|
| Status |
Public on Aug 01, 2017 |
| Title |
tomato leaves at 12 hpt with water, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
leaves at 12 hpt with water
|
| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: Summer sweet
treatment: water
time (post-treatment): 12 hours
tissue: leaves
|
| Treatment protocol |
Tomato plants were sprayed thoroughly with NPA or water until run-off. For preparation of NPA, 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.
|
| Growth protocol |
Seedlings of tomato were grown on a mixture of peat moss, perlite and vermiculite at 27oC under a 12 hour photoperiod.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed 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 12 hours after water treatment
|
| 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 5.5 in all of the chips were considered to be the result of nonspecific hybridization, and then resulted in 8488 probes.
|
| |
|
| 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) |
| GSE40163 |
Transcriptome analysis of tomato in response to treatment with neutralized phosphorous acid (NPA) |
| GSE40214 |
Transcriptome analysis of neutralized phosphorous acid (NPA)-induced resistance in tomato against Phytophthora parasitica |
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