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Sample GSM320452 Query DataSets for GSM320452
Status Public on Sep 16, 2008
Title protocol: Cot filtration (CF) - genotype: Mo17 maize inbred - rep3
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 ( 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 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
AFFX-BioB-3_at 645.02 P 0.0113843
AFFX-BioB-5_at 520.8 P 0.000445958
AFFX-BioB-M_at 638.2 P 0.00448384
AFFX-BioC-3_at 835.71 P 0.000224712
AFFX-BioC-5_at 1289.5 P 0.000169266
AFFX-BioDn-3_at 4118.2 P 4.43055e-05
AFFX-BioDn-5_at 2646.6 P 7.00908e-05
AFFX-CreX-3_at 8240.7 P 4.43055e-05
AFFX-CreX-5_at 7393 P 4.43055e-05
AFFX-DapX-3_at 27.455 A 0.559354
AFFX-DapX-5_at 34.459 A 0.185131
AFFX-DapX-M_at 5.3825 A 0.932322
AFFX-LysX-3_at 16.68 A 0.39692
AFFX-LysX-5_at 7.7609 A 0.51489
AFFX-LysX-M_at 8.4991 A 0.969024
AFFX-PheX-3_at 17.779 A 0.937071
AFFX-PheX-5_at 9.6394 A 0.699394
AFFX-PheX-M_at 5.2126 A 0.963431
AFFX-r2-Bs-dap-3_at 18.827 A 0.123873
AFFX-r2-Bs-dap-5_at 10.486 A 0.733153

Total number of rows: 17734

Table truncated, full table size 637 Kbytes.

Supplementary file Size Download File type/resource
GSM320452.CEL.gz 2.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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