Transcriptomics

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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

SECONDARY ACCESSION(S): GSE29642PRJNA141221

REPOSITORIES: GEO, ArrayExpress

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Publications


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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