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Sample GSM324489 Query DataSets for GSM324489
Status Public on Jun 30, 2009
Title Si- B+ rep3
Sample type RNA
Source name no silicon, disease inoculation
Organism Triticum aestivum
Characteristics wheat cultivar AC Drummond, age = 7weeks
Treatment protocol Wheat plants were grown in the presence (Si+) or absence (Si-) of Si and inoculated (B+) or not (B-) with Bgt for a total of four treatments: Si-B-, Si+B-, Si-B+, and Si+B+. These treatments were applied in the following manner. One week after sowing, distilled water was replaced by a Hoagland solution amended or not with potassium silicate (Kasil 6, PQ Corp etc) at a concentration of 1.7 mM (Si+ Hoagland). Twice a week, Si was added to the Si+ nutrient solution in order to maintain Si concentration at 1.7 mM. Every other week, both Si- and Si+ Hoagland solutions were renewed and the pH adjusted to 5.8 in all systems at each Si addition or nutrient solution renewal. Four weeks after sowing (i.e. three weeks after Si amendment started), half the plants were inoculated with Bgt as described previously. Briefly, one day prior to inoculation, reservoir wheat plants heavily infected with Bgt were gently shaken to remove old spores and to stimulate the production of fresh ones. The inoculation was performed by shaking the heavily infected wheat plants over the experimental plants.
Growth protocol Hydroponic systems were used to precisely control Si feeding of plants and to reduce external Si contamination. Seeds of wheat cultivar AC Drummond, chosen for its known high susceptibility to Bgt, were sown in 9-cm pots in a nylon bed consisting of nylon stockings cut into small ribbons. Hydroponic systems were set up to immerse roots for 15 minutes every 30 minutes. The plants were grown in a greenhouse (16 h light at 22°C and 8h dark at 18°C, 80% humidity). Plants were immersed in distilled water only during the first week following sowing.
Extracted molecule total RNA
Extraction protocol Plants were individually harvested, flash frozen in liquid nitrogen and kept at -80°C until used. Leaves of each plant were separately ground with a pestle and mortar in liquid nitrogen. Total RNA was extracted with RNeasy plant kit (Qiagen, Hilden, Germany). Concentration and quality of RNA were assessed on a Nanodrop spectrophotometer (Nanodrop, Wilmington, De, USA) and 2100 Bioanalyser (Agilent, Palo Alto, Ca, USA).
Label biotin
Label protocol Biotin-labeled cRNAs were synthesized using MessageAmp II-Biotin Enhanced Kit (Ambion, Austin, Tx, USA) following the manufacturer’s instructions using 1 µg total RNA. Labelled cRNA was then fragmented using 5X Array Fragmentation Buffer supplied with the MessageAmp II-Biotin Enhanced Kit.
Hybridization protocol The labelled samples were added to an Affymetrix GeneChip® Wheat Genome Array (Affymetrix, Santa Clara, CA, USA), according to the manufacturer’s instructions. The chips were hybridized for 16 h at 45 °C in a rotisserie oven at 60 rpm
Scan protocol Following hybridization, the arrays were washed and stained in an Affymetrix Fluidics Station 450, according to the standard protocol from Affymetrix, and scanned using an Affymetrix Scanner 3000.
Description Si-B+3
Data processing The R 2.6 software and Bioconductor were used to perform data analysis using dedicated packages Limma , Affy , and AffyPLM available on the Bioconductor website ( Data quality assessment was performed as described. These packages were also used to correct for background (RMA method), normalize the microarray data (quantile method) and generate lists of differentially expressed genes according to the fold change and t-test p-values.
Submission date Sep 25, 2008
Last update date May 26, 2009
Contact name Florian Chain
Organization name INRA
Department Institut Micalis
Lab Probihote
Street address Domaine de Vilvert
City Jouy en Josas
ZIP/Postal code 78352
Country France
Platform ID GPL3802
Series (1)
GSE12936 Transcriptomic analysis of the effect of silicon on wheat plants infected or uninfected with powdery mildew

Data table header descriptions
VALUE Data are obtained after background correction (RMA method) and normalization (quantile method)

Data table
AFFX-BioB-3_at 7.49460421007682
AFFX-BioB-5_at 8.08638586814886
AFFX-BioB-M_at 7.60230482358252
AFFX-BioC-3_at 9.45135604630518
AFFX-BioC-5_at 8.94424724056958
AFFX-BioDn-3_at 11.6092113589644
AFFX-BioDn-5_at 10.2650004712764
AFFX-CreX-3_at 13.2120180047957
AFFX-CreX-5_at 12.6667311639375
AFFX-DapX-3_at 2.94946285127208
AFFX-DapX-5_at 3.01693941817660
AFFX-DapX-M_at 3.13132486413954
AFFX-LysX-3_at 3.12806228960401
AFFX-LysX-5_at 2.76514380223663
AFFX-LysX-M_at 3.17658039894501
AFFX-PheX-3_at 5.44549616792151
AFFX-PheX-5_at 3.18515108611852
AFFX-PheX-M_at 2.82378013267402
AFFX-r2-Bs-dap-3_at 2.81882407408825
AFFX-r2-Bs-dap-5_at 3.30003424231656

Total number of rows: 61290

Table truncated, full table size 2160 Kbytes.

Supplementary file Size Download File type/resource
GSM324489.CEL.gz 4.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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