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Sample GSM320466 Query DataSets for GSM320466
Status Public on Sep 16, 2008
Title protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: B73 maize inbred - rep2
Sample type genomic
Source name leaf (protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: B73 maize inbred)
Organism Zea mays
Characteristics B73 (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 Amplified fragment length polymorphism (AFLP)
Label biotin
Label protocol BioPrime DNA labeling system for AFLP
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 17713 P 0.000972217
AFFX-BioB-5_at 14139 P 5.16933e-05
AFFX-BioB-M_at 18837 P 0.000856576
AFFX-BioC-3_at 33149 P 5.16933e-05
AFFX-BioC-5_at 44635 P 4.43055e-05
AFFX-BioDn-3_at 141560 P 4.43055e-05
AFFX-BioDn-5_at 87284 P 9.45344e-05
AFFX-CreX-3_at 259740 P 4.43055e-05
AFFX-CreX-5_at 251510 P 4.43055e-05
AFFX-DapX-3_at 115.6 A 0.876428
AFFX-DapX-5_at 304.62 A 0.368438
AFFX-DapX-M_at 270.92 A 0.559354
AFFX-LysX-3_at 337.34 A 0.156732
AFFX-LysX-5_at 323.47 A 0.368438
AFFX-LysX-M_at 148.95 A 0.945787
AFFX-PheX-3_at 523.14 A 0.834139
AFFX-PheX-5_at 127.22 A 0.67292
AFFX-PheX-M_at 84.514 A 0.916408
AFFX-r2-Bs-dap-3_at 126.76 A 0.328321
AFFX-r2-Bs-dap-5_at 508.06 A 0.328321

Total number of rows: 17734

Table truncated, full table size 602 Kbytes.

Supplementary file Size Download File type/resource
GSM320466.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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