Search   for 
Find Your Gene ·  Publications ·  Tools ·  Gene List Suite ·  Expression Atlases ·  About PLEXdb ·  Feedback
Login ID:
Password:
Plants
Arabidopsis
Barley
Brachypodium
Citrus
Cotton
Grape
Maize
Medicago
Poplar
Rice
Soybean
Sugarcane
Tomato
Wheat
Pathogens & Symbionts
Search Experiments
Download Data
Gene List Suite
Tools
Your Account
Documentation
News
Personnel
Links
 Data Release Policy 
PLEXdb is committed to making expression data publicly available to researchers world-wide...
complete policy
 

Browse MaizePLEX Experiment Data

Choose an experiment:
Responses of Zea mays root tissue to inoculation with the necrotrophic root pathogen Phytophthora cinnamomi
Jane Allardyce, Deakin University, Waurn Ponds, Australia (janealis@deakin.edu.au)
Experiment design (12 hybridizations)
time
•6 hrs •24 hrs
pathogen inoculation
•control •inoculated

This experiment has been imported by PLEXdb from NCBI GEO (GSE27626)

Series_summary:
Phytophthora cinnamomi is a devastating soil-bor...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

Show
Experiment Name: Responses of Zea mays root tissue to inoculation with the necrotrophic root pathogen Phytophthora cinnamomi
Accession No: ZM43
Microarray: maize18k
Visibility: public
Experiment Type:
Experiment Factor(s):
time
•6 hrs  •24 hrs
pathogen inoculation
•control   •inoculated
Quality Control: biological replicates
Treatment summary:
 time  pathogen inoculation  # replicates
 6 hrs  control  3
 6 hrs  inoculated  3
 24 hrs  control  3
 24 hrs  inoculated  3
Total hybridizations: 12
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE27626)

Series_summary:
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.

Series_overall_design:
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.
Publication: none
Created: 2011-08-05 12:19:00
Last Update: 2011-08-10 12:32:16
Released: 2011-08-10
GEO Accession GSE27626
Submitter: PLEXdb Curator
Name: Jane Allardyce
Institution: Deakin University, Waurn Ponds, Australia
Head of Laboratory: Jane Allardyce
email(s):
Homepage:

 
Copyright@2001-2013 The PLEXdb Group
All rights reserved.

For problems with the webpages contact PLEXdb webmasters