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Series GSE5620 Query DataSets for GSE5620
Status Public on Jan 08, 2007
Title AtGenExpress: Stress Treatments (Control plants)
Organism Arabidopsis thaliana
Experiment type Expression profiling by array
Summary 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.
Stress treatments
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 uEinstein/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 = Cecilia D`Angelo, Joachim Kilian, Joerg Kudla, Oliver Batistic, Stefan Weinl
Experimenter institute = AtGenExpress
Keywords: time_series_design; growth_condition_design; stimulus_or_stress_design
 
Overall design 36 samples were used in this experiment
 
Contributor(s) D`Angelo C, Kilian J, Kudla J, Batistic O, Weinl S, Townsend H, Emmerson Z, Schildknecht B
Citation(s) 17376166
Wanke D, Berendzen KW, Kilian J, Harter K. Insights into Arabidopsis abiotic stress response from the AtGenExpress expression profile dataset. In "Plant Stress Biology: Genomics Goes Systems Biology", WILEY-VCH, 2009.
Submission date Aug 25, 2006
Last update date Aug 28, 2018
Contact name Nottingham Arabidopsis Stock Centre (NASC)
E-mail(s) affy@arabidopsis.info
Phone +44 (0)115 951 3237
Fax +44 (0)115 951 3297
URL http://arabidopsis.info/
Organization name Nottingham Arabidopsis Stock Centre (NASC)
Department School of Biosciences, University of Nottingham
Street address Sutton Bonington Campus
City Loughborough
ZIP/Postal code LE12 5RD
Country United Kingdom
 
Platforms (1)
GPL198 [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array
Samples (36)
GSM131223 AtGen_6-0011_Control-Shoots-0h_Rep1
GSM131224 AtGen_6-0012_Control-Shoots-0h_Rep2
GSM131225 AtGen_6-0021_Control-Roots-0h_Rep1
Relations
Affiliated with GSE69995
BioProject PRJNA96919

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE5620_RAW.tar 80.1 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file

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