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Browse BarleyBase Experiment Data

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Response of barley roots during the host interaction with the plasmodiophorid virus vector Polymyxa graminis
Graham RD McGrann, Broom’s Barn Research Centre. (Rothamsted Research Dept of Applied Crop Science) (graham.mcgrann@bbsrc.ac.uk, effie.mutasa@bbsrc.ac.uk)
Experiment design (6 hybridizations)
pathogen isolates
•Mock •Polymyxa graminis

Transcriptional changes were monitored in roots of the barley cultivar Regina following inoculation with zoospores of the adapted plasmodiophorid v...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Response of barley roots during the host interaction with the plasmodiophorid virus vector Polymyxa graminis
Accession No: BB74
Microarray: Barley1
Visibility: public
Experiment Type:
Experiment Factor(s):
pathogen isolates
•Mock   •Polymyxa graminis
Quality Control: biological replicates
Treatment summary:
 pathogen isolates  # replicates
 Mock  3
 Polymyxa graminis  3
Total hybridizations: 6
Description: Transcriptional changes were monitored in roots of the barley cultivar Regina following inoculation with zoospores of the adapted plasmodiophorid virus vector Polymyxa graminis 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. graminis 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: 'Barley elicits a similar early basal defence response during host and non-host interactions with Polymyxa root parasites', 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
Created: 2009-07-12 07:07:30
Last Update: 2009-07-13 08:24:07
GEO Accession GSE17238
Submitter: Graham Robert David McGrann
Name: Graham RD McGrann
Institution: Broom’s Barn Research Centre. (Rothamsted Research Dept of Applied Crop Science)
Head of Laboratory: Effie Mutasa-Göttgens
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