|
| Status |
Public on Apr 26, 2024 |
| Title |
Pst DC3000, day1, biological rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
Solanum lycopersicum L. cv. Micro-Tom
|
| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: Micro-Tom
organ: Leaves
treatment: Pst DC3000
|
| Treatment protocol |
One-half of the 30-day-old Micro-Tom plants were exposed to 1000 Hz (at 90 dB for 2 h for 3 consecutive days) using a wireless speaker and the Audacy software in an anechoic chamber. One-half of the untreated controls and 1000 Hz-pretreated plants were dipped upside down in 200 mL bacterial suspension (2 x 108 cfu per ml) containing 0.02% of the surfactant Silwet L-77 and 10 mM MgCl2 (mock solution); the other half of plants were dipped in 200 mL of mock solution. Then, the plants were returned to the growth chamber and leaf samples were collected after 1 day or 3 days of sound/Pst DC3000 treatments.
|
| Growth protocol |
Tomato seeds were surface sterilized and germinated in Petri dishes lined with moistened filter paper. Uniformly germinated seeds were then transferred to soaked peat moss pots (Jiffy pots) and watered as required. Plants were grown in a controlled growth chamber for 30 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 100 mg of leaf samples using RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChipTM WT PLUS Reagent Kit, 2017, Affymetrix).
|
| |
|
| Hybridization protocol |
Following Fragment and Label Single-Stranded cDNA, 0.75 ug of biotin-labeled ss-cDNA sample were hybridized for 20 h at 48ºC on GeneChip® Tomato Gene 1.1 ST Array Strip (Affymetrix, 902296). Arrays were washed and stained in GeneAtlas System.
|
| Scan protocol |
GeneChips were scanned using GeneAtlas System scanner.
|
| Description |
Gene expression data from leaves of 30-day-old tomato plants incubated for 2 h for 3 consecutive days in anechoic box and inoculated with Pst DC300 after 1 dpi
|
| Data processing |
The data were analyzed with robust multi-array average (RMA) using Affymetrix default analysis settings and global scaling as normalization method.
|
| |
|
| Submission date |
Jul 27, 2023 |
| Last update date |
Apr 26, 2024 |
| Contact name |
Antonio A Calderón |
| E-mail(s) |
antonio.calderon@upct.es
|
| Organization name |
Universidad Politécnica de Cartagena
|
| Street address |
Paseo Alfonso XIII, 48
|
| City |
Cartagena |
| State/province |
Outside North America |
| ZIP/Postal code |
30203 |
| Country |
Spain |
| |
|
| Platform ID |
GPL21525 |
| Series (1) |
| GSE239448 |
Expression data from leaves of tomato (Solanum lycopersicum L. cv. MicroTom) plants subjected to 1000 Hz sound vibration (at 90 dB for 2 h for 3 consecutive days) and/or inoculated with Pst DC300. |
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