Transcriptomics

Dataset Information

60

Transcription profiling by array of Arabidopsis after exposure to heat stress


ABSTRACT: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana. The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate. Seeds of Arabidopsis thaliana Wild Type (col-0) were sown on rafts in Magenta boxes containing MS-Agar-media. After 2 days in the cold room (4°C, dark) the boxes were transferred to the long day chamber. Long day conditions were 16/8 hrs light/dark, 24°C, 50% humidity and 150 µEinstein/cm2 sec light intensity. At day 11 the rafts were transferred in Magenta boxes containing MS-liquid-media. At day 16 stress treatment started at 3 hrs of light period; samples taken at 0.5, 1, 3, 6, 12, 24 h after treatment (in selected indicated cases 0.25h and 4.0h too), control samples include 0h; roots and shoots were prepared separately; all treatments and preparations were done on the same batch of seedlings in one place (Lab J.Kudla/Ulm, Germany) by coworkers from the indicated groups. Experimenter name = Lutz Nover , Pascal von Koskull-Döring; Experimenter institute = AtGenExpress Experiment Overall Design: 32 samples were used in this experiment

INSTRUMENT(S): 418 [Affymetrix]

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Nottingham Arabidopsis Stock Centre (NASC)   

PROVIDER: E-GEOD-5628 | ArrayExpress| 2012-02-21

SECONDARY ACCESSION(S): GSE5628PRJNA96935

REPOSITORIES: GEO, ArrayExpress

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Publications

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

Kilian Joachim J   Whitehead Dion D   Horak Jakub J   Wanke Dierk D   Weinl Stefan S   Batistic Oliver O   D'Angelo Cecilia C   Bornberg-Bauer Erich E   Kudla Jörg J   Harter Klaus K  

The Plant journal : for cell and molecular biology 20070321 2


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 iden  ...[more]

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