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The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses

The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses
The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses
The tolerance responses of plants to many abiotic stresses are conjectured to be controlled by complex gene networks. In the frame of the AtGenExpress project a comprehensive Arabidopsis thaliana genome transcript expression study was performed using the Affymetrix ATH1 microarray in order to understand these regulatory networks in detail. In contrast to earlier studies, we subjected, side-by-side and in a high-resolution kinetic series, Arabidopsis plants, of identical genotype grown under identical conditions, to different environmental stresses comprising heat, cold, drought, salt, high osmolarity, UV-B light and wounding. Furthermore, the harvesting of tissue and RNA isolation were performed in parallel at the same location using identical experimental protocols. Here we describe the technical performance of the experiments. We also present a general overview of environmental abiotic stress-induced gene expression patterns and the results of a model bioinformatics analysis of gene expression in response to UV-B light, drought and cold stress. Our results suggest that the initial transcriptional stress reaction of Arabidopsis might comprise a set of core environmental stress response genes which, by adjustment of the energy balance, could have a crucial function in various stress responses. In addition, there are indications that systemic signals generated by the tissue exposed to stress play a major role in the coordination and execution of stress responses. In summary, the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress.
AtGenExpress, bioinformatics, gene expression, microarray, abiotic stress
0960-7412
347-363
Kilian, Joachim
ae4c4b8b-6752-4559-b5d3-ec21e05a8b30
Whitehead, Dion
d4912294-eabc-4ffb-815b-d78f599e22dd
Horak, Jakub
67c19704-c134-4c21-a0e9-91d2cf937bed
Wanke, Dierk
11997b48-9b6b-4b6f-bc7e-2c963b1e5c60
Weinl, Stefan
2f78f0c7-3be9-4b12-8ddf-364731ab5071
Batistic, Oliver
e36a3a07-28aa-4549-87f9-88a791fdf1eb
D'Angelo, Cecilia
0d35b03b-684d-43aa-a57a-87212ab07ee1
Bornberg-Bauer, Erich
59bf0725-91ac-4a09-b492-b6ce238b8e0a
Kudla, Jörg
662352ce-945f-459d-9572-e8875d39b2f3
Harter, Klaus
c05227a4-f56e-4e9c-8b2a-571130c1ecea
Kilian, Joachim
ae4c4b8b-6752-4559-b5d3-ec21e05a8b30
Whitehead, Dion
d4912294-eabc-4ffb-815b-d78f599e22dd
Horak, Jakub
67c19704-c134-4c21-a0e9-91d2cf937bed
Wanke, Dierk
11997b48-9b6b-4b6f-bc7e-2c963b1e5c60
Weinl, Stefan
2f78f0c7-3be9-4b12-8ddf-364731ab5071
Batistic, Oliver
e36a3a07-28aa-4549-87f9-88a791fdf1eb
D'Angelo, Cecilia
0d35b03b-684d-43aa-a57a-87212ab07ee1
Bornberg-Bauer, Erich
59bf0725-91ac-4a09-b492-b6ce238b8e0a
Kudla, Jörg
662352ce-945f-459d-9572-e8875d39b2f3
Harter, Klaus
c05227a4-f56e-4e9c-8b2a-571130c1ecea

Kilian, Joachim, Whitehead, Dion, Horak, Jakub, Wanke, Dierk, Weinl, Stefan, Batistic, Oliver, D'Angelo, Cecilia, Bornberg-Bauer, Erich, Kudla, Jörg and Harter, Klaus (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. The Plant Journal, 50 (2), 347-363. (doi:10.1111/j.1365-313X.2007.03052.x). (PMID:17376166)

Record type: Article

Abstract

The tolerance responses of plants to many abiotic stresses are conjectured to be controlled by complex gene networks. In the frame of the AtGenExpress project a comprehensive Arabidopsis thaliana genome transcript expression study was performed using the Affymetrix ATH1 microarray in order to understand these regulatory networks in detail. In contrast to earlier studies, we subjected, side-by-side and in a high-resolution kinetic series, Arabidopsis plants, of identical genotype grown under identical conditions, to different environmental stresses comprising heat, cold, drought, salt, high osmolarity, UV-B light and wounding. Furthermore, the harvesting of tissue and RNA isolation were performed in parallel at the same location using identical experimental protocols. Here we describe the technical performance of the experiments. We also present a general overview of environmental abiotic stress-induced gene expression patterns and the results of a model bioinformatics analysis of gene expression in response to UV-B light, drought and cold stress. Our results suggest that the initial transcriptional stress reaction of Arabidopsis might comprise a set of core environmental stress response genes which, by adjustment of the energy balance, could have a crucial function in various stress responses. In addition, there are indications that systemic signals generated by the tissue exposed to stress play a major role in the coordination and execution of stress responses. In summary, the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress.

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More information

Published date: April 2007
Keywords: AtGenExpress, bioinformatics, gene expression, microarray, abiotic stress
Organisations: Ocean and Earth Science

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Local EPrints ID: 349899
URI: http://eprints.soton.ac.uk/id/eprint/349899
ISSN: 0960-7412
PURE UUID: 78b210f6-3426-4079-a7e7-3013b194b0d3

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Date deposited: 13 Mar 2013 11:59
Last modified: 27 Apr 2022 09:44

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Contributors

Author: Joachim Kilian
Author: Dion Whitehead
Author: Jakub Horak
Author: Dierk Wanke
Author: Stefan Weinl
Author: Oliver Batistic
Author: Erich Bornberg-Bauer
Author: Jörg Kudla
Author: Klaus Harter

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