|
| Status |
Public on Jun 22, 2009 |
| Title |
Infected_hypocotyls_6h_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
soybean hypocotyls infected with P. sojae, 6h
|
| Organisms |
Glycine max; Phytophthora sojae |
| Characteristics |
specimen: soybean
cultivar: Harosoy (soybean)
tissue: soybean hypocotyl
infection: P. sojae
strain: P6497, race 2 (P. sojae)
time: 6h
|
| Growth protocol |
P. sojae was grown on V8 agar medium. Soybean seeds were sown in vermiculite and grown for 8d in darkness.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Qiagen kit.
|
| Label |
biotin
|
| Label protocol |
Biotinylated complimentary RNA (cRNA) was prepared from 10 μg of total RNA as per the Ambion MessageAmp II protocol (Ambion, Austin, TX). Double-stranded cDNA was synthesized using ArrayScript and oligo(dT) primers with a T7 promoter. Biotin-labeled cRNA was prepared by cDNA in vitro transcription using MEGAscript. External spike-in controls (Affymetrix, Santa Clara, CA) were used.
|
| |
|
| Hybridization protocol |
A cocktail containing 10 μg of labeled cRNA was hybridized to the Soybean GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an anti-streptavidin antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).
|
| Description |
P. sojae was grown on V8 agar medium. Soybean seeds were sown in vermiculite and grown for 8d in darkness. Seedlings were placed in trays and each hypocotyl inoculated with a P. sojae mycelia plug, 5mm diameter, excised from V8 agar plates. Infected plant tissues were harvested at specified time point. Total RNA was extracted with Qiagen kit.
|
| Data processing |
Probe level signal intensities (.cel files) were generated using GCOS1.4 (Affymetrix Inc., Santa Clara, CA). Gene level data (.chp files) were generated using MAS5 default values for the Statistical Expression algorithm parameters and a Target Signal of 150 for all probe sets and a Normalization Value of 1.
|
| |
|
| Submission date |
Mar 04, 2009 |
| Last update date |
Jun 22, 2009 |
| Contact name |
Mark Gijzen |
| E-mail(s) |
mark.gijzen@agr.gc.ca
|
| Phone |
519-457-1470
|
| Fax |
519-457-3997
|
| Organization name |
Agriculture and Agri-Food Canada
|
| Street address |
1391 Sandford Street
|
| City |
London |
| State/province |
Ontario |
| ZIP/Postal code |
N5V 4T3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL4592 |
| Series (1) |
| GSE15100 |
Gene expression in Phytophthora sojae mycelia, germinating zoospores, and during infection of soybean hypocotyls |
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