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Series GSE17240 Query DataSets for GSE17240
Status Public on Jul 24, 2009
Title Response of barley roots during the non-host interaction with the plasmodiophorid virus vector Polymyxa betae
Organism Hordeum vulgare
Experiment type Expression profiling by array
Summary Transcriptional changes were monitored in roots of the barley cultivar Regina following inoculation with zoospores of the nonadapted plasmodiophorid virus vector Polymyxa betae using the Affymetrix Barley1 GeneChip®. Barley cv. Regina seeds were imbibed in distilled water over night and then transferred on to moist heat treated (90°C over night) sand in plastic trays that were sealed. Trays were incubated at room temperature for 4 days to allow the seeds to germinate to Zadocks stage 07 of the decimal code for the growth stages of cereals (Tottman et al., 1979 Annals of Applied Biology, 93: 221-234; Zadocks et al., 1974 Weed Research, 14: 415-421). 110 barley (cv. Regina) seedling (Zadocks stage 07) were placed into a 90 mm diameter plastic Petri dish (3 Petri dishes per treatment) and 60 mL of P. betae zoospore suspension added (1 x 10 6 spores mL-1). Control plants were treated exactly the same way except zoospore-free buffer (0.1 g L-1 Phostrogen, 0.5% Bovine serum albumen) was added. Zoospore challenge (and control) occurred at an ambient temperature of 22°C. Roots were excised from ten plants per treatment at ten time points (15’, 30’, 45’ 1h, 2h, 3h, 4h, 5h, 6h, 7h) and frozen in liquid nitrogen. Three independent biological replicate experiments were done. Total RNA was isolated from each sample using TRI-reagent following the manufacturer’s instructions (Invitrogen) and then treated with DNase I (Ambion, Texas, USA) according to the manufacturer’s protocol. RNA samples for microarray hybridisation were further purified using RNeasy Mini Spin column purification (Qiagen, Hilden, Germany). The integrity of the RNA samples was confirmed using the BioAnalyzer 2100 (Agilent Technologies). Affymetrix GeneChip processing, including RNA quality control, microarray hybridisation and data acquisition was performed through contract research services by Geneservice Ltd (www.geneservice.co.uk). A total of six hybridisations were performed.
Publication: European Journal of Plant Pathology 123(1):5-15.<br>

****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Graham McGrann. The equivalent experiment is BB75 at PLEXdb.]
 
Overall design pathogen isolates: Mock inoculated control(3-replications); pathogen isolates: Polymyxa betae(3-replications)
Web link http://www.plexdb.org/modules/PD_browse/experiment_browser.php?experiment=BB75
 
Contributor(s) McGrann G
Citation Barley elicits a similar early basal defence response during host and non-host interactions with Polymyxa root parasites, 2009, Graham R. D. McGrann, Belinda J. Townsend, John F. Antoniw, Michael J. C. Asher, Effie S. Mutasa-Göttgens, European Journal of Plant Pathology 123(1):5-15, DOI:10.1007/s10658-008-9332-z
Submission date Jul 21, 2009
Last update date Mar 21, 2012
Contact name PLEXdb Curator, Sudhansu Dash
Organization name Iowa State University
Department Virtual Reality Application Center
Lab PLEXdb
Street address 1023 Crop Genomes Informatics Lab (Iowa State University)
City Ames
State/province IA
ZIP/Postal code 50011
Country USA
 
Platforms (1)
GPL1340 [Barley1] Affymetrix Barley Genome Array
Samples (6)
GSM431568 pathogen isolates: Mock inoculated control - rep1
GSM431569 pathogen isolates: Mock inoculated control - rep2
GSM431570 pathogen isolates: Mock inoculated control - rep3
Relations
BioProject PRJNA118961

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE17240_RAW.tar 11.6 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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