|
| Status |
Public on Feb 19, 2010 |
| Title |
PN24W_bio2_tech2 |
| Sample type |
RNA |
| |
|
| Source name |
Pinot Noir leaf, water, 24h
|
| Organism |
Vitis vinifera |
| Characteristics |
tissue: leaf
infection: water
time point: 24h
cultivar: Pinot Noir
|
| Biomaterial provider |
Dr. Annalisa Polverari (University of Verona)
|
| Treatment protocol |
Fully expanded leaves of 8 to 10-week-old in vitro grapevine plants were mock-inoculated by application of 50μL drops of distilled water on the adaxial leaf surface as a control, with the same procedure. Leaf disks corresponding to infected tissue were cut and collected at 12 and 24 hours post-inoculation (hpi), immediately frozen in liquid nitrogen and stored at -80°C
|
| Growth protocol |
In vitro plants of Vitis vinifera cv. Pinot Noir grown at 27°C and a 16 h photoperiod (50 μE/m2/s) as described in Blaich (1977)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated form leaves of V. vinifera cv Pinot Noir according to Reid et al., 2006.
|
| Label |
Alexa Fluor 647
|
| Label protocol |
Total RNA (1 ug) was amplified by using the SuperScript Indirect RNA Amplification System (Invitrogen), to incorporate amino-allyl UTP molecules (aRNA) and fluorescently labelled by using the Alexa Fluor 647 reactive Dye
|
| |
|
| Hybridization protocol |
Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 1% SDS, 0.2% BSA) for 60 minutes at 37 °C.
Hybridization was performed at 37°C for 16 hours in hybridization solution (6X SSPE, 0.8% BSA, 12% DI Formamide, 2.5% SDS).
Hybridization washings were performed as following:
- wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20).
- wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20).
- 2 washes with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20).
|
| Scan protocol |
Scanning was performed using Perkin Elmer ScanArray 4000XL microarray scanner and ScanArray Express 4.0 acquisition software. Laser was set at 60% of power. PMT gain was set at 60%.
|
| Description |
All the procedures provided were performed as indicated by Combimatrix protocols available at Combimatrix website (www.combimatric.com)
|
| Data processing |
Raw data was extracted using Microarray Imager 5.8.0 software (Combimatrix). Data were quantile-normalized using Blist 0.6 software (Combimatrix).
|
| |
|
| Submission date |
Oct 14, 2009 |
| Last update date |
Feb 19, 2010 |
| Contact name |
Alberto Ferrarini |
| E-mail(s) |
alberto.ferrarini@univr.it
|
| Phone |
+39-045-802-7058
|
| Organization name |
University of Verona
|
| Department |
Scientific and Technological Department
|
| Lab |
Plant Functional Genomics Centre
|
| Street address |
Strada le Grazie, 15
|
| City |
Verona |
| State/province |
Veneto |
| ZIP/Postal code |
37134 |
| Country |
Italy |
| |
|
| Platform ID |
GPL8025 |
| Series (1) |
| GSE18596 |
RNAs expression profiling in a resistant and a susceptible grapevine cultivar to Plasmopara viticola |
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