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Sample GSM320464 Query DataSets for GSM320464
Status Public on Sep 16, 2008
Title protocol: Methylation filtration (MF) - genotype: CML69 maize inbred - rep3
Sample type genomic
Source name leaf (protocol: Methylation filtration (MF) - 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 Methylation Filtration (MF)
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 1403.8 P 0.000389851
AFFX-BioB-5_at 1132.3 P 0.00010957
AFFX-BioB-M_at 1574.3 P 0.000126831
AFFX-BioC-3_at 2267.7 P 5.16933e-05
AFFX-BioC-5_at 3275.1 P 4.43055e-05
AFFX-BioDn-3_at 9665 P 4.43055e-05
AFFX-BioDn-5_at 6625.2 P 5.16933e-05
AFFX-CreX-3_at 19311 P 4.43055e-05
AFFX-CreX-5_at 19531 P 5.16933e-05
AFFX-DapX-3_at 21.673 A 0.574038
AFFX-DapX-5_at 44.955 A 0.216524
AFFX-DapX-M_at 9.9888 A 0.921998
AFFX-LysX-3_at 19.728 A 0.340661
AFFX-LysX-5_at 23.225 A 0.39692
AFFX-LysX-M_at 22.24 A 0.953518
AFFX-PheX-3_at 41.142 A 0.891021
AFFX-PheX-5_at 68.218 A 0.239063
AFFX-PheX-M_at 8.9508 A 0.963431
AFFX-r2-Bs-dap-3_at 18.135 A 0.5
AFFX-r2-Bs-dap-5_at 11.307 A 0.761547

Total number of rows: 17734

Table truncated, full table size 633 Kbytes.

Supplementary file Size Download File type/resource
GSM320464.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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