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Sample GSM322368 Query DataSets for GSM322368
Status Public on Sep 09, 2009
Title genotype: Incrocio Manzoni - disease type: Bois Noir infected - rep2
Sample type RNA
 
Source name leaf vein (genotype: Incrocio Manzoni - disease type: Bois Noir infected)
Organism Vitis vinifera
Characteristics Cultivar Incrocio Manzoni 60.13 (Riesling Renano x Pinot Bianco) (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 Incrocio Manzoni 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 8169.7 P 0
1606427_at 637.49 P 0
1606428_at 11.778 A 0
1606429_at 13.922 A 0
1606430_at 2391.1 P 0
1606431_at 883.62 P 0
1606432_at 430.12 P 0
1606433_at 1874.5 P 0
1606434_at 710.33 P 0
1606435_at 490.07 P 0
1606436_s_at 9754.7 P 0
1606437_at 1099.6 P 0
1606438_at 1006.6 P 0
1606439_s_at 3899.5 P 0
1606440_at 13.644 A 0
1606441_at 20.575 P 0
1606442_at 1587 P 0
1606443_at 20.29 P 0
1606444_at 138.73 P 0
1606445_a_at 516.36 P 0

Total number of rows: 16602

Table truncated, full table size 359 Kbytes.




Supplementary file Size Download File type/resource
GSM322368.CEL.gz 3.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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