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 AraPLEX Experiment Data

Choose an experiment:
Impact of Type III effectors on plant defense responses
Marta de Torres Zabala, Department of Agricultural Sciences, Imperial College at Wye
Experiment design (27 hybridizations)
compound
•Mock •DC3000 •DC3000hrpA •DC3000::avrRpm1
time
•2hr •4hr •12hr

This experiment submission is a courtesy of the Nottingham Arabidopsis Stock Centre's microarray database (http://ssbdjc2.nottingham.ac.uk/narrays/...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

Show
Experiment Name: Impact of Type III effectors on plant defense responses
Accession No: AT13
Microarray: ATH1-121501
Visibility: public
Experiment Type:
Experiment Factor(s):
compound
•Mock  •DC3000   •DC3000hrpA  •DC3000::avrRpm1
time
•2hr  •4hr  •12hr
Quality Control: biological replicates
Treatment summary:
 compound  time  # replicates
 Mock  2hr  3
 Mock  4hr  3
 Mock  12hr  3
 DC3000  2hr  3
 DC3000  4hr  3
 DC3000  12hr  3
 DC3000hrpA  2hr  3
 DC3000hrpA  4hr  3
 DC3000hrpA  12hr  3
Total hybridizations: 27
Description: This experiment submission is a courtesy of the Nottingham Arabidopsis Stock Centre's microarray database (http://ssbdjc2.nottingham.ac.uk/narrays/experimentbrowse.pl). The data was generated from NASC's Affymetrix service and offered for public access at BarleyBase.

If you publish with this data, please reference data from NASC/GARNet:

Craigon DJ., James N., Okyere J., Higgins J., Jotham J., May S.
NASCArrays: A repository for Microarray Data generated by NASC's Transcriptomics Service.
Nucleic Acids Research, (2004). volume 32, Database issue D575-D577.

Following is the original experiment description:

About the Experimenter
Name: Dr Marta de Torres Zabala
Head of Lab Name: Dr Murray Grant
Address: Department of Agricultural Sciences, Imperial College at Wye, Wye
Postcode: TN25 5AH
Country: UK
Telephone Number: 02075942883
Fax Number: 02075942640

Experiment Type: gene_overexpression; time_course; normal_diseased;
Experimental Parameters:
Quality Control Measures Taken: no-plants-pooled 4 leaves/plant; 18 plants/time point.

Experiment: Impact of Type III effectors on plant defense responses
Experiment Description:
Our interest lie in how plants respond to bacterial pathogens. Over the past three years we have identified and documented reproducible, landmark biochemical and molecular events following challenge of Arabidopsis with the phytopathogenic enterobacteria P. syringae. Significantly, our studies revealed 60% of cDNA-AFLP differentials not present on the 8,200 feature GeneChips and 20% absent from public EST databases (de Torres in press). We now seek to exploit this background using carefully defined time-points to analyse global changes in the Arabidopsis transcriptome using challenges selected to define gene targets implicated in (i) expression of basal immunity (ii) the establishment of successful parasitism (resistance) by a virulent pathogen (host). The results will provide a rationale for future functional assays of the identified pathways using transgenic knockouts and mutant analyses. Additionally, data will provide underpinning support for comparative proteomics of the defense response currently in progress with GARNet support using the same experimental parameters (BBSRC 32/P14635).

We propose the following treatments:

(i) Mock vs. DC3000hrpA @ 60 min: 60 minutes is subsequent to host immediate-early stress responses and will catalogue the innate responses induced by pathogen associated molecular patterns. The hrpA lesion will ensure no type III effectors influence transcriptional responses. Gene products induced at this time are predicted to potentiate latter host responses (2 treatments X 3 biological replicates = 6 chips).

(ii) Mock vs. DC3000 vs. DC3000hrpA vs. DC3000::avrRpm1 @ 4 hours: A key time point previously defined where no macroscopic symptoms are visible but significant differences exist between compatible and incompatible interactions at the molecular and physiological levels. These treatments will serve to define the earliest genes induced by the complement of DC3000 type III effector and will specifically define genes/pathways suppressed by virulence factors in addition to those implicated in orchestration of the hypersensitive cell death. We will also include an incompatible interaction on a transgenic line expressing an RPM1 interacting protein, which fails to mount an HR but exhibits hyper-resistance. We predict this challenge will separate the resistance response (pathogen restriction) from that associated with hypersensitive cell death (5 treatments X 3 biological replicates = 15 chips).

(iii) Mock vs. DC3000 vs. DC3000hrpA @ 14 hours: At 10 h before phenotypes are apparent in the DC3000 background, Type III effector delivery is well advanced and impact on host transcription maximal (3 treatments X 3 biological replicates = 9 chips).
Publication: none
Created: 2004-06-10 09:37:57
Last Update: 2008-08-05 10:58:29
GEO Accession GSE6176
Submitter: PLEXdb Curator
Name: Marta de Torres Zabala
Institution: Department of Agricultural Sciences, Imperial College at Wye
Head of Laboratory: Dr Murray Grant
email(s):
Homepage:

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

For problems with the webpages contact PLEXdb webmasters