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Sample GSM322361 Query DataSets for GSM322361
Status Public on Sep 09, 2009
Title genotype: Chardonnay - disease type: Bois Noir infected - rep1
Sample type RNA
 
Source name leaf vein (genotype: Chardonnay - disease type: Bois Noir infected)
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 Field-grown Chardonnay plant naturally infected with Bois Noir phytoplasma
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 8871 P 0
1606427_at 448.79 P 0
1606428_at 2.8409 A 0
1606429_at 25.939 A 0
1606430_at 2010.4 P 0
1606431_at 675.51 P 0
1606432_at 412.99 P 0
1606433_at 1548.2 P 0
1606434_at 549.47 P 0
1606435_at 341.8 P 0
1606436_s_at 10723 P 0
1606437_at 532.76 P 0
1606438_at 750.61 P 0
1606439_s_at 3920.2 P 0
1606440_at 5.54 A 0
1606441_at 30.279 M 0
1606442_at 2270.7 P 0
1606443_at 28.533 M 0
1606444_at 81.135 P 0
1606445_a_at 532.94 P 0

Total number of rows: 16602

Table truncated, full table size 360 Kbytes.




Supplementary file Size Download File type/resource
GSM322361.CEL.gz 3.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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