Transcriptomics,Multiomics

Dataset Information

5

Transcriptional profiling of Zea mays roots infected by necrotrophic pathogen Phytophthora cinnamomi for 6 or 24 hours against mock-infected controls


ABSTRACT: Phytophthora cinnamomi is a devastating soil-borne oomycete with a very broad host range however there remains a major gap in the understanding of plant resistance responses to the pathogen, furthermore, necrotrophic plant-pathogen interactions, particularly those of root pathogens, remain poorly understood. Zea mays exhibits non-host resistance to the pathogen and has been well characterised as a model species. Using the maize Affymetrix GeneChip array we conducted genome-wide gene expression profiling to elucidate the defence genes and pathways which are induced in the root tissue of a resistant plant species to the pathogen. Each experimental repeat consisted of 60 Z. mays seedlings in total: 15 control and 15 inoculated plants per timepoint. Root tissue was harvested and snap frozen in liquid nitrogen and stored at -80°C until required. All harvested root tissue within each treatment group at each time point was pooled for total RNA extractions. Three technical repeats were conducted resulting in a total of 180 sampled plants and 12 samples of purified total RNA for microarray analysis. Total RNA was labelled, hybridised and scanned using standard Affymetrix protocols and resulted in 12 .CEL files. Raw data was processed using Partek Genomics Suite software and normalised using Robust Multi-Chip Average Software. Differentially expressed genes were defined by a fold difference of >1.5 (log2) and those with a P value cutoff of <0.05 were considered statistically significant.

REANALYSED by: E-GEOD-27626

OTHER RELATED OMICS DATASETS IN: PRJNA138239

ORGANISM(S): Zea mays  

SUBMITTER: Jane A Allardyce   Jane Allardyce 

PROVIDER: E-GEOD-27626 | ArrayExpress | 2011-03-02

SECONDARY ACCESSION(S): GSE27626PRJNA138239

REPOSITORIES: GEO, ArrayExpress

Dataset's files

Source:
Action DRS
E-GEOD-27626.idf.txt Idf
E-GEOD-27626.processed.1.zip Processed
E-GEOD-27626.raw.1.zip Raw
E-GEOD-27626.sdrf.txt Txt
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Publications

Transcriptional profiling of Zea mays roots reveals roles for jasmonic acid and terpenoids in resistance against Phytophthora cinnamomi.

Allardyce Jane Alisa JA   Rookes James Edward JE   Hussain Hashmath Inayath HI   Cahill David Miles DM  

Functional & integrative genomics 20130222 2


Phytophthora cinnamomi is a soil-borne plant pathogen that has caused widespread damage to vulnerable native ecosystems and agriculture systems across the world and shows no sign of abating. Management of the pathogen in the natural environment is difficult and the options are limited. In order to discover more about how resistant plants are able to defend themselves against this generalist pathogen, a microarray study of plant gene expression following root inoculation with P. cinnamomi was und  ...[more]

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