|
| Status |
Public on Oct 06, 2012 |
| Title |
Ponderosa stem_mock inoculation_biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Water-inoculated stems of susceptible cultivar Ponderosa, 1dpi
|
| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: stem
cultivar: Susceptible cultivar Ponderosa
inoculum: Distilled water
|
| Treatment protocol |
Seedlings at the five to six leaf-stage were inoculated on their stems just above the cotyledon by cutting to one-third the stem depth with a knife, adding a drop of bacterial suspension or distilled water to the opening, and then clipping the wound site to avoid bending. Inoculated plants were grown in a growth chamber at 30ºC under 30,000 lux light intensity for 12 h a day.
|
| Growth protocol |
Seedlings were raised individually in peat moss pellets and grown in a green house at 25ºC. About 30 days after sowing, seedlings at the five to six leaf-stage were used. R. solanacearum strain 8107S was grown in selective TZC medium containing 200 µg/ml streptomycin sulfate for 1 day at 30ºC, with shaking. Bacteria were collected by centrifugation and re-suspended in distilled water. The suspension was adjusted to 1e+9 cfu/ml by means of a colorimeter and then diluted to 1e+6 cfu/ml.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using an RNeasy Plant Mini Kit (Qiagen) in accordance with the manufacture's protocol.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (3' IVT Express Kit User Manual, 2008, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on tomato GeneChip Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with Hybridization, Wash and Stain Kit.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GCS3000 scanner.
|
| Description |
Gene expression data from mock-inoculated Ponderosa stems. RNA from 15 plants was used.
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 500.
|
| |
|
| Submission date |
Aug 31, 2011 |
| Last update date |
Oct 06, 2012 |
| Contact name |
Takeaki Ishihara |
| Organization name |
National Agriculture and Food Research Organization
|
| Department |
National Agricultural Research Center
|
| Lab |
Plant Protection Division
|
| Street address |
3-1-1 Kannondai
|
| City |
Tsukuba |
| State/province |
Ibaraki |
| ZIP/Postal code |
305-8666 |
| Country |
Japan |
| |
|
| Platform ID |
GPL4741 |
| Series (1) |
| GSE31807 |
Expression data from Ralstonia solanacearum-inoculated tomato stem |
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