|
| Status |
Public on Aug 06, 2015 |
| Title |
NahG-Désirée_4dpi_mock_bottomLeaf_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
NahG-Désirée_whole mock-inoculated bottom leaf_4dpi
|
| Organism |
Solanum tuberosum |
| Characteristics |
genotype/variation: NahG-Désirée
treatment: mock-inoculation
time point: 4 dpi
leaf location: bottom
|
| Treatment protocol |
After 4 weeks of growth in soil, the potato plants were inoculated with PVYNTN (isolate NIB-NTN, AJ585342) as described in [Plant Pathol 2010, 59:1121-1132]. For the mock-inoculated plants, the same procedures were performed with sap from healthy potato plants.
|
| Growth protocol |
Two weeks after node segmentation, they were transferred to soil in a growth chamber, and kept at 21 ±2 °C in the light and 18 ±1 °C in the dark, at a relative humidity of 75% ±2%, with 70-90 μmol/m2/s2 radiation (L36W/77 lamp, Osram, Germany) and a 16-h photoperiod
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from the inoculated leaves was extracted, treated, purified, and quality controlled as described previously (Baebler ret al., MPP, 2009)
|
| Label |
Cy 3
|
| Label protocol |
100 ng total RNA per sample were introduced into an RT-IVT reaction. Prior to RT-IVT, the total RNA samples were spiked with in-vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix, Agilent Technologies). The spiked total RNA was reverse transcribed into cDNA and then converted into labeled cRNA by in-vitro transcription (Low Input Quick-Amp Labeling Kit One-Color, Agilent Technologies) incorporating Cyanine-3-CTP.
|
| |
|
| Hybridization protocol |
Hybridization mixture was set up using Gene Expression Hybridization Kit (Agilent Technologies) and applied to the microarray. The hybridization at 65°C for 17 h was followed by washing with increasing stringency using Gene Expression Wash Buffers (Agilent) and drying with acetonitrile (SIGMA). All these steps were performed at IMGM Laboratories GmbH, Germany
|
| Scan protocol |
Fluorescent signal intensities were detected with Scan Control A8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies). All these steps were performed at IMGM Laboratories GmbH, Germany.
|
| Description |
nah_moc_b-04-1
|
| Data processing |
Data was analyzed in R environment with limma and Agi4x44PreProcess packages. Robust spline normalization was used (rsn), background was not subtracted.
|
| |
|
| Submission date |
Jun 17, 2014 |
| Last update date |
Aug 06, 2015 |
| Contact name |
Ziva Ramsak |
| E-mail(s) |
ziva.ramsak@nib.si
|
| Organization name |
National Institute of Biology
|
| Department |
Department of Biotechnology and Systems Biology
|
| Street address |
Večna pot 111
|
| City |
Ljubljana |
| ZIP/Postal code |
1000 |
| Country |
Slovenia |
| |
|
| Platform ID |
GPL14365 |
| Series (1) |
| GSE58593 |
Dynamics of tolerant potato-potato virus Y interaction |
|
