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Sample GSM320451 Query DataSets for GSM320451
Status Public on Sep 16, 2008
Title protocol: Cot filtration (CF) - genotype: Mo17 maize inbred - rep2
Sample type genomic
 
Source name leaf (protocol: Cot filtration (CF) - genotype: Mo17 maize inbred)
Organism Zea mays
Characteristics Mo17 (Germplasm Name); PO:0009025 leaf, (Organism Part); PO:0007134 A vegetative growth, PO:0007071 2.02 main shoot and axillary shoots visible at two nodes (Development Stage); 2 week old (Age); Scotts MetroMix 200 (Growth Media).
Growth protocol Growth Description: glasshouse
Extracted molecule genomic DNA
Extraction protocol Cot Filtration (CF)
Label biotin
Label protocol BioPrime DNA labeling system for CF/MF
 
Hybridization protocol Affy- Eukaryotic Target Hybridization
Scan protocol Affy- Array Scanning
Description Plants grown in glasshouse for 2 weeks.
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 13, 2008
Last update date Sep 15, 2008
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 GPL4032
Series (1)
GSE12770 Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes

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
AFFX-BioB-3_at 570.39 P 0.0429619
AFFX-BioB-5_at 593.99 P 0.00124757
AFFX-BioB-M_at 623.98 P 0.00227503
AFFX-BioC-3_at 827.13 P 0.000445958
AFFX-BioC-5_at 1146.7 P 0.000340357
AFFX-BioDn-3_at 4125.3 P 5.16933e-05
AFFX-BioDn-5_at 2125.2 P 7.00908e-05
AFFX-CreX-3_at 7562.5 P 4.43055e-05
AFFX-CreX-5_at 6824.8 P 5.16933e-05
AFFX-DapX-3_at 57.092 A 0.39692
AFFX-DapX-5_at 34.476 A 0.368438
AFFX-DapX-M_at 5.9023 A 0.937071
AFFX-LysX-3_at 27.776 A 0.32708
AFFX-LysX-5_at 6.4515 A 0.544588
AFFX-LysX-M_at 16.874 A 0.749204
AFFX-PheX-3_at 20.299 A 0.932322
AFFX-PheX-5_at 25.096 A 0.440646
AFFX-PheX-M_at 13.639 A 0.843268
AFFX-r2-Bs-dap-3_at 23.292 A 0.266847
AFFX-r2-Bs-dap-5_at 7.1968 A 0.856998

Total number of rows: 17734

Table truncated, full table size 636 Kbytes.




Supplementary file Size Download File type/resource
GSM320451.CEL.gz 2.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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