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Series GSE6176 Query DataSets for GSE6176
Status Public on Jan 22, 2007
Title Impact of Type III effectors on plant defense responses
Organism Arabidopsis thaliana
Experiment type Expression profiling by array
Summary Our interest lies in how plants respond to bacterial pathogens. Over the past three years we have identified and documented reproducible, landmark biochemical and molecular events following the 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).
Keywords: time_series_design; pathogenicity_design; compound_treatment_design
Overall design Number of plants pooled:4 leaves/plant; 18 plants/time point
Contributor(s) de Torres Zabala M
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Submission date Oct 27, 2006
Last update date Aug 28, 2018
Contact name Nottingham Arabidopsis Stock Centre (NASC)
Phone +44 (0)115 951 3237
Fax +44 (0)115 951 3297
Organization name Nottingham Arabidopsis Stock Centre (NASC)
Department School of Biosciences, University of Nottingham
Street address Sutton Bonington Campus
City Loughborough
ZIP/Postal code LE12 5RD
Country United Kingdom
Platforms (1)
GPL198 [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array
Samples (27)
GSM142829 GM001_ATH1_A11-Torres-5N3
GSM142830 GM001_ATH1_A14-Torres-4N3_repeat2
GSM142831 GM001_ATH1_A30-Torres-9N6_repeat1
Affiliated with GSE69995
BioProject PRJNA100641

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE6176_RAW.tar 61.6 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file

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