|
| Status |
Public on May 08, 2015 |
| Title |
WT_root_epidermis+cotrex_5uM_Zn_Rep1 |
| Sample type |
RNA |
| |
|
| Source name |
25 days old tomato plants exposed to 5 uM Zn for 15 days
|
| Organism |
Solanum lycopersicum |
| Characteristics |
organ: roots
tissue: epidermis + cortex (EC)
genotype: var. Beta wild type
|
| Treatment protocol |
The plants of the same size were transferred to basic nutrient solution (1/4 Knop's medium) supplemented with 5 µM Zn (added as ZnS04) for 15 days.
|
| Growth protocol |
Seeds were surface-sterilized in 70% ethanol and rinsed with sterile deionised water. Germination and the first stage of seedlings development took place in the glass jars containing the basic medium supplemented with 2% (w/v) sucrose solidified with 1% agar (w/v) for 10 days. Obtained 10-day-old seedlings were transferred to 2-L pots and grown for 15 days under hydroponic conditions on quarter-strength Knop’s medium. The nutrient solution was replaced every 2 days. Plants were grown in a controlled growth chamber, at 23/16°C day/night temperatures, 40–50% humidity, with a 16-h photoperiod at a quantum flux density (PAR) of 250 μmol m−2 s−1 using fluorescent Flora tubes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PicoPure RNA Isolation Kit (Arcturus Engineering) following the manufacturer’s instructions, including treatment with the RNase-Free DNase Set (Qiagen, USA). Isolated RNA was amplified with the RiboAmp HS PLUS (Arcturus Engineering) amplification system following the manufacturer’s protocol.
|
| Label |
biotin
|
| Label protocol |
Labelling of RNA samples was performed by use of the Affymetrix 3’ IVT-Express kit (Affymetrix UK Ltd., High Wycombe, UK) following standard Affymetrix protocols (Affymetrix UK Ltd., High Wycombe, UK).
|
| |
|
| Hybridization protocol |
RNA hybridization to tomato cDNA microarray Affymetrix Tomato Genome Array was conducted at Corelab, Laboratory of Microarray Analyses (University of Warsaw and Institute of Biochemistry and Biophysics, PAS) using GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix) according to manufacturer’s protocol
|
| Scan protocol |
GeneChip® Scanner 3000 7G (Affymetrix UK Ltd., High Wycombe, UK)
|
| Description |
gene expression in LCM -excised epidermis + cortex from roots of Wild type tomato
|
| Data processing |
Microarray hybridization signals were recorded and processed using Affymetrix® GeneChip® Command Console® Software (AGCC).
|
| |
|
| Submission date |
May 07, 2015 |
| Last update date |
May 08, 2015 |
| Contact name |
Maria Kendziorek |
| E-mail(s) |
zyzka@o2.pl
|
| Organization name |
Uniwersity of Warsaw
|
| Department |
Biology
|
| Street address |
Miecznikowa 1
|
| City |
Warsaw |
| ZIP/Postal code |
02-096 |
| Country |
Poland |
| |
|
| Platform ID |
GPL4741 |
| Series (2) |
| GSE68639 |
Expression data from root tissues of 35S:AtHMA4 and wild-type tomato plants grown in the presence of Zn |
| GSE68641 |
35S:AtHMA4 and wild-type tomato plants grown in the presence of Zn |
|
