrs  3
 control  54 hrs  3
 control  246 hrs  3
Total hybridizations: 18
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE19297)

Series_summary:
Background: Solubilized aluminum (Al) is rhizotoxic and can be present in acid soils at levels that inhibit root growth. Acid soils are found throughout the world and often support forests. However, unlike in herbaceous plants, little is known about the mechanisms by which forest trees respond to and tolerate Al. To begin to elucidate these mechanisms, we characterized transcriptomic changes in response to Al in roots of aspen (Populus tremula L.).
Results: Aspen roots were treated with Al in solution culture for 6 h, 54 h, and 246 h. Transcriptomic changes were assessed by the Affymetrix GeneChip Poplar Genome Array. The analysis revealed 176 induced and 66 suppressed genes. The majority of these genes were regulated at 6 h, presumably reflecting root growth, which was strongly inhibited at 6 h and partially was recovered at 2 d and 10 d. Enrichment analysis identified sets of functionally related genes whose members were statistically over-represented compared to the genes on the microarray. These sets included genes related to cell wall modification, oxidative stress, cell death, and transport processes. Two of the genes involved in transport were related to the Arabidopsis Al tolerance genes AtALS3 (aluminum sensitive 3), possibly mediating redistribution of Al, and AtMATE (multi-drug and toxin extrusion), facilitating exudation of citrate. Expression patterns in response to Al in different plant tissues indicated that the two aspen genes are homologs of AtALS3 and AtMATE, suggesting that aspen and Arabidopsis share common mechanisms to cope with Al.
Conclusion: This is the first survey of transcriptomic changes in response to Al in a forest tree. The results of our study provide a valuable set of data, which will help to further our understanding of the mechanisms and their regulation that enable aspen to grow in environments with toxic levels of Al.

Series_overall_design:
Aspen roots were treated with Al in solution culture for 6 h, 54 h, 246 h to cover a broad range of exposure times. Transcriptomic changes were assessed by the Affymetrix GeneChip Poplar Genome Array. For each time point, root tips of three independant plants were analyzed.
Publication: 'Transcriptome responses to aluminum stress in roots of aspen (Populus tremula).', Grisel N, Zoller S, Künzli-Gontarczyk M, Lampart T, Münsterkötter M, Brunner I, Bovet L, Métraux JP, Sperisen C.
BMC Plant Biol 2010 Aug 23;10:185.
pubmed: 20727216
Created: 2010-12-17 11:42:31
Last Update: 2010-12-17 12:06:25
Released: 2011-01-28
GEO Accession GSE19297
Submitter: PLEXdb Curator
Name: Stefan Zoller
Institution: University and ETH Zurich, Department of Functional Genomics Center Zurich, Zurich, Switzerland
Head of Laboratory: Christoph Sperisen
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