|
| Status |
Public on Aug 01, 2017 |
| Title |
tomato leaves at 3 dpt with NPA, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
leaves at 3 days post treatment with NPA
|
| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: Summer sweet
treatment: NPA
time (post-treatment): 3 hours
inoculation: none
time (post-inoculation): none
tissue: leaves
|
| Treatment protocol |
The aerial parts of the tomato plants were sprayed with NPA (1 g/L) or water till run-off. For preparation of the NPA solution, 1 g phosphorous acid (Sigma-Aldrich, St. Louis, MO, USA) was mixed with 1 L ddH2O, followed by the addition of 1 g potassium hydroxide (Sigma-Aldrich), to adjust the pH to 6.3. At 3 days post treatment, plants were further inoculated with zoospores of P. parasitica till run-off, and kept in a moist chamber (humidity > 90%) to facilitate disease development.
|
| Growth protocol |
Seedlings of tomato were grown on a mixture of peat moss, perlite, and vermiculite at 27oC under a 12-hour photoperiod. After pathogen inoculation, plants were kept in a moist chamber (humidity > 90%) under a 12-hour photoperiod.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated by using the Trizol Reagent according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNAs were prepared with 10 μg of plant total RNA according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 μg of cRNA were hybridized with GeneChip Tomato Genome Array at 45oC for 16 hours. Subsequently, GeneChips were washed and stained in the Affymetrix GeneChip fluidics station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip scanner 3000.
|
| Description |
Gene expression data from tomato leaves at 3 days post treatment with NPA
|
| Data processing |
The raw data were analyzed by using Gene-Spring® GX 10 (Agilent Technologies) based on the Robust Multi-array Average (RMA) algorithm. The processes included background correction, log2 transformation, quantile normalization, and conversion to obtain an expression measure for each probe set on each array. As referring to the histogram of the expression value, normalized probe signal values less than 5.8 in all of the chips were considered to be the result of nonspecific hybridization, and then resulted in 8664 probes.
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| |
|
| Submission date |
Aug 16, 2012 |
| Last update date |
Aug 01, 2017 |
| Contact name |
Ruey-Fen Liou |
| E-mail(s) |
rfliou@ntu.edu.tw
|
| Organization name |
National Taiwan University
|
| Department |
Plant Pathology and Microbiology
|
| Street address |
1, Sec. 4, Roosevelt Road
|
| City |
Taipei |
| ZIP/Postal code |
106 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL4741 |
| Series (2) |
| GSE40164 |
Transcriptome analysis of phosphonate-pretreated tomato in response to inoculation with Phytophthora parasitica |
| GSE40214 |
Transcriptome analysis of neutralized phosphorous acid (NPA)-induced resistance in tomato against Phytophthora parasitica |
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