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Browse BarleyBase Experiment Data

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Transcript profiling of local and adjacent leaf responses in barley following inoculation with Pseudomonas syringae
Ellen Colebrook, John Innes Centre (ellen.colebrook@bbsrc.ac.uk,graham.mcgrann@bbsrc.ac.uk,lesley.boyd@bbsrc.ac.uk)
Experiment design (12 hybridizations)
tissue type name
•Local •Adjacent
treatment
•Inoculated •Control

Transcriptional changes were monitored in the barley cultivar Golden Promise 24 hours post inoculation (hpi) with the bacteria Pseudomonas syringae...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Transcript profiling of local and adjacent leaf responses in barley following inoculation with Pseudomonas syringae
Accession No: BB92
Microarray: Barley1
Visibility: public
Experiment Type:
Experiment Factor(s):
tissue type name
•Local   •Adjacent
treatment
•Inoculated   •Control
Quality Control: biological replicates
Treatment summary:
 tissue type name  treatment  # replicates
 Local  Inoculated  3
 Local  Control  3
 Adjacent  Inoculated  3
 Adjacent  Control  3
Total hybridizations: 12
Description: Transcriptional changes were monitored in the barley cultivar Golden Promise 24 hours post inoculation (hpi) with the bacteria Pseudomonas syringae pv. tomato DC3000 avrRpm1 (PstavrRpm1) using the Affymetrix Barley genome array GeneChip®.

Seedlings of Golden Promise were grown to growth stage 12-13 (Zadoks et al., 1974) before inoculating with either PstavrRpm1 or water (for the mock inoculation control) by infiltration. Plants were grown under a 18 °C / 16 h light period; 12 °C / 8 h dark period, with artificial lighting (100 µmol m-2 s-1) and a relative humidity of 75 – 85 %.


Leaf samples from three seedlings were collected 24 hpi for RNA extraction and transcriptomics analysis from the area infiltrated (local) and from the area next to the infiltrated region (adjacent) from three biological replicates. Leaf tissue was ground under liquid nitrogen and total RNA extracted using the RNeasy miniprep kit (Qiagen), following the manufacturer’s instructions. RNA was DNase treated using Turbo DNase (Ambion) according to the manufacturer instructions. RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent). The two cycle-target labeling method was used following the Affymetrix protocol.

Affymetrix GeneChip processing, including RNA quality control, microarray hybridisation and data acquisition was performed through contract research services by Cogenics (North Carolina, U.S.A.). A total of twelve hybridisations were performed.

Submitted at NCBI GEO via PLEXdb.

Publication: 'Broad-spectrum acquired resistance in barley induced by the Pseudomonas pathosystem shares transcriptional components with Arabidopsis SAR.', Colebrook EH, Creissen G, McGrann GRD, Dreos R, Lamb C and Boyd LA
Molecular Plant-Microbe Interactions 25, No. 5, pp. 658-667 (2012)
pubmed: 22250583
Created: 2010-04-09 06:33:06
Last Update: 2010-04-27 12:02:07
GEO Accession GSE43906
Submitter: Graham Robert David McGrann
Name: Ellen Colebrook
Institution: John Innes Centre
Head of Laboratory: Lesley Boyd
email(s):
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