GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM320441 Query DataSets for GSM320441
Status Public on Sep 16, 2008
Title protocol: mRNA - genotype: Mo17 maize inbred - rep1
Sample type RNA
Source name leaf (protocol: mRNA - genotype: Mo17 maize inbred)
Organism Zea mays
Characteristics Mo17 (Germplasm Name); PO:0009025 leaf, (Organism Part); PO:0007134 A vegetative growth, PO:0007088 2.04 main shoot and axillary shoots visible at four nodes (Development Stage); 4 week old (Age); Scotts MetroMix 200 (Growth Media).
Growth protocol Growth Description: glasshouse
Extracted molecule total RNA
Extraction protocol Total RNA Isolation in Maize
Label biotin
Label protocol Affymetrix one-cycle target labeling
Hybridization protocol Affy- Eukaryotic Target Hybridization
Scan protocol Affy- Array Scanning
Description Plants grown in glasshouse for 4-weeks (April to May). No supplemental lighting.
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 174.79 P 6.0233e-05
AFFX-BioB-5_at 143.85 P 0.00202266
AFFX-BioB-M_at 183.29 P 7.00908e-05
AFFX-BioC-3_at 778.65 P 4.43055e-05
AFFX-BioC-5_at 460.45 P 5.16933e-05
AFFX-BioDn-3_at 2659.5 P 4.43055e-05
AFFX-BioDn-5_at 1079 P 4.43055e-05
AFFX-CreX-3_at 8336.9 P 4.43055e-05
AFFX-CreX-5_at 5940.3 P 5.16933e-05
AFFX-DapX-3_at 3626 P 4.43055e-05
AFFX-DapX-5_at 1294.5 P 4.43055e-05
AFFX-DapX-M_at 2415.3 P 5.16933e-05
AFFX-LysX-3_at 683.98 P 4.43055e-05
AFFX-LysX-5_at 200.25 P 4.43055e-05
AFFX-LysX-M_at 238.36 P 6.0233e-05
AFFX-PheX-3_at 321.84 P 4.43055e-05
AFFX-PheX-5_at 329.78 P 4.43055e-05
AFFX-PheX-M_at 275.53 P 6.0233e-05
AFFX-r2-Bs-dap-3_at 3442.4 P 0.00167288
AFFX-r2-Bs-dap-5_at 1799.5 P 0.00167288

Total number of rows: 17734

Table truncated, full table size 627 Kbytes.

Supplementary file Size Download File type/resource
GSM320441.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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