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Series GSE65046 Query DataSets for GSE65046
Status Public on Feb 29, 2016
Title Temporal analysis of physiological, metabolite and transcriptome responses during drought identifies distinct early and late phases in Arabidopsis
Organism Arabidopsis thaliana
Experiment type Expression profiling by array
Summary Water availability is the biggest single limitation on plant productivity worldwide. In Arabidopsis, adjustments to drought stress, involving changes in metabolism and gene expression drive increased drought tolerance and initiate diverse drought avoidance and escape responses. To address regulatory processes that integrate these complex responses we hypothesised that we needed to identify genes that govern early responses to drought. To this end, we produced a high-resolution time series transcriptomics dataset, coupled with detailed physiological and metabolic analyses of plants subjected to a slow transition from well-watered to the onset of drought conditions. 1825 differentially expressed genes (DEGs) were identified which showed no significant enrichment in gene ontology terms associated with dehydration responses and abscisic acid (ABA) regulation, confirming that the gene expression time series had targeted events prior to severe drought stress. Initial changes in gene expression coincided with a drop in carbon assimilation, not the later increase in foliar ABA content. Thus the early physiological and gene expression responses to drought were not driven by changes in leaf ABA content. In order to identify gene regulatory networks (GRNs) linked to early events, we used Bayesian network modelling of differentially expressed transcription factor (TF) genes. This approach identified AGAMOUS-LIKE 22 as key hub gene in a TF GRN. AGL22 is involved in the transition from vegetative state to flowering. Loss of AGL22 expression affected flowering time and drying rate providing a link between early changes in metabolism and the subsequent initiation of developmental responses to stress that govern plant productivity.
Overall design A novel experimental design strategy (A Mead et al, in preparation), based on the principle of the “loop design”, was developed to enable efficient extraction of information about key sample comparisons using a two-color hybridization experimental system. With 108 distinct samples (four biological replicates, at each of 13 time points in control and droughted conditions, plus a shared time zero set) to be compared, the experimental design included 216 two-color microarray slides, allowing four technical replicates of each sample to be observed. One third of the slides were devoted to assessment of changes in gene expression between time points, using a simple loop design to link samples from time points across the sampled times, directly comparing samples collected on adjacent sampling times (i.e. day 1 with day 2, day 2 with day 3, etc.). With the remaining slides, four separate loops were constructed comparing treatments, biological replicates and sampling times.
All of the samples in the microarray experiment were Col-0.
Contributor(s) Bechtold U, Lawson T, Penfold CA, Jenkins D, Legaie R, Moore JD, Subramaniam S, Baker NR, Florance H, Feil R, Lunn JE, Smirnoff N, Denby K, Buchanan-Wollaston V, Beynon J, Wild D, Rand D, Ott S, Mullineaux PM
Citation(s) 26842464
Submission date Jan 16, 2015
Last update date Nov 28, 2016
Contact name Jonathan David Moore
Organization name The Genome Analysis Centre
Department Platforms and Pipelines
Street address Norwich Research Park
City Norwich
ZIP/Postal code NR4 7UH
Country United Kingdom
Platforms (1)
GPL16132 CATMA Arabidopsis V4 TAIR V9 spotted cDNA array
Samples (108)
GSM1586255 0 zero a
GSM1586256 1 control a
GSM1586257 2 control a
BioProject PRJNA272977

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
GSE65046_RAW.tar 647.8 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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