|
| Status |
Public on May 30, 2008 |
| Title |
78_2006.2A.R146P, Experimental replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
Soybean cultivar RIL 146 - RNA taken from entire inoculated area inoculated with water + agar(mock sample): Timepoint: NA
|
| Organism |
Glycine max |
| Characteristics |
cultivar - RIL 146
Tissue/Cell Type: Soybean root/hypocotyls - P.sojae mycelium from minimal medium
|
| Treatment protocol |
Soybean plants were grown in growth chambers and transferred to trays prior to inoculation. There were 3 trays for each treatment type having 10 plants each. P.sojae materials were inoculated onto the roots of the host plant and RNA extraction was carried out either on 3rd day or 5th day post inoculation. For mock inoculation, the plants were inoculated with pure water with agar. For RIL experiments the RILS had no specific time points but the checks did.
|
| Growth protocol |
Soybean plants were grown in growth chambers and later transferred to trays with clothes soaked in water
|
| Extracted molecule |
total RNA |
| Extraction protocol |
QIAGEN RNeasy Kit : As recommended by manufacturer
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA. RNA is is first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction is carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling. The biotinylated cRNA targets are then cleaned up, fragmented, and hybridized to GeneChip expression arrays(Affymetrix Technical manual - 2004)
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| |
|
| Hybridization protocol |
hybridization cocktail is prepared, including the fragmented target, probe array controls, BSA, and herring sperm DNA. It is then hybridized to the probe array during a 16-hour incubation(Affymetrix technical manual - 2004)
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000
|
| Description |
Data was collected from the hypocotyl regions of Soybean plants at different time points
|
| Data processing |
The data were analyzed with RMA suite from R package version 2.4.0. Background correction was using RMA followed by quantile normalization and data was summarized using median polish method
|
| |
|
| Submission date |
May 29, 2008 |
| Last update date |
May 30, 2008 |
| Contact name |
sucheta Tripathy |
| E-mail(s) |
sutripa@vbi.vt.edu
|
| Phone |
5402318138
|
| Organization name |
Virginia Tech
|
| Department |
Virginia Bioinformatics Institute
|
| Lab |
Tyler lab
|
| Street address |
1, Washington street
|
| City |
Blacksburg |
| State/province |
VA |
| ZIP/Postal code |
24061 |
| Country |
USA |
| |
|
| Platform ID |
GPL4592 |
| Series (1) |
| GSE11611 |
Combined gene expression and QTL analysis of soybean quantitative resistance to Phytophthora sojae |
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