Dataset Information


Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis (time series)

ABSTRACT: 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-colour hybridisation experimental system. With 192 distinct samples (four biological replicates at each of 24 time points in mock and treated conditions) to be compared, the experimental design included 288 two-colour 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 24 sampled times, directly comparing samples collected on adjacent sampling times (i.e. 2 hrs post-infection with 4 hrs post-infection, 4 hrs post-infection with 6 hrs post-infection, etc.). With the remaining slides, four separate loops were constructed comparing treatments, biological replicates and samplling times. infected vs. mock, 24 time points, randomized loop, 576 Imagene files

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Susanna Atwell  Christopher Penfold   Oliver Stegle   Richard Hickman   Dafyd Jenkins   Jim Beynon   Steven Kiddle   David L Wild   Vicky Buchanan-Wollaston   Jonathan David Moore   Andrew Mead   Emily Breeze   David Rand   Youn-sung Kim   Sascha Ott   Oliver Windram   Roxane Legaie   Laura Baxter   Cunjin Zhang   Karsten Borgwardt   Priyadharshini Madhou   Jonathan Moore   Stuart McHattie   Alex Tabrett   Emma Cooke   Dan Kliebenstein   Katherine Denby   Claire Hill   Bärbel Finkenstädt   Johanna Rhodes    

PROVIDER: E-GEOD-29642 | ArrayExpress | 2012-10-02



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Transcriptional reprogramming forms a major part of a plant's response to pathogen infection. Many individual components and pathways operating during plant defense have been identified, but our knowledge of how these different components interact is still rudimentary. We generated a high-resolution time series of gene expression profiles from a single Arabidopsis thaliana leaf during infection by the necrotrophic fungal pathogen Botrytis cinerea. Approximately one-third of the Arabidopsis genom  ...[more]

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