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Sample GSM299461 Query DataSets for GSM299461
Status Public on Jun 20, 2009
Title C_ni_rep1
Sample type RNA
 
Source name Rpv1-/Rpv2+, mock-inoculated with water
Organism Vitis rotundifolia
Characteristics Vitis (41528 population) - Age: 13 month. Dev.stage (Boyes et al. Plant Cell 2001): green cuttings with 10 developed leaves.
Treatment protocol Name:ni - pathogen - control,pathogen infection,mock inoculation:time 6hour . The sixth leaves from the top of plants were used. One leaf disc (14 mm diameter) was punched from each of the 18 plants and mock inoculated with sterile bidistilled water by contact of the abaxial leaf surface in one petri dish. Six hours later, discs were collected and frozen.
Growth protocol leaf - Plants were grown in the greenhouse in potting soil (compost) during three months (March, April, May)
Extracted molecule total RNA
Extraction protocol C_ni_rep1:91.2ug.
Label Biotin
Label protocol labelling Biotin direct, amplification=yes, RNAa 20 ug.
 
Hybridization protocol labelled extract quantity: 10ug
Scan protocol GCOS, Biotin:pmt voltage 570nm,650V,laser power 1
Description Grapevine downy mildew caused by the Oomycete Plasmopara viticola is one of the most important diseases affecting Vitis spp. However, all cultivated European grapevine varieties are susceptible to P. viticola and the resistance needs to be introduced from other Vitaceae. Segregating populations derived from Muscadinia rotundifolia, a species closely related to Vitis, lead to the identification and mapping of two resistance genes, named Rpv1 and Rpv2. The macroscopic phenotypes of the resistance mediated by the two loci are different. Rpv2 plants completely inhibit P. viticola sporulation and produce very small necrotic lesions. In contrast, Rpv1 plants allow a rather limited but visible sporulation of P. viticola. The aim of the study is to understand the gene expression changes associated with downy mildew resistance mediated by these two loci. Gene expression patterns after P. viticola inoculation or mock inoculation are compared in incompatible (resistant plants bearing Rpv1 or Rpv2 locus) and compatible (susceptible plants with no resistance loci) interactions, using the Vitis vinifera GeneChip from Affymetrix.
Data processing The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).
 
Submission date Jun 23, 2008
Last update date Jun 23, 2008
Contact name sandrine balzergue
Organization name INRA
Lab IRHS
Street address Rue G. Morel
City Beaucouze
ZIP/Postal code 49000
Country France
 
Platform ID GPL1320
Series (1)
GSE11857 Gene expression patterns associated with grapevine resistance to downy mildew mediated by the Rpv1 and Rpv2 genes

Data table header descriptions
ID_REF ID number
VALUE Normalized data by GCRMA

Data table
ID_REF VALUE
1606368_s_at 12.82
1606427_at 6.44
1606428_at 3.04
1606429_at 13.41
1606430_at 9.70
1606431_at 9.74
1606432_at 7.59
1606433_at 8.42
1606434_at 8.60
1606435_at 4.17
1606436_s_at 12.59
1606437_at 9.58
1606438_at 8.29
1606439_s_at 10.82
1606440_at 2.26
1606441_at 2.69
1606442_at 10.32
1606443_at 2.76
1606444_at 6.67
1606445_a_at 8.38

Total number of rows: 16602

Table truncated, full table size 265 Kbytes.




Supplementary file Size Download File type/resource
GSM299461.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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