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Browse WheatPLEX Experiment Data

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Transcription profiling of wheat interacting with incompatible and compatible yellow rust in a Yr1-containing genotype
Osman Bozkurt, Middle East Technical University, Department of Chemistry, Biochemistry and Biotechnology Programs, Ankara, TR-06531, Turkey (tolga76er@yahoo.com, graham.mcgrann@bbsrc.ac.uk,akkayams@metu.edu.tr)
Experiment design (9 hybridizations)
pathogen isolates
•Mock inoculated (Control) •Yr1-avirulent wheat yellow rust isolate 232E137 •Yr1-virulent wheat yellow rust isolate 169E136

Transcriptional changes were monitored in the wheat cultivar Avocet*6/Yr1 following inoculation with avirulent and virulent wheat yellow rust (Pucc...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Transcription profiling of wheat interacting with incompatible and compatible yellow rust in a Yr1-containing genotype
Accession No: TA25
Microarray: Wheat
Visibility: public
Experiment Type:
Experiment Factor(s):
pathogen isolates
•Mock inoculated (Control)   •Yr1-avirulent wheat yellow rust isolate 232E137   •Yr1-virulent wheat yellow rust isolate 169E136
Quality Control: biological replicates
Treatment summary:
 pathogen isolates  # replicates
 Mock inoculated (Control)  3
 Yr1-avirulent wheat yellow rust isolate 232E137  3
 Yr1-virulent wheat yellow rust isolate 169E136  3
Total hybridizations: 9
Description: Transcriptional changes were monitored in the wheat cultivar Avocet*6/Yr1 following inoculation with avirulent and virulent wheat yellow rust (Puccinia striiformis f.sp. tritici) isolates using the Affymetrix wheat genome array GeneChip®. Seedlings of Avocet*6/Yr1 were grown to growth stage 12-13 (Zadoks et al., 1974) before inoculating with either the P.s. f.sp. tritici isolate 169E136 (Yr1-virulent) or 232E137 (Yr1-avirulent) or with talc for the Mock inoculation (Boyd and Minchin 2001). Plants were grown under a 16/8 hour photoperiod cycle, supplemented with sodium lighting (240 μmol m-2 s-1) at day/night temperatures of 20°C/15°C and a relative humidity of 60%, both before and after inoculation, in a spore-free, containment level 2 greenhouse. Leaf samples from six seedlings were collected 6, 12, 24, 48 and 72 hpi for RNA extraction and transcriptomics analysis from three independent biological experiments. Leaf tissue was ground under liquid nitrogen and total RNA extracted using the TRIzol reagent method, following the manufacturer’s instructions (Invitrogen, Carlsbad, CA). RNA from each time point (16 μg) were pooled to obtain 80 μg of total RNA for each treatment (mock inoculated control; avirulent isolate inoculated; virulent isolate inoculated). Pooled RNA samples were further purified using the Qiagen RNeasy mini-kit according to the manufacturer instructions (Qiagen) and RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent). Affymetrix GeneChip processing, including RNA quality control, microarray hybridisation and data acquisition was performed through contract research services by the John Innes Genome Laboratory, John Innes Centre, Norwich, U.K. A total of nine hybridisations were performed.

Submitted at NCBI GEO via PLEXdb.

Publication: none
Created: 2009-01-30 08:16:11
Last Update: 2009-05-21 00:06:53
Released: 2010-08-04
GEO Accession GSE31761
Submitter: Graham Robert David McGrann
Name: Osman Bozkurt
Institution: Middle East Technical University, Department of Chemistry, Biochemistry and Biotechnology Programs, Ankara, TR-06531, Turkey
Head of Laboratory: Mahinur Akkaya
email(s):
Homepage:

 
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