|
| Status |
Public on Mar 05, 2018 |
| Title |
Nt-PC48-rep3 |
| Sample type |
RNA |
| |
|
| Source name |
N. tabacum infected with CIPC48 replicate3
|
| Organism |
Nicotiana tabacum |
| Characteristics |
cultivar: Xanthi NN
tissue: Leaves and apex
dpi: 8
|
| Treatment protocol |
Batches of 8-week-old N. tabacum plants were inoculated with ≈5 µg of RNA of each viral genotype by abrasion of the third true leaf. Inoculations were done in two experimental blocks, first one including HC-Pro:AS13, HC-Pro:CLA2, HC-Pro:CLA11, NIb:PC95 and their controls, and second one including CI:PC48, CI:PC55 and their controls. All infected tobacco plants showed symptoms 5–8 dpi (not HC-Pro:AS13 infected plants). At 8 dpi virus-infected leafs and apexes for each plant were collected individually (HC-Pro:AS13 infected plants that were collected at 15 dpi). Plant tissue was frozen, homogenized, aliquoted and stored at -80ºC.
|
| Growth protocol |
All plants were at similar growth stages and were maintained in a Biosafety Level-2 greenhouse at 25ºC under a 16-h light and 8-h dark photoperiod.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction from 100 mg of fresh tissue per plant was performed using Agilent Plant RNA Isolation Mini Kit (Agilent Technologies) following the manufacturer’s instructions. The integrity of the RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent) before and after hybridization.
|
| Label |
Cy3
|
| Label protocol |
Sample RNA (200 ng) was amplified and labeled with the Agilent Low Input Quick Amp Labeling Kit (Agilent 5190-2306).
|
| |
|
| Hybridization protocol |
Hybridization and slide washing were performed with the Gene Expression Hybridization Kit (Agilent 5188-5242) and Gene Expression Wash Buffers (Agilent 5188-5326) as detailed in G4140-90040 GeneExpression one Color v6.6 procedure. An Agilent One color Spike-In Kit (Agilent 5188-5282) was used to assess the labeling and hybridization efficiencies.
|
| Scan protocol |
Slides were scanned in GenePix 4000B (Axon) microarray scanner, at 5 µm resolution. Image files were extracted with the Feature Extraction software 9.5.1.
|
| Description |
Experimental block 2
CIPC48_24
|
| Data processing |
Interarray analyses were performed with the Babelomics 5 software.
|
| |
|
| Submission date |
Jun 08, 2017 |
| Last update date |
Mar 05, 2018 |
| Contact name |
Héctor Cervera Benet |
| E-mail(s) |
heccerbe@posgrado.upv.es
|
| Organization name |
CSIC-UPV
|
| Department |
IBMCP
|
| Lab |
2.04
|
| Street address |
Ingeniero Fausto Elio s/n
|
| City |
Valencia |
| State/province |
Valencia |
| ZIP/Postal code |
46022 |
| Country |
Spain |
| |
|
| Platform ID |
GPL10098 |
| Series (1) |
| GSE99838 |
Viral fitness correlates with the magnitude and direction of the perturbation induced in the host's transcriptome: the tobacco etch potyvirus - tobacco case study. |
|
