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Sample GSM320456 Query DataSets for GSM320456
Status Public on Sep 16, 2008
Title protocol: Methylation filtration (MF) - genotype: B73 maize inbred - rep1
Sample type genomic
Source name leaf (protocol: Methylation filtration (MF) - 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 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 1677.9 P 0.000581276
AFFX-BioB-5_at 1315.9 P 0.00010957
AFFX-BioB-M_at 2011 P 7.00908e-05
AFFX-BioC-3_at 2606.5 P 6.0233e-05
AFFX-BioC-5_at 3070.7 P 5.16933e-05
AFFX-BioDn-3_at 9501.6 P 4.43055e-05
AFFX-BioDn-5_at 6957.3 P 5.16933e-05
AFFX-CreX-3_at 18604 P 4.43055e-05
AFFX-CreX-5_at 17955 P 5.16933e-05
AFFX-DapX-3_at 11.982 A 0.794268
AFFX-DapX-5_at 53.836 A 0.102165
AFFX-DapX-M_at 4.852 A 0.979978
AFFX-LysX-3_at 39.466 A 0.123572
AFFX-LysX-5_at 32.892 A 0.300606
AFFX-LysX-M_at 7.8219 A 0.949771
AFFX-PheX-3_at 29.459 A 0.932322
AFFX-PheX-5_at 36.844 A 0.41138
AFFX-PheX-M_at 5.0364 A 0.932322
AFFX-r2-Bs-dap-3_at 3.3441 A 0.5
AFFX-r2-Bs-dap-5_at 37.019 A 0.266847

Total number of rows: 17734

Table truncated, full table size 635 Kbytes.

Supplementary file Size Download File type/resource
GSM320456.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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