GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM320470 Query DataSets for GSM320470
Status Public on Sep 16, 2008
Title protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: Mo17 maize inbred - rep3
Sample type genomic
Source name leaf (protocol: Amplified fragment restriction polymorphism (AFLP) - 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 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 17845 P 0.000581276
AFFX-BioB-5_at 15673 P 5.16933e-05
AFFX-BioB-M_at 21406 P 0.000445958
AFFX-BioC-3_at 33055 P 5.16933e-05
AFFX-BioC-5_at 45346 P 4.43055e-05
AFFX-BioDn-3_at 146410 P 4.43055e-05
AFFX-BioDn-5_at 98176 P 7.00908e-05
AFFX-CreX-3_at 267760 P 4.43055e-05
AFFX-CreX-5_at 275000 P 5.16933e-05
AFFX-DapX-3_at 140.62 A 0.949771
AFFX-DapX-5_at 265.71 A 0.32708
AFFX-DapX-M_at 52.13 A 0.969024
AFFX-LysX-3_at 236.32 A 0.227636
AFFX-LysX-5_at 343.09 A 0.156732
AFFX-LysX-M_at 149.75 A 0.712257
AFFX-PheX-3_at 606.67 A 0.712257
AFFX-PheX-5_at 111.62 A 0.86462
AFFX-PheX-M_at 98.578 A 0.883887
AFFX-r2-Bs-dap-3_at 19.977 A 0.761547
AFFX-r2-Bs-dap-5_at 101.3 A 0.671679

Total number of rows: 17734

Table truncated, full table size 603 Kbytes.

Supplementary file Size Download File type/resource
GSM320470.CEL.gz 1.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap