NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM714441 Query DataSets for GSM714441
Status Public on Apr 28, 2011
Title 21/66_12PV_bio2_tech1
Sample type RNA
 
Source name F1 21/66_infected_12h
Organism Vitis vinifera
Characteristics genotype: F1 21/66 (Merzling x Teroldego cross)
tissue: leaf
infection: Plasmopara viticola
time point: 12h
Treatment protocol Sporangiophores of P. viticola (Berk. and Curt) Berl. et De Toni were collected from infected leaves of V. vinifera cv Pinot Gris plants by brushing the white mould present on the underside of the leaves in cold bidistilled water. Fully expanded leaves of 8 to 10 week old grafted plants were inoculated by spraying a conidial suspension of 10^4/10^5 spores/ml onto the abaxial leaf surface and were kept overnight in the dark in a growth chamber at 24°C with 80% RH . The infected plants were then transferred to the greenhouse and kept in the same conditions as described above. Mock-inoculated plants were obtained by spraying distilled water in the greenhouse. Leaves for the analysis (the second and third from the apex) were collected from two biological replicates each of F1 21/66, F1 22/73 and Teroldego at 12 and 96 hours post infection (hpi) and at 0 hours post mock-inoculation (hpmi), immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction.
Growth protocol F1 individuals from Merzling x Teroldego cross were replicated annually by grafting wood cuttings onto rootstock KOBER 5BB. The plants were kept in a growth chamber in 1L pots filled with soil:sand:peat:vermiculite (3:1:3:3, v/v) in greenhouse at 25°C/20°C day/night temperature, 16 h photoperiod and a relative humidity (RH) of 70 ± 10%.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from frozen leaves according to Moser et al., 2004
Label Cy5
Label protocol Total RNA (1 microgram) was amplified using the Amino Allyl MessageAmpII aRNA Amplification kit (Ambion, USA) and the resulted amminoallyl-aRNA was conjugated to a fluorescent label (Cy-5). The purified labeled aaRNA was quantified by spectrophotometry (ATI Unicam) and 2 micrograms were hybridized to the custom Combimatrix array according to the manufacters directions.
 
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 The arrays were scanned with a ScanArray4000XL (Perkin Elmer, USA) and TIF images were exported to MicroArray Imager 5.8 (Combimatrix, USA) for densometric analysis.
Description 21/66_12PV_D1
Data processing Raw data was extracted using Microarray Imager 5.8.0 software (Combimatrix). Spot flagging and visual inspection of the images was carried out in order to exclude bad spots (based on spot saturation and heterogeneity). The raw signals were analyzed and negatively flagged spots were excluded from further analysis by assigning them a zero weight. Only probes with a signal intensity of at least 500 fluorescence units (Galbraith, 2003) for all biological replicates were considered for further analysis. A scaling normalization was further performed using Actin and Ufgt (UDP-glucose:flavonoid 3-O-glucosyltransferase) as reference genes. A mean expression value from normalized values of technical replicates for each probe was calculated.
 
Submission date Apr 26, 2011
Last update date Aug 18, 2011
Contact name Giulia Malacarne
E-mail(s) giulia.malacarne@fmach.it
Phone +39-0461-615387
Organization name Edmund Mach Foundation
Department Genomics and Biology of Fruit Crops Department
Street address Via Edmund Mach,1
City S. Michele a/Adige
State/province Trento
ZIP/Postal code 38010
Country Italy
 
Platform ID GPL13450
Series (1)
GSE28851 Resistance to Plasmopara viticola in a grapevine segregating population is associated with stilbenoid accumulation and with specific host transcriptional responses

Data table header descriptions
ID_REF
VALUE Normalized value

Data table
ID_REF VALUE
4Cl_145_179 502.3602361
4Cl_209_243 704.2271507
A01_36_71 1308.385988
A01_92_127 2470.851035
A01_RC_200_235 2681.369389
A01_RC_256_293 4558.731695
A02_108_142 1247.249151
A02_31_65 2588.798989
A02_RC_22_56 11548.80619
A02_RC_4_38 1553.510099
A03-7_199_237 3590.635648
A03-7_97_131 4169.705312
A04-3_RC_120_158 3043.287928
A04-3_RC_8_43 4437.323165
A08-2_RC_130_164 1794.30849
A08-2_RC_171_205 4573.727523
A10-3_112_147 1118.342707
A10-3_88_124 1387.402466
A10-3_RC_8_43 10178.7066
A12-6_113_147 3749.82213

Total number of rows: 814

Table truncated, full table size 23 Kbytes.




Supplementary file Size Download File type/resource
GSM714441.txt.gz 116.9 Kb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.