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| Status |
Public on Dec 26, 2018 |
| Title |
res tomato mutant, roots, control condition, rep. 3 |
| Sample type |
RNA |
| |
|
| Source name |
res mutant roots, control condition
|
| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: root
genotype: res mutant
background cultivar: Moneymaker
age: six-week old plants
condition: control (optimal growth condition)
|
| Treatment protocol |
Salt stress was applied in hydroponics to six-week old WT and res plants, and consisted in ½ Hoagland plus 200 mM NaCl for 5 days. Leaflets from the first fully-expanded leaf and roots were harvested and immediately frozen in liquid N2 prior to stress application (control) and after 5 days of salt treatment. Three biological replicates (each one including three plants) were considered for each genotype and treatment.
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| Growth protocol |
Plants of the res mutant and Solanum lycopersicum L. cv. Moneymaker (background genotype), were used. Seeds were germinated in darkness, in a 8:3 (v/v) mixture of peat:perlite, at 28ºC temperature and 90% of relative humidity (RH). After emergence, plants were grown in a controlled growth chamber with 16 h light/8 h darkness photoperiod, with light of a photosynthetic photon flux (400-700 nm) of 350 µmol m-2 s-1 at the plant level, provided by fluorescent tubes (Philips Master TL-D 58W/840 REFLEX, Holland), and 25 ºC and 50-60% of temperature and RH, respectively. Two-week old plantlets were transferred to hydroponics. The hydroponic system consisted in tanks of 50 L volume (219 x 20 x 17 cm) filled with half-strength (½) Hoagland nutritive solution (Hoagland and Arnon, 1950), which was continuously aerated by means of a compressor (Puska N-150-150, with a 115 L min-1 flow, 10 Kg cm-2 maximum pressure). The nutritive solution was controlled by monitoring pH and electrical conductivity (EC), renewing it at least once per week.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from 24 samples was extracted by means of Rneasy Mini Kit (Qiagen) according to instrutions from manufacturer.The amount and quality of the RNA was checked by Bioanalyzer and spectrophotometrically by Nanodrop.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 100ng of total RNA (GeneChip WT Plus Reagent Kit. Manual Target Preparation for GeneChip Whole Transcript (WT) Expression Arrays).
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| |
|
| Hybridization protocol |
Following fragmentation and labeling, 3.5 ug of cDNA was hybridized for 20 hr at 48ºC on TomGene-1-1-st-v1 array using the GeneAtlas Hybridization Station. After hybridization, arrays were washed and stained in the GeneAtlas Fluidics Station (GeneAtlasTM System, Affymetrix)
|
| Scan protocol |
GeneChips were scanned using the GeneAtlas Imaging Station (GeneAtlasTM System, Affymetrix)
|
| Description |
res tomato mutant, roots, control condition, replicate 3
|
| Data processing |
Data were analyzed with RMA (Robust Multiarray Analysis) using Affymetrix default analysis settings and global scaling as normalization method. Non-supervised Principal Components Analysis (PCA) and hierarchical clustering were performed and they showed that samples tend to separate according to genotype and condition. Partek Genomics Suite and Partek Pathways software (Partek Incorporated, St. Louis, USA) were used for obtaining the annotation of probesets and performing the statistical analysis. An ANOVA test was applied with a restrictive threshold at p-value ≤ 0.05, and multiple test corrections was performed using the FDR (Benjamini and Hochberg, 1995).
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| |
|
| Submission date |
Oct 25, 2017 |
| Last update date |
Dec 26, 2018 |
| Contact name |
Irene Albaladejo |
| E-mail(s) |
iralca@gmail.com
|
| Organization name |
CEBAS-CSIC
|
| Street address |
Campus Universitario Espinardo
|
| City |
Espinardo |
| State/province |
Murcia |
| ZIP/Postal code |
30100 |
| Country |
Spain |
| |
|
| Platform ID |
GPL21525 |
| Series (1) |
| GSE106149 |
Expression data from leaflets and roots of the tomato res mutant and its background genotype, wild-type (WT) (Solanum lycopersicum L. cv. Moneymaker), grown in control conditions and salt stress |
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