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Sample GSM786259 Query DataSets for GSM786259
Status Public on Aug 27, 2011
Title year: 2006 - developmental stage: UD:0000034 33E-L - rep2
Sample type RNA
 
Source name fruit_year 2006_developmental stage: UD:0000034 33E-L
Organism Vitis vinifera
Characteristics germplasm name: clone entav 115
organism part: PO: 0009001 fruit
development stage: UD:0000034 33E-L
growth media: field soil
Extracted molecule total RNA
Extraction protocol hot borate RNA extraction protocol
Label biotin
Label protocol Affy-Eukaryotic Target Preparation
 
Hybridization protocol Affy-Eukaryotic Target Hybridization
Scan protocol Affy-Array Scanning
Description Ten clusters of Pinot Noir, clone ENTAV 115, were collected on 07/05/2006 (5 weeks after flowering) in the vineyard "Ai Molini" at IASMA research center. 50 berries were randomly detached and immediately frozen. Three sub-pools of 8 berries each were then obtained and regarded as biological replicas. Total RNA was extracted, purified, labelled and used for Affymetrix Vitis GeneChip v1.0 hybridization.
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 Aug 25, 2011
Last update date Aug 27, 2011
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)
GSE31674 Pinot Noir berry transcriptome during ripening.

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 10425 P 0.000218932
1606427_at 749.97 P 0.000265668
1606428_at 28.615 A 0.204022
1606429_at 48.17 P 0.00306674
1606430_at 1928.9 P 0.000218932
1606431_at 1061.9 P 0.000218932
1606432_at 472.71 P 0.000265668
1606433_at 94.161 P 0.00189169
1606434_at 1211.8 P 0.000218932
1606435_at 87.871 P 0.0149365
1606436_s_at 4489.3 P 0.000265668
1606437_at 1041.5 P 0.000218932
1606438_at 695.53 P 0.000218932
1606439_s_at 3549 P 0.000218932
1606440_at 20.882 P 0.0247109
1606441_at 33.862 P 0.00189169
1606442_at 2840.4 P 0.000218932
1606443_at 65.85 P 0.00135392
1606444_at 353.75 P 0.000804664
1606445_a_at 865.09 P 0.000218932

Total number of rows: 16602

Table truncated, full table size 503 Kbytes.




Supplementary file Size Download File type/resource
GSM786259_20_06.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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