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Sample GSM322365 Query DataSets for GSM322365
Status Public on Sep 09, 2009
Title genotype: Chardonnay - disease type: Healthy - rep2
Sample type RNA
 
Source name leaf vein (genotype: Chardonnay - disease type: Healthy)
Organism Vitis vinifera
Characteristics Cultivar Chardonnay (Germplasm Name); PO:0020138 leaf vein, (Organism Part); PO:0009012 plant growth and development stages (Development Stage); field soil (Growth Media).
Extracted molecule total RNA
Extraction protocol Tris-LiCl
Label biotin
Label protocol Affy-Eukaryotic Target Preparation
 
Hybridization protocol Affy- Eukaryotic Target Hybridization
Scan protocol Affy- Array Scanning
Description Phytoplasma-free field-grown Chardonnay plant
Data processing The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.
 
Submission date Sep 18, 2008
Last update date Sep 09, 2009
Contact name PLEXdb Curator, Sudhansu Dash
Organization name Iowa State University
Department Virtual Reality Application Center
Lab PLEXdb
Street address 1023 Crop Genomes Informatics Lab (Iowa State University)
City Ames
State/province IA
ZIP/Postal code 50011
Country USA
 
Platform ID GPL1320
Series (1)
GSE12842 Gene expression in grapevine in response to Bois noir infection

Data table header descriptions
ID_REF Affymetrix probe set id
VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
1606368_s_at 7595 P 0
1606427_at 344.02 P 0
1606428_at 5.3928 A 0
1606429_at 27.606 P 0
1606430_at 1532.2 P 0
1606431_at 689.83 P 0
1606432_at 341.31 P 0
1606433_at 932.71 P 0
1606434_at 324.99 P 0
1606435_at 464.34 P 0
1606436_s_at 10106 P 0
1606437_at 629.73 P 0
1606438_at 701.05 P 0
1606439_s_at 4837.4 P 0
1606440_at 17.465 A 0
1606441_at 39.523 P 0
1606442_at 2671.9 P 0
1606443_at 25.345 A 0
1606444_at 60.965 P 0
1606445_a_at 722.21 P 0

Total number of rows: 16602

Table truncated, full table size 360 Kbytes.




Supplementary file Size Download File type/resource
GSM322365.CEL.gz 3.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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