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Sample GSM320473 Query DataSets for GSM320473
Status Public on Sep 16, 2008
Title protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: CML69 maize inbred - rep3
Sample type genomic
Source name leaf (protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: CML69 maize inbred)
Organism Zea mays
Characteristics CML69 (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 21827 P 0.000389851
AFFX-BioB-5_at 16075 P 5.16933e-05
AFFX-BioB-M_at 28838 P 0.000296757
AFFX-BioC-3_at 36672 P 4.43055e-05
AFFX-BioC-5_at 51301 P 4.43055e-05
AFFX-BioDn-3_at 169290 P 4.43055e-05
AFFX-BioDn-5_at 106800 P 7.00908e-05
AFFX-CreX-3_at 298190 P 4.43055e-05
AFFX-CreX-5_at 285980 P 5.16933e-05
AFFX-DapX-3_at 146.04 A 0.724854
AFFX-DapX-5_at 210.68 A 0.382599
AFFX-DapX-M_at 185.81 A 0.876428
AFFX-LysX-3_at 266.05 A 0.544588
AFFX-LysX-5_at 128.78 A 0.559354
AFFX-LysX-M_at 65.694 A 0.989683
AFFX-PheX-3_at 454.58 A 0.843268
AFFX-PheX-5_at 148.89 A 0.67292
AFFX-PheX-M_at 43.814 A 0.910522
AFFX-r2-Bs-dap-3_at 79.537 A 0.296856
AFFX-r2-Bs-dap-5_at 85.481 A 0.761547

Total number of rows: 17734

Table truncated, full table size 603 Kbytes.

Supplementary file Size Download File type/resource
GSM320473.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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