GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM322367 Query DataSets for GSM322367
Status Public on Sep 09, 2009
Title genotype: Incrocio Manzoni - disease type: Bois Noir infected - rep1
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 ( 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 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
1606368_s_at 9327.5 P 0
1606427_at 863.44 P 0
1606428_at 1.8692 A 0
1606429_at 1.3024 A 0
1606430_at 1974.1 P 0
1606431_at 818.48 P 0
1606432_at 431.94 P 0
1606433_at 937.28 P 0
1606434_at 771.19 P 0
1606435_at 241.62 P 0
1606436_s_at 11326 P 0
1606437_at 804.07 P 0
1606438_at 708.19 P 0
1606439_s_at 6994.1 P 0
1606440_at 16.312 A 0
1606441_at 26.802 A 0
1606442_at 1640.2 P 0
1606443_at 24.091 A 0
1606444_at 65.557 P 0
1606445_a_at 521.54 P 0

Total number of rows: 16602

Table truncated, full table size 360 Kbytes.

Supplementary file Size Download File type/resource
GSM322367.CEL.gz 3.1 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap